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);
}
private void addContainerExpression(ProteinExpressionDTO proteinExpressionDTO, IndividualProtein protein, MoleculeExpressionContainer moleculeExpressionContainer)
{
var expressionDTO = new ExpressionContainerDTO {
MoleculeName = protein.Name, ContainerName = moleculeExpressionContainer.Name
};
_expressionContainerDTOUpdater.UpdateProperties(expressionDTO, moleculeExpressionContainer);
proteinExpressionDTO.AddProteinExpression(expressionDTO);
}
protected override void Context()
{
base.Context();
_command = A.Fake <ICommand>();
_expressionContainerDTO = new ExpressionContainerDTO {
RelativeExpressionParameter = new ParameterDTO(_relativeExpressionParameter)
};
A.CallTo(() => _moleculeExpressionTask.SetRelativeExpressionInSimulationFor(_relativeExpressionParameter, _value)).Returns(_command);
}
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 void SetRelativeExpression(ExpressionContainerDTO expressionContainerDTO, double value)
{
AddCommand(_moleculeExpressionTask.SetRelativeExpressionFor(_protein, expressionContainerDTO.ContainerName, value));
}
public void SetFavorite(ExpressionContainerDTO protein, bool isFavorite)
{
SetFavorite(protein.RelativeExpressionParameter, isFavorite);
}
public void SetRelativeExpression(ExpressionContainerDTO protein, double valueInGuiUnit)
{
AddCommand(_moleculeExpressionTask.SetRelativeExpressionInSimulationFor(protein.RelativeExpressionParameter.Parameter, valueInGuiUnit));
}
public void SetFavorite(ExpressionContainerDTO expressionContainerDTO, bool isFavorite)
{
SetFavorite(expressionContainerDTO.RelativeExpressionParameter, isFavorite);
}
