private ExpressionContainerDTO expressionContainerFor(IParameter relativeExpression, IParameter relativeExpressioNorm)
{
var expressionContainerDTO = new ExpressionContainerDTO();
var moleculeName = relativeExpression.ParentContainer.Name;
var simulation = _executionContext.Get <Simulation>(relativeExpression.Origin.SimulationId);
var molecule = simulation.Individual?.MoleculeByName <IndividualMolecule>(moleculeName);
var isTransporter = moleculeIsTransporter(molecule);
expressionContainerDTO.RelativeExpressionParameter = _containerParameterMapper.MapFrom(relativeExpression, expressionContainerDTO, x => x.RelativeExpression, x => x.RelativeExpressionParameter);
expressionContainerDTO.RelativeExpressionNormParameter = _containerParameterMapper.MapFrom(relativeExpressioNorm, expressionContainerDTO, x => x.RelativeExpressionNorm, x => x.RelativeExpressionNormParameter);
IGroup group;
if (parameterIsGlobalExpression(relativeExpression))
{
if (isTransporter)
{
return(null);
}
group = _groupRepository.GroupByName(CoreConstants.Groups.VASCULAR_SYSTEM);
expressionContainerDTO.ContainerPathDTO = _representationInfoRepository.InfoFor(RepresentationObjectType.CONTAINER, containerNameForGlobalExpression(relativeExpression.Name)).ToPathElement();
expressionContainerDTO.Sequence = relativeExpression.Sequence;
}
else if (expressionShouldBeTreatedAsGlobal(relativeExpression, isTransporter))
{
return(null);
}
else if (relativeExpression.HasAncestorNamed(CoreConstants.Organ.Lumen))
{
group = _groupRepository.GroupByName(CoreConstants.Groups.GI_LUMEN);
expressionContainerDTO.ContainerPathDTO = _representationInfoRepository.InfoFor(relativeExpression.ParentContainer.ParentContainer).ToPathElement();
}
else if (relativeExpression.HasAncestorNamed(CoreConstants.Compartment.Mucosa))
{
group = _groupRepository.GroupByName(CoreConstants.Groups.GI_MUCOSA);
//Mucosa rel exp are for instance in Mucosa/Duodnum/interstitial
expressionContainerDTO.ContainerPathDTO = _representationInfoRepository.InfoFor(relativeExpression.ParentContainer.ParentContainer.ParentContainer).ToPathElement();
}
else
{
var expressionContainer = expressionContainerFor(relativeExpression);
group = _groupRepository.GroupByName(isGiTractOrgan(expressionContainer) ? CoreConstants.Groups.GI_NON_MUCOSA_TISSUE : CoreConstants.Groups.ORGANS_AND_TISSUES);
expressionContainerDTO.ContainerPathDTO = _representationInfoRepository.InfoFor(expressionContainer).ToPathElement();
}
expressionContainerDTO.GroupingPathDTO = _representationInfoRepository.InfoFor(RepresentationObjectType.GROUP, group.Name).ToPathElement();
//May have been set previously
if (expressionContainerDTO.Sequence == 0)
{
expressionContainerDTO.Sequence = group.Sequence;
}
expressionContainerDTO.MoleculeName = moleculeName;
expressionContainerDTO.ParameterPath = _fullPathDisplayResolver.FullPathFor(relativeExpression);
return(expressionContainerDTO);
}
public SchemaItemDTO MapFrom(SchemaItem schemaItem)
{
var schemaItemDTO = new SchemaItemDTO(schemaItem);
schemaItemDTO.DoseParameter = _parameterDTOMapper.MapFrom(schemaItem.Dose, schemaItemDTO, x => x.Dose, x => x.DoseParameter);
schemaItemDTO.StartTimeParameter = _parameterDTOMapper.MapFrom(schemaItem.StartTime, schemaItemDTO, x => x.StartTime, x => x.StartTimeParameter);
return(schemaItemDTO);
}
public IdentificationParameterDTO MapFrom(IdentificationParameter identificationParameter)
{
var identificationParameterDTO = new IdentificationParameterDTO(identificationParameter);
identificationParameterDTO.StartValueParameter = _parameterMapper.MapFrom(identificationParameter.StartValueParameter, identificationParameterDTO, x => x.StartValue, x => x.StartValueParameter);
identificationParameterDTO.MinValueParameter = _parameterMapper.MapFrom(identificationParameter.MinValueParameter, identificationParameterDTO, x => x.MinValue, x => x.MinValueParameter);
