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 bool Edit(IParameter tableParameter)
{
_tableParameterPresenter.Edit(tableParameter);
_view.Caption = PKSimConstants.UI.EditTableParameter(_fullPathDisplayResolver.FullPathFor(tableParameter), tableParameter.Editable);
_view.CancelVisible = tableParameter.Editable;
plotTable();
_view.Display();
return(tableParameter.Editable && !_view.Canceled);
}
private void addParameterNode(ITreeNode node, IParameter parameter, PathElement pathElementDTO)
{
var representation = new RepresentationInfo {
DisplayName = pathElementDTO.DisplayName, IconName = pathElementDTO.IconName
};
var parameterNode = _treeNodeFactory.CreateFor(parameter, representation);
parameterNode.ToolTip = _toolTipPartCreator.ToolTipFor(_fullPathDisplayResolver.FullPathFor(parameter));
node.AddChild(parameterNode);
}
private void displayMissingParametersMessage(ValidationResult validationResult)
{
if (validationResult.ValidationState == ValidationState.Valid)
{
return;
}
var missingParameters = validationResult.Messages.Select(x => _fullPathDisplayResolver.FullPathFor(x.Object));
_dialogCreator.MessageBoxInfo(PKSimConstants.Warning.MissingSimulationParametersWereOverwritten(missingParameters));
}
public PopulationAnalysisParameterField CreateFor(IParameter parameter)
{
var field = new PopulationAnalysisParameterField
{
ParameterPath = _entityPathResolver.PathFor(parameter),
Name = _fullPathDisplayResolver.FullPathFor(parameter),
};
updateDimension(parameter, field);
return(field);
}
public ParameterScalingDTO MapFrom(ParameterScaling parameterScaling)
{
var parameterScalingDTO = new ParameterScalingDTO(parameterScaling)
{
ParameterFullPathDisplay = _fullPathDisplayResolver.FullPathFor(parameterScaling.SourceParameter),
SourceParameter = _parameterDTOMapper.MapFrom(parameterScaling.SourceParameter),
TargetParameter = _parameterDTOMapper.MapFrom(parameterScaling.TargetParameter),
ScalingMethod = parameterScaling.ScalingMethod
};
return(parameterScalingDTO);
}
private void validateScalingForSharedOutputMappings(OutputMapping mapping, ParameterIdentification parameterIdentification, ValidationResult validationResult)
{
var allOutputScalings = scalingsMappedForOutput(mapping, parameterIdentification);
if (allOutputScalings.Count() == 1)
{
return;
}
var displayPathAsString = _fullPathDisplayResolver.FullPathFor(parameterIdentification, addSimulationName: true);
validationResult.AddMessage(NotificationType.Error, parameterIdentification, Error.OutputsDoNotAllHaveTheSameScaling(displayPathAsString));
}
public ValidationMessageDTO MapFrom(ValidationMessage validationMessage)
{
var dto = new ValidationMessageDTO
{
Message = validationMessage.Text,
ObjectDescription = _fullPathDisplayResolver.FullPathFor(validationMessage.Object),
Status = validationMessage.NotificationType,
Icon = iconFrom(validationMessage.NotificationType)
};
dto.AddDetails(validationMessage.Details);
return(dto);
}
private IEnumerable <object> anatomyAndPhysiologyFor(Individual individual)
{
var report = new List <object>();
var allParameters = _containerTask.CacheAllChildrenSatisfying <IParameter>(individual, valueShouldBeExportedForAnatomy);
if (!allParameters.Any())
{
report.Add(PKSimConstants.UI.Default);
return(report);
}
var dataTable = new DataTable {
TableName = PKSimConstants.UI.AnatomyAndPhysiology
};
dataTable.AddColumn(PKSimConstants.UI.Parameter);
dataTable.AddColumn(PKSimConstants.UI.Value);
dataTable.AddColumn(PKSimConstants.UI.DefaultValue);
foreach (var parameter in allParameters)
{
var row = dataTable.NewRow();
row[PKSimConstants.UI.Parameter] = _fullPathDisplayResolver.FullPathFor(parameter);
row[PKSimConstants.UI.Value] = ParameterMessages.DisplayValueFor(parameter);
row[PKSimConstants.UI.DefaultValue] = ParameterMessages.DisplayValueFor(parameter, parameter.DefaultValue.GetValueOrDefault(parameter.Value));
dataTable.Rows.Add(row);
}
var table = new Table(dataTable.DefaultView, new Text(dataTable.TableName));
var reference = new Reference(table);
var text = new Text(PKSimConstants.UI.AnatomyAndPhysiologyText, reference);
report.Add(text);
report.Add(table);
return(report);
}
private string uniqueNameFor(SensitivityAnalysis sensitivityAnalysis, IParameter parameter)
{
var defaultName = _fullPathDisplayResolver.FullPathFor(parameter);
return(_containerTask.CreateUniqueName(sensitivityAnalysis.AllSensitivityParameters, defaultName, canUseBaseName: true));
}
public string DisplayNameFor(IObjectBase objectBase)
{
return(_fullPathDisplayResolver.FullPathFor(objectBase));
}
public string SensitivityParameterNameForParameter(IParameter parameter) => _fullPathDisplayResolver.FullPathFor(parameter);