public override void GlobalContext()
{
base.GlobalContext();
_simulation = DomainFactoryForSpecs.CreateDefaultSimulation();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
var compoundProperties = _simulation.CompoundPropertiesList.First();
_compoundName = compoundProperties.Compound.Name;
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _compoundName, QuantityType = QuantityType.Drug
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Enzyme", QuantityType = QuantityType.Enzyme
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Metabolite", QuantityType = QuantityType.Metabolite
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Protein", QuantityType = QuantityType.OtherProtein
});
var specificBindingSelection = new ProcessSelection {
CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Specific Binding"
};
var metabolizationSelection = new EnzymaticProcessSelection {
CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Metabolism"
};
_complexProductName = specificBindingSelection.ProductName(CoreConstants.Molecule.Complex);
_metaboliteProductName = specificBindingSelection.ProductName(CoreConstants.Molecule.Metabolite);
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _complexProductName, QuantityType = QuantityType.Complex
});
compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(specificBindingSelection);
compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(metabolizationSelection);
}
public override Task <IProcessMapping> MapToModel(CompoundProcessSelection snapshot, Model.CompoundProcess process)
{
IProcessMapping processMapping;
switch (process)
{
case SystemicProcess systemicProcess:
processMapping = new SystemicProcessSelection
{
ProcessType = systemicProcess.SystemicProcessType,
};
break;
case EnzymaticProcess _:
processMapping = new EnzymaticProcessSelection
{
MetaboliteName = snapshot.MetaboliteName,
};
break;
case InteractionProcess _:
processMapping = new InteractionSelection();
break;
default:
processMapping = new ProcessSelection();
break;
}
processMapping.ProcessName = snapshot.Name;
processMapping.CompoundName = process.ParentCompound.Name;
processMapping.MoleculeName = snapshot.MoleculeName;
return(Task.FromResult(processMapping));
}
protected override async Task Context()
{
await base.Context();
_noProcessSelection = new EnzymaticProcessSelection
{
MoleculeName = "CYP",
};
}
protected override Task Context()
{
sut = new ProcessMappingMapper();
_compound = new Compound
{
Name = "COMP",
};
_enzymaticProcess = new EnzymaticProcess().WithName("MetaProcess");
_enzymaticProcessSelection = new EnzymaticProcessSelection
{
CompoundName = _compound.Name,
MetaboliteName = "META",
MoleculeName = "CYP",
ProcessName = _enzymaticProcess.Name
};
_specificBindingProcess = new SpecificBindingPartialProcess().WithName("BindingProcess");
_specificBindingPartialProcessSelection = new ProcessSelection
{
CompoundName = _compound.Name,
MoleculeName = "BINDER",
ProcessName = _specificBindingProcess.Name
};
_transportSystemicProcess = new SystemicProcess
{
Name = "SystemicTransport",
SystemicProcessType = SystemicProcessTypes.GFR
};
_transportSystemicProcessSelection = new SystemicProcessSelection
{
CompoundName = _compound.Name,
ProcessName = _transportSystemicProcess.Name,
ProcessType = _transportSystemicProcess.SystemicProcessType
};
_interactionProcess = new InductionProcess().WithName("InteractionProcess");
_interactionSelection = new InteractionSelection
{
CompoundName = _compound.Name,
ProcessName = _interactionProcess.Name,
MoleculeName = "INHIBITOR"
};
_compound.AddProcess(_enzymaticProcess);
_compound.AddProcess(_transportSystemicProcess);
_compound.AddProcess(_interactionProcess);
_compound.AddProcess(_specificBindingProcess);
return(_completed);
}
protected override void Context()
{
base.Context();
_compound = new Compound().WithName("Comp");
_metabolite = new Compound().WithName("Metabolite");
_simulation = new IndividualSimulation();
_simulation.Properties = new SimulationProperties();
_simulation.Properties.AddCompoundProperties(new CompoundProperties {
Compound = _compound
});
_simulation.Properties.AddCompoundProperties(new CompoundProperties {
Compound = _metabolite
});
var enzymaticProcessSelection = new EnzymaticProcessSelection {
CompoundName = _compound.Name, MetaboliteName = _metabolite.Name
};
_simulation.CompoundPropertiesFor(_compound).Processes.MetabolizationSelection.AddPartialProcessSelection(enzymaticProcessSelection);
}
public override Task <IProcessMapping> MapToModel(CompoundProcessSelection snapshot, CompoundProcessSnapshotContext snapshotContext)
{
IProcessMapping processMapping;
var process = snapshotContext.Process;
switch (process)
{
case SystemicProcess systemicProcess:
processMapping = new SystemicProcessSelection
{
ProcessType = systemicProcess.SystemicProcessType,
};
break;
case EnzymaticProcess _:
processMapping = new EnzymaticProcessSelection
{
MetaboliteName = snapshot.MetaboliteName,
};
break;
case InteractionProcess _:
processMapping = new InteractionSelection();
break;
default:
processMapping = new ProcessSelection();
break;
}
processMapping.ProcessName = ModelValueFor(snapshot.Name);
//Parent compound may be null for process that are representing a non existent selection
processMapping.CompoundName = ModelValueFor(process.ParentCompound?.Name);
processMapping.MoleculeName = ModelValueFor(snapshot.MoleculeName);
return(Task.FromResult(processMapping));
}
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);
}
protected override async Task Because()
{
_processSelection = await sut.MapToModel(_snapshot, _enzymaticProcess) as EnzymaticProcessSelection;
}
protected override void Because()
{
_result = sut.Clone(A.Fake <ICloneManager>()) as EnzymaticProcessSelection;
}
protected override async Task Because()
{
_processSelection = await sut.MapToModel(_snapshot, new CompoundProcessSnapshotContext(_enzymaticProcess, new SnapshotContext())) as EnzymaticProcessSelection;
}
