protected override Task Context()
{
_alternativeMapper = A.Fake <AlternativeMapper>();
_parameterMapper = A.Fake <ParameterMapper>();
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMapper = A.Fake <CompoundProcessMapper>();
_compoundFactory = A.Fake <ICompoundFactory>();
sut = new CompoundMapper(_parameterMapper, _alternativeMapper, _calculationMethodCacheMapper, _processMapper, _compoundFactory);
_compound = new Model.Compound
{
Name = "Compound",
Description = "Description"
};
addPkAParameters(_compound, 0, 8, CompoundType.Base);
addPkAParameters(_compound, 1, 4, CompoundType.Acid);
addPkAParameters(_compound, 2, 7, CompoundType.Neutral);
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.IS_SMALL_MOLECULE));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue((int)PlasmaProteinBindingPartner.Glycoprotein).WithName(CoreConstants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER));
_partialProcess = new EnzymaticProcess().WithName("EnzymaticProcess");
_systemicProcess = new SystemicProcess().WithName("SystemicProcess");
_compound.AddProcess(_partialProcess);
_compound.AddProcess(_systemicProcess);
_calculationMethodCacheSnapshot = new CalculationMethodCache();
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compound.CalculationMethodCache)).Returns(_calculationMethodCacheSnapshot);
_snapshotProcess1 = new CompoundProcess();
_snapshotProcess2 = new CompoundProcess();
A.CallTo(() => _processMapper.MapToSnapshot(_partialProcess)).Returns(_snapshotProcess1);
A.CallTo(() => _processMapper.MapToSnapshot(_systemicProcess)).Returns(_snapshotProcess2);
return(_completed);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_alternativeMapper = A.Fake <AlternativeMapper>();
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMapper = A.Fake <CompoundProcessMapper>();
_compoundFactory = A.Fake <ICompoundFactory>();
_valueOriginMapper = A.Fake <ValueOriginMapper>();
sut = new CompoundMapper(_parameterMapper, _alternativeMapper, _calculationMethodCacheMapper, _processMapper, _valueOriginMapper, _compoundFactory);
_compound = new Model.Compound
{
Name = "Compound",
Description = "Description"
};
_pkaValueOrigin = new ValueOrigin {
Method = ValueOriginDeterminationMethods.InVitro, Description = "PKA"
};
_snapshotValueOrigin = new Snapshots.ValueOrigin {
Method = ValueOriginDeterminationMethodId.InVivo, Description = "PKA"
};
addPkAParameters(_compound, 0, 8, CompoundType.Base);
addPkAParameters(_compound, 1, 4, CompoundType.Acid);
addPkAParameters(_compound, 2, 7, CompoundType.Neutral);
_compoundIntestinalPermeabilityAlternativeGroup = createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY);
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY));
_compound.AddParameterAlternativeGroup(_compoundIntestinalPermeabilityAlternativeGroup);
_compoundIntestinalPermeabilityAlternativeGroup.DefaultAlternative.IsDefault = true;
//Calculated alternative will not be the default alternative for intestinal perm
_calculatedAlternative = new ParameterAlternative {
Name = PKSimConstants.UI.CalculatedAlernative, IsDefault = false
};
_compoundIntestinalPermeabilityAlternativeGroup.AddAlternative(_calculatedAlternative);
//Mapping of a calculated alternative returns null
A.CallTo(() => _alternativeMapper.MapToSnapshot(_calculatedAlternative)).Returns(Task.FromResult <Alternative>(null));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.IS_SMALL_MOLECULE));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue((int)PlasmaProteinBindingPartner.Glycoprotein).WithName(CoreConstants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER));
_partialProcess = new EnzymaticProcess().WithName("EnzymaticProcess");
_systemicProcess = new SystemicProcess().WithName("SystemicProcess");
_compound.AddProcess(_partialProcess);
_compound.AddProcess(_systemicProcess);
_calculationMethodCacheSnapshot = new CalculationMethodCache();
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compound.CalculationMethodCache)).Returns(_calculationMethodCacheSnapshot);
_snapshotProcess1 = new CompoundProcess();
_snapshotProcess2 = new CompoundProcess();
A.CallTo(() => _processMapper.MapToSnapshot(_partialProcess)).Returns(_snapshotProcess1);
A.CallTo(() => _processMapper.MapToSnapshot(_systemicProcess)).Returns(_snapshotProcess2);
_molweightParameter = DomainHelperForSpecs.ConstantParameterWithValue(400).WithName(Constants.Parameters.MOL_WEIGHT);
_molweightParameter.ValueOrigin.Method = ValueOriginDeterminationMethods.InVivo;
//Do not update F value origin to ensure that it's being synchronized when mapping from snapshot
_halogenFParameter = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(Constants.Parameters.F);
_compound.Add(_molweightParameter);
_compound.Add(_halogenFParameter);
return(_completed);
}
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);
}