identificationParameterDTO.MaxValueParameter = _parameterMapper.MapFrom(identificationParameter.MaxValueParameter, identificationParameterDTO, x => x.MaxValue, x => x.MaxValueParameter);
return(identificationParameterDTO);
}
private TypePKaDTO typePKaFor(IList <IParameter> compoundParameters, string parameterPka1, string parameterCompoundType1)
{
var pKaParameter = compoundParameters.FindByName(parameterPka1);
var compoundTypeParameter = compoundParameters.FindByName(parameterCompoundType1);
var dto = new TypePKaDTO();
dto.CompoundTypeParameter = _parameterMapper.MapFrom(compoundTypeParameter, dto, x => x.CompoundTypeValue, x => x.CompoundTypeParameter);
dto.PKaParameter = _parameterMapper.MapFrom(pKaParameter, dto, x => x.PKa, x => x.PKaParameter);
return(dto);
}
public SchemaDTO MapFrom(Schema schema)
{
var schemaDTO = new SchemaDTO(schema, schema.TimeBetweenRepetitions.Dimension);
schemaDTO.TimeBetweenRepetitionsParameter = _parameterDTOMapper.MapFrom(schema.TimeBetweenRepetitions, schemaDTO, x => x.TimeBetweenRepetitions, x => x.TimeBetweenRepetitionsParameter);
schemaDTO.StartTimeParameter = _parameterDTOMapper.MapFrom(schema.StartTime, schemaDTO, x => x.StartTime, x => x.StartTimeParameter);
schemaDTO.NumberOfRepetitionsParameter = _parameterDTOMapper.MapFrom(schema.NumberOfRepetitions, schemaDTO, x => x.NumberOfRepetitions, x => x.NumberOfRepetitionsParameter);
schema.SchemaItems.OrderBy(x => x.Name).Each(item => schemaDTO.AddSchemaItem(_schemaItemDtoMapper.MapFrom(item)));
return(schemaDTO);
}
private void addTypePKaFor(CompoundTypeDTO compoundTypeDTO, IList <IParameter> compoundParameters, string parameterPka1, string parameterCompoundType1)
{
var pKaParameter = compoundParameters.FindByName(parameterPka1);
var compoundTypeParameter = compoundParameters.FindByName(parameterCompoundType1);
var typePKaDTO = new TypePKaDTO();
typePKaDTO.CompoundTypeParameter = _parameterMapper.MapFrom(compoundTypeParameter, typePKaDTO, x => x.CompoundTypeValue, x => x.CompoundTypeParameter);
typePKaDTO.PKaParameter = _parameterMapper.MapFrom(pKaParameter, typePKaDTO, x => x.PKa, x => x.PKaParameter);
compoundTypeDTO.AddTypePKa(typePKaDTO);
}
public OutputIntervalDTO MapFrom(OutputInterval outputInterval)
{
var outputIntervalDTO = new OutputIntervalDTO {
OutputInterval = outputInterval
};
outputIntervalDTO.StartTimeParameter = _parameterDTOMapper.MapFrom(outputInterval.StartTime, outputIntervalDTO, x => x.StartTime, x => x.StartTimeParameter);
outputIntervalDTO.EndTimeParameter = _parameterDTOMapper.MapFrom(outputInterval.EndTime, outputIntervalDTO, x => x.EndTime, x => x.EndTimeParameter);
outputIntervalDTO.ResolutionParameter = _parameterDTOMapper.MapFrom(outputInterval.Resolution, outputIntervalDTO, x => x.Resolution, x => x.ResolutionParameter);
return(outputIntervalDTO);
}
public SensitivityParameterDTO MapFrom(SensitivityParameter sensitivityParameter)
{
var sensitivityParameterDTO = new SensitivityParameterDTO(sensitivityParameter);
sensitivityParameterDTO.NumberOfStepsParameter = _parameterMapper.MapFrom(sensitivityParameter.NumberOfStepsParameter, sensitivityParameterDTO, x => x.NumberOfSteps, x => x.NumberOfStepsParameter);
sensitivityParameterDTO.VariationRangeParameter = _parameterMapper.MapFrom(sensitivityParameter.VariationRangeParameter, sensitivityParameterDTO, x => x.VariationRange, x => x.VariationRangeParameter);
sensitivityParameterDTO.DisplayPath = sensitivityParameter.Parameter != null?_quantityDisplayPathMapper.DisplayPathAsStringFor(sensitivityParameter.Parameter, addSimulationName : true) : sensitivityParameter.ParameterSelection.Path;
return(sensitivityParameterDTO);
}
public MoleculePropertiesDTO MapFrom(IndividualMolecule molecule)
{
var dto = new MoleculePropertiesDTO(molecule)
{
MoleculeType = _objectTypeResolver.TypeFor(molecule)
};
dto.ReferenceConcentrationParameter = _parameterMapper.MapFrom(molecule.ReferenceConcentration, dto, x => x.ReferenceConcentration, x => x.ReferenceConcentrationParameter);
dto.HalfLifeLiverParameter = _parameterMapper.MapFrom(molecule.HalfLifeLiver, dto, x => x.HalfLifeLiver, x => x.HalfLifeLiverParameter);
dto.HalfLifeIntestineParameter = _parameterMapper.MapFrom(molecule.HalfLifeIntestine, dto, x => x.HalfLifeIntestine, x => x.HalfLifeIntestineParameter);
return(dto);
}
public SolubilityAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var solubilityAlternativeDTO = new SolubilityAlternativeDTO(parameterAlternative);
var solubility = parameterAlternative.Parameter(CoreConstants.Parameter.SolubilityAtRefpH);
var refPh = parameterAlternative.Parameter(CoreConstants.Parameter.RefpH);
var gainPerCharge = parameterAlternative.Parameter(CoreConstants.Parameter.SolubilityGainPerCharge);
solubilityAlternativeDTO.SolubilityParameter = _parameterDTOMapper.MapFrom(solubility, solubilityAlternativeDTO, dto => dto.Solubility, dto => dto.SolubilityParameter);
solubilityAlternativeDTO.RefpHParameter = _parameterDTOMapper.MapFrom(refPh, solubilityAlternativeDTO, dto => dto.RefpH, dto => dto.RefpHParameter);
solubilityAlternativeDTO.GainPerChargeParameter = _parameterDTOMapper.MapFrom(gainPerCharge, solubilityAlternativeDTO, dto => dto.GainPerCharge, dto => dto.GainPerChargeParameter);
return(solubilityAlternativeDTO);
}
public PermeabilityAlternativeDTO MapFrom(ParameterAlternative parameterAlternative, string parameterName)
{
var permeability = parameterAlternative.Parameter(parameterName);
var permeabilityAlternativeDTO = new PermeabilityAlternativeDTO(parameterAlternative, permeability.ValueOrigin);
permeabilityAlternativeDTO.PermeabilityParameter = _parameterDTOMapper.MapFrom(permeability, permeabilityAlternativeDTO, dto => dto.Permeability, dto => dto.PermeabilityParameter);
return(permeabilityAlternativeDTO);
}
public void UpdateProperties(ExpressionContainerDTO expressionDTO, MoleculeExpressionContainer expressionContainer)
{
var group = _groupRepository.GroupByName(expressionContainer.GroupName);
var groupInfo = _representationInfoRepository.InfoFor(RepresentationObjectType.GROUP, expressionContainer.GroupName);
var containerInfo = _representationInfoRepository.InfoFor(RepresentationObjectType.CONTAINER, expressionContainer.ContainerName);
expressionDTO.GroupingPathDTO = groupInfo.ToPathElement();
expressionDTO.ContainerPathDTO = containerInfo.ToPathElement();
expressionDTO.Sequence = group.Sequence;
expressionDTO.RelativeExpressionParameter =
_parameterMapper.MapFrom(expressionContainer.RelativeExpressionParameter, expressionDTO,
x => x.RelativeExpression, x => x.RelativeExpressionParameter);
expressionDTO.RelativeExpressionNormParameter =
_parameterMapper.MapFrom(expressionContainer.RelativeExpressionNormParameter, expressionDTO,
x => x.RelativeExpressionNorm, x => x.RelativeExpressionNormParameter);
}
public LipophilictyAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var lipophilicity = parameterAlternative.Parameter(CoreConstants.Parameters.LIPOPHILICITY);
var lipophilictyAlternativeDTO = new LipophilictyAlternativeDTO(parameterAlternative, lipophilicity.ValueOrigin);
lipophilictyAlternativeDTO.LipophilictyParameter = _parameterDTOMapper.MapFrom(lipophilicity, lipophilictyAlternativeDTO, dto => dto.Lipophilicty, dto => dto.LipophilictyParameter);
return(lipophilictyAlternativeDTO);
}
public FractionUnboundAlternativeDTO MapFrom(ParameterAlternativeWithSpecies parameterAlternative)
{
var fractionUnbound = parameterAlternative.Parameter(CoreConstants.Parameters.FRACTION_UNBOUND_PLASMA_REFERENCE_VALUE);
var fractionUnboundAlternativeDTO = new FractionUnboundAlternativeDTO(parameterAlternative, fractionUnbound.ValueOrigin);
fractionUnboundAlternativeDTO.FractionUnboundParameter = _parameterDTOMapper.MapFrom(fractionUnbound, fractionUnboundAlternativeDTO, dto => dto.FractionUnbound, dto => dto.FractionUnboundParameter);
return(fractionUnboundAlternativeDTO);
}
public LipophilictyAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var lipophilictyAlternativeDTO = new LipophilictyAlternativeDTO(parameterAlternative);
var lipophilicity = parameterAlternative.Parameter(CoreConstants.Parameter.Lipophilicity);
lipophilictyAlternativeDTO.LipophilictyParameter = _parameterDTOMapper.MapFrom(lipophilicity, lipophilictyAlternativeDTO, dto => dto.Lipophilicty, dto => dto.LipophilictyParameter);
return(lipophilictyAlternativeDTO);
}
public FractionUnboundAlternativeDTO MapFrom(ParameterAlternativeWithSpecies parameterAlternative)
{
var fractionUnboundAlternativeDTO = new FractionUnboundAlternativeDTO(parameterAlternative);
var lipophilicity = parameterAlternative.Parameter(CoreConstants.Parameter.FractionUnbound);
fractionUnboundAlternativeDTO.FractionUnboundParameter = _parameterDTOMapper.MapFrom(lipophilicity, fractionUnboundAlternativeDTO, dto => dto.FractionUnbound, dto => dto.FractionUnboundParameter);
return(fractionUnboundAlternativeDTO);
}
public SolubilityAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var solubilityAtRefPh = parameterAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_AT_REFERENCE_PH);
var solubilityTable = parameterAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_TABLE);
var solubilityParameter = solubilityTable.Formula.IsTable() ? solubilityTable : solubilityAtRefPh;
var solubilityAlternativeDTO = new SolubilityAlternativeDTO(parameterAlternative, solubilityParameter.ValueOrigin);
solubilityAlternativeDTO.SolubilityParameter = _parameterDTOMapper.MapFrom(solubilityParameter, solubilityAlternativeDTO, dto => dto.Solubility, dto => dto.SolubilityParameter);
var refPh = parameterAlternative.Parameter(CoreConstants.Parameters.REFERENCE_PH);
solubilityAlternativeDTO.RefpHParameter = _parameterDTOMapper.MapFrom(refPh, solubilityAlternativeDTO, dto => dto.RefpH, dto => dto.RefpHParameter);
var gainPerCharge = parameterAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_GAIN_PER_CHARGE);
solubilityAlternativeDTO.GainPerChargeParameter = _parameterDTOMapper.MapFrom(gainPerCharge, solubilityAlternativeDTO, dto => dto.GainPerCharge, dto => dto.GainPerChargeParameter);
return(solubilityAlternativeDTO);
}
public EventMappingDTO MapFrom(IEventMapping eventMapping, PKSim.Core.Model.Simulation simulation)
{
var eventMappingDTO = new EventMappingDTO(eventMapping);
eventMappingDTO.StartTimeParameter = _parameterDTOMapper.MapFrom(eventMapping.StartTime, eventMappingDTO, x => x.StartTime, x => x.StartTimeParameter);
var templateEvent = _buildingBlockRepository.All <PKSim.Core.Model.PKSimEvent>().FindById(eventMapping.TemplateEventId);
var usedEvent = simulation.UsedBuildingBlockByTemplateId(eventMapping.TemplateEventId);
//simulation was already using an event based on template. Retrieved the building block used
if (usedEvent != null)
{
templateEvent = _buildingBlockInSimulationManager.TemplateBuildingBlockUsedBy <PKSim.Core.Model.PKSimEvent>(usedEvent);
}
eventMappingDTO.Event = templateEvent;
return(eventMappingDTO);
}
private TExpressionParameterDTO createExpressionContainerParameterDTOFrom(string containerName, string compartmentName,
string groupName, IParameter moleculeParameter)
{
var moleculeName = moleculeParameter.ParentContainer.Name;
var group = _groupRepository.GroupByName(groupName);
var dto = new TExpressionParameterDTO
{
MoleculeName = moleculeName,
ContainerName = containerName,
CompartmentName = compartmentName,
GroupName = groupName,
GroupingPathDTO = _representationInfoRepository.PathElementFor(RepresentationObjectType.GROUP, groupName),
ContainerPathDTO = _representationInfoRepository.PathElementFor(RepresentationObjectType.CONTAINER, containerName),
CompartmentPathDTO = _representationInfoRepository.PathElementFor(RepresentationObjectType.CONTAINER, compartmentName),
Sequence = group.Sequence
};
dto.Parameter = _parameterMapper.MapFrom(moleculeParameter, dto, x => x.Value, x => x.Parameter);
return(dto);
}