private void updateAlternativeSelection(CompoundGroupSelection snapshotCompoundGroupSelection, ModelCompoundProperties compoundProperties)
{
var compoundGroupSelection = compoundProperties.CompoundGroupSelections.Find(x => x.GroupName == snapshotCompoundGroupSelection.GroupName);
if (compoundGroupSelection == null)
{
_logger.AddError(PKSimConstants.Error.CompoundGroupNotFoundFor(snapshotCompoundGroupSelection.GroupName, compoundProperties.Compound.Name));
return;
}
var alternativeGroup = compoundProperties.Compound.ParameterAlternativeGroup(snapshotCompoundGroupSelection.GroupName);
if (alternativeGroup == null)
{
_logger.AddError(PKSimConstants.Error.CompoundGroupNotFoundFor(snapshotCompoundGroupSelection.GroupName, compoundProperties.Compound.Name));
return;
}
var alternative = alternativeGroup.AlternativeByName(snapshotCompoundGroupSelection.AlternativeName);
if (alternative == null)
{
_logger.AddError(PKSimConstants.Error.CompoundAlternativeNotFoundFor(snapshotCompoundGroupSelection.AlternativeName, alternativeGroup.DefaultAlternative?.Name, snapshotCompoundGroupSelection.GroupName, compoundProperties.Compound.Name));
return;
}
compoundGroupSelection.AlternativeName = snapshotCompoundGroupSelection.AlternativeName;
}
public CompoundProperties MapFrom(Compound compound)
{
var compoundProperties = new CompoundProperties {
Compound = compound
};
foreach (var category in _categoryRepository.All())
{
var compoundCalculationMethod = compound.CalculationMethodFor(category) ?? category.DefaultItem;
compoundProperties.AddCalculationMethod(compoundCalculationMethod);
}
//update default mapping for alternatives in compound
foreach (var alternativeGroup in compound.AllParameterAlternativeGroups())
{
var compoundGroupSelection = new CompoundGroupSelection {
AlternativeName = alternativeGroup.DefaultAlternative.Name, GroupName = alternativeGroup.Name
};
compoundProperties.AddCompoundGroupSelection(compoundGroupSelection);
}
return(compoundProperties);
}
private IParameter getParameterForAlternative(Compound compound, CompoundProperties compoundProperties, CompoundGroupSelection alternativeSelection)
{
if (compound == null)
{
return(null);
}
var alternativeGroup = compound.ParameterAlternativeGroup(alternativeSelection.GroupName);
if (alternativeGroup == null)
{
return(null);
}
var alternative = alternativeGroup.AlternativeByName(alternativeSelection.AlternativeName);
if (alternative == null)
{
return(null);
}
var parameter = alternative.AllVisibleParameters().FirstOrDefault();
if (parameter == null)
{
return(null);
}
if (!CoreConstants.Groups.GroupsWithCalculatedAlternative.Contains(alternativeSelection.GroupName))
{
return(parameter);
}
//this is a calculated alternative. We need to retrieve the value depending on the selected lipophilicity
IEnumerable <IParameter> allParameters;
if (alternativeGroup.Name == CoreConstants.Groups.COMPOUND_PERMEABILITY)
{
allParameters = _compoundAlternativeTask.PermeabilityValuesFor(compound);
}
else
{
allParameters = _compoundAlternativeTask.IntestinalPermeabilityValuesFor(compound);
}
var lipophilicityName = compoundProperties.CompoundGroupSelections
.Where(x => x.GroupName == CoreConstants.Groups.COMPOUND_LIPOPHILICITY)
.Select(x => x.AlternativeName).FirstOrDefault();
return(allParameters.FirstOrDefault(x => x.IsNamed(lipophilicityName)));
}
protected override Task Context()
{
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMappingMapper = A.Fake <ProcessMappingMapper>();
_logger = A.Fake <ILogger>();
_project = new PKSimProject();
_calculationMethodSnapshot = new CalculationMethodCache();
sut = new CompoundPropertiesMapper(_calculationMethodCacheMapper, _processMappingMapper, _logger);
_compoundGroupSelectionOneAlternative = new CompoundGroupSelection
{
AlternativeName = "ALT1",
GroupName = "ALTERNATIVE_GROUP_1"
};
_compoundGroupSelectionTwoAlternatives = new CompoundGroupSelection
{
AlternativeName = "ALT2",
GroupName = "ALTERNATIVE_GROUP_2"
};
_compound = new Compound
{
Name = "COMP",
};
_protocol = new SimpleProtocol
{
Name = "PROTOCOL"
};
_parameterAlternativeGroupWithOneAlternative = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionOneAlternative.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionTwoAlternatives.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT1"
});
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT2"
});
