private Individual createIndividual()
{
var originData = new OriginData
{
Species = CoreConstants.Species.HUMAN,
Population = CoreConstants.Population.ICRP,
Age = new Parameter
{
Value = 30,
Unit = "year(s)",
},
Weight = new Parameter
{
Value = 75,
Unit = "kg",
},
Height = new Parameter
{
Value = 175,
Unit = "cm",
},
Gender = CoreConstants.Gender.MALE
};
var modelOriginData = _originDataMapper.MapToModel(originData, new SnapshotContext()).Result;
var individual = _individualFactory.CreateAndOptimizeFor(modelOriginData);
return(individual);
}
protected override void Context()
{
base.Context();
var originData = new OriginData
{
Species = CoreConstants.Species.HUMAN,
Population = CoreConstants.Population.ICRP,
};
originData.AddCalculationMethods("SurfaceAreaPlsInt_VAR1");
_settings = new PopulationSettings
{
Individual = new Individual
{
OriginData = originData
},
Age = new ParameterRange
{
Min = 0,
Max = 80,
Unit = "year(s)",
},
Weight = new ParameterRange
{
Min = 70,
Unit = "kg",
},
NumberOfIndividuals = 10,
ProportionOfFemales = 70
};
_moleculeOntogenies = new [] { new MoleculeOntogeny("CYP3A4", "CYP3A4"), new MoleculeOntogeny("CYP2D6", "CYP2D6") };
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_moleculeMapper = A.Fake <MoleculeMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
sut = new IndividualMapper(_parameterMapper, _moleculeMapper, _originDataMapper, _individualFactory);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Liver, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Kidney, "PKidney");
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_enzyme = new IndividualEnzyme
{
Name = "Enz",
};
_individual.AddMolecule(_enzyme);
_transporter = new IndividualTransporter
{
Name = "Trans",
};
_individual.AddMolecule(_transporter);
_enzymeSnapshot = new Molecule {
Type = QuantityType.Enzyme
};
_transporterSnapshot = new Molecule {
Type = QuantityType.Transporter
};
A.CallTo(() => _moleculeMapper.MapToSnapshot(_enzyme)).Returns(_enzymeSnapshot);
A.CallTo(() => _moleculeMapper.MapToSnapshot(_transporter)).Returns(_transporterSnapshot);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > .That.Contains(_parameterKidney))).Returns(new[] { _localizedParameterKidney });
return(_completed);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionProfileMapper = A.Fake <ExpressionProfileMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <ModelIndividual> >();
sut = new IndividualMapper(_parameterMapper, _expressionProfileMapper, _originDataMapper, _individualFactory, _moleculeExpressionTask);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
var kidney = _individual.EntityAt <IContainer>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY);
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.LIVER, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY, "PKidney");
_parameterKidneyRelExp = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.REL_EXP);
_parameterKidneyRelExp.DefaultValue = 10;
kidney.Add(_parameterKidneyRelExp);
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_parameterKidneyRelExp.Value = 50;
_parameterKidneyRelExp.ValueDiffersFromDefault().ShouldBeTrue();
_expressionProfile1 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(moleculeName: "Enz");
_expressionProfile2 = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>(moleculeName: "Trans");
_individual.AddExpressionProfile(_expressionProfile1);
_individual.AddExpressionProfile(_expressionProfile2);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > ._))
