protected override async Task Context()
{
await base.Context();
_compoundCalculationMethod = new OSPSuite.Core.Domain.CalculationMethodCache();
_calculationMethodSnapshot = new CalculationMethodCache();
_categorialParameterIdentificationRunMode = new CategorialParameterIdentificationRunMode {
AllTheSame = false
};
_categorialParameterIdentificationRunMode.CalculationMethodsCache["C1"] = _compoundCalculationMethod;
A.CallTo(() => _calculationMethodMapper.MapToSnapshot(_compoundCalculationMethod)).Returns(_calculationMethodSnapshot);
}
public CalculationMethodCache CalculationMethodCacheFor(string compoundName)
{
if (AllTheSame)
{
return(AllTheSameSelection);
}
if (!CalculationMethodsCache.Contains(compoundName))
{
CalculationMethodsCache[compoundName] = new CalculationMethodCache();
}
return(CalculationMethodsCache[compoundName]);
}
protected override Task Context()
{
_calculationMethodRepository = A.Fake <ICalculationMethodRepository>();
_calculationMethodCategoryRepository = A.Fake <ICalculationMethodCategoryRepository>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new CalculationMethodCacheMapper(_calculationMethodRepository, _calculationMethodCategoryRepository, _logger);
_singleCategory = new CalculationMethodCategory {
Name = "Multiple"
};
_multipleCategory = new CalculationMethodCategory {
Name = "Single"
};
_calculationMethodWithMultipleOptions = new CalculationMethod
{
Name = "CM1",
DisplayName = "CM1",
Category = _multipleCategory.Name
};
_calculationMethodWithSingleOption = new CalculationMethod
{
Name = "CM2",
DisplayName = "CM2",
Category = _singleCategory.Name
};
_anotherCalculationMethodInMultipleOptions = new CalculationMethod
{
Name = "Another CM",
Category = _multipleCategory.Name
};
A.CallTo(() => _calculationMethodRepository.All()).Returns(new[] { _calculationMethodWithMultipleOptions, _anotherCalculationMethodInMultipleOptions, _calculationMethodWithSingleOption, });
_singleCategory.Add(_calculationMethodWithSingleOption);
_multipleCategory.Add(_calculationMethodWithMultipleOptions);
_multipleCategory.Add(_anotherCalculationMethodInMultipleOptions);
_calculationMethodCache = new CalculationMethodCache();
_calculationMethodCache.AddCalculationMethod(_calculationMethodWithMultipleOptions);
_calculationMethodCache.AddCalculationMethod(_calculationMethodWithSingleOption);
A.CallTo(() => _calculationMethodCategoryRepository.FindBy(_singleCategory.Name)).Returns(_singleCategory);
A.CallTo(() => _calculationMethodCategoryRepository.FindBy(_multipleCategory.Name)).Returns(_multipleCategory);
return(Task.FromResult(true));
}
public virtual CompoundProperties Clone(ICloneManager cloneManager)
{
var clone = new CompoundProperties
{
CalculationMethodCache = CalculationMethodCache.Clone(),
Processes = Processes.Clone(cloneManager),
ProtocolProperties = ProtocolProperties.Clone(),
//do not clone: simply update reference that should be changed if required
Compound = Compound
};
CompoundGroupSelections.Each(clone.AddCompoundGroupSelection);
return(clone);
}
protected override ParameterIdentificationRunMode CreateRunMode()
{
var calculationMethodRepository = IoC.Resolve <ICompoundCalculationMethodRepository>();
_categorialRunMode = new CategorialParameterIdentificationRunMode {
AllTheSame = false
};
_calculationMethod1 = calculationMethodRepository.All().ElementAt(0);
_calculationMethod2 = calculationMethodRepository.All().ElementAt(1);
_calculationMethodCache1 = new CalculationMethodCache();
_calculationMethodCache2 = new CalculationMethodCache();
_calculationMethodCache1.AddCalculationMethod(_calculationMethod1);
_calculationMethodCache1.AddCalculationMethod(_calculationMethod2);
_calculationMethodCache2.AddCalculationMethod(_calculationMethod2);
_categorialRunMode.CalculationMethodsCache.Add("Drug1", _calculationMethodCache1);
_categorialRunMode.CalculationMethodsCache.Add("Drug2", _calculationMethodCache2);
return(_categorialRunMode);
}
protected override void Context()
{
base.Context();
sut.AllTheSame = false;
var cacheComp1 = new CalculationMethodCache();
cacheComp1.AddCalculationMethod(_calculationMethod1);
cacheComp1.AddCalculationMethod(_calculationMethod2);
var cacheComp2 = new CalculationMethodCache();
cacheComp2.AddCalculationMethod(_calculationMethod3);
cacheComp2.AddCalculationMethod(_calculationMethod2);
sut.CalculationMethodsCache["Comp1"] = cacheComp1;
sut.CalculationMethodsCache["Comp2"] = cacheComp2;
sut.AllTheSameSelection.AddCalculationMethod(_calculationMethod1);
sut.AllTheSameSelection.AddCalculationMethod(_calculationMethod2);
sut.AllTheSameSelection.AddCalculationMethod(_calculationMethod3);
}
public virtual OriginData Clone()
{
return(new OriginData
{
Age = Age,
AgeUnit = AgeUnit,
Comment = Comment,
Height = Height,
HeightUnit = HeightUnit,
BMI = BMI,
BMIUnit = BMIUnit,
SpeciesPopulation = SpeciesPopulation,
Gender = Gender,
Species = Species,
SubPopulation = SubPopulation,
Weight = Weight,
WeightUnit = WeightUnit,
GestationalAge = GestationalAge,
CalculationMethodCache = CalculationMethodCache.Clone()
});
}
public virtual OriginData Clone()
{
var clone = new OriginData
{
Age = Age,
AgeUnit = AgeUnit,
Comment = Comment,
Height = Height,
HeightUnit = HeightUnit,
BMI = BMI,
BMIUnit = BMIUnit,
SpeciesPopulation = SpeciesPopulation,
Gender = Gender,
Species = Species,
SubPopulation = SubPopulation,
Weight = Weight,
WeightUnit = WeightUnit,
GestationalAge = GestationalAge,
CalculationMethodCache = CalculationMethodCache.Clone()
};
clone.UpdateValueOriginFrom(ValueOrigin);
return(clone);
}
private void updateCalculationMethodCache(OSPSuite.Core.Domain.CalculationMethodCache modelCalculationMethodCache, CalculationMethodCache snapshotCalculationMethodCache)
{
_calculationMethodCacheMapper.UpdateCalculationMethodCache(modelCalculationMethodCache, snapshotCalculationMethodCache, oneCalculationMethodPerCategory: false);
}
public OriginData()
{
CalculationMethodCache = new CalculationMethodCache();
}
public Compound() : base(PKSimBuildingBlockType.Compound)
{
CalculationMethodCache = new CalculationMethodCache();
}
public ModelProperties()
{
CalculationMethodCache = new CalculationMethodCache();
}
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);
}
public OriginData()
{
CalculationMethodCache = new CalculationMethodCache();
ValueOrigin = new ValueOrigin();
}