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithOneAlternative);
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithTwoAlternatives);
_compoundProperties = new Model.CompoundProperties();
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionOneAlternative);
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionTwoAlternatives);
_compoundProperties.Compound = _compound;
_enzymaticProcess = new EnzymaticProcess {
Name = "EnzymaticProcess"
};
_anotherEnzymaticProcess = new EnzymaticProcess {
Name = "AnotherEnzymaticProcess", MoleculeName = "CYP3A4"
};
_specificBindingProcess = new SpecificBindingPartialProcess {
Name = "SpecificBinding"
};
_gfrTransportProcess = new SystemicProcess {
Name = "Transport", SystemicProcessType = SystemicProcessTypes.GFR
};
_hepaticEnzymaticProcess = new SystemicProcess {
Name = "Plasma Clearance", SystemicProcessType = SystemicProcessTypes.Hepatic
};
_compound.AddProcess(_enzymaticProcess);
_compound.AddProcess(_specificBindingProcess);
_compound.AddProcess(_gfrTransportProcess);
_compound.AddProcess(_hepaticEnzymaticProcess);
_enzymaticPartialProcessSelection = new EnzymaticProcessSelection {
ProcessName = _enzymaticProcess.Name
};
_noEnzymaticSystemicProcessSelection = new SystemicProcessSelection {
ProcessType = SystemicProcessTypes.Hepatic
};
_specificBindingPartialProcessSelection = new ProcessSelection {
ProcessName = _specificBindingProcess.Name
};
_transportSystemicProcessSelection = new SystemicProcessSelection {
ProcessName = _gfrTransportProcess.Name, ProcessType = _gfrTransportProcess.SystemicProcessType,
};
_noEnzymaticPartialProcessSelection = new EnzymaticProcessSelection {
MoleculeName = _anotherEnzymaticProcess.MoleculeName
};
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_enzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_noEnzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddSystemicProcessSelection(_noEnzymaticSystemicProcessSelection);
_compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(_specificBindingPartialProcessSelection);
_compoundProperties.Processes.TransportAndExcretionSelection.AddSystemicProcessSelection(_transportSystemicProcessSelection);
_snapshotProcess1 = new CompoundProcessSelection {
Name = _enzymaticPartialProcessSelection.ProcessName
};
_snapshotProcess2 = new CompoundProcessSelection {
Name = _specificBindingPartialProcessSelection.ProcessName
};
_snapshotProcess3 = new CompoundProcessSelection {
Name = _transportSystemicProcessSelection.ProcessName
};
_snapshotProcess4 = new CompoundProcessSelection {
SystemicProcessType = _noEnzymaticSystemicProcessSelection.ProcessType.SystemicProcessTypeId.ToString()
};
_snapshotProcess5 = new CompoundProcessSelection {
MoleculeName = _noEnzymaticPartialProcessSelection.MoleculeName
};
_formulation = new Formulation
{
Id = "123456"
};
_compoundProperties.ProtocolProperties.Protocol = _protocol;
_compoundProperties.ProtocolProperties.AddFormulationMapping(new FormulationMapping
{
FormulationKey = "F1",
TemplateFormulationId = _formulation.Id
});
_project.AddBuildingBlock(_formulation);
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compoundProperties.CalculationMethodCache)).Returns(_calculationMethodSnapshot);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_enzymaticPartialProcessSelection)).Returns(_snapshotProcess1);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_specificBindingPartialProcessSelection)).Returns(_snapshotProcess2);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_transportSystemicProcessSelection)).Returns(_snapshotProcess3);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticSystemicProcessSelection)).Returns(_snapshotProcess4);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticPartialProcessSelection)).Returns(_snapshotProcess5);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess1, _enzymaticProcess)).Returns(_enzymaticPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess2, _specificBindingProcess)).Returns(_specificBindingPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess3, _gfrTransportProcess)).Returns(_transportSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess4, A <NotSelectedSystemicProcess> ._)).Returns(_noEnzymaticSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess5, A <EnzymaticProcess> ._)).Returns(_noEnzymaticPartialProcessSelection);
return(_completed);
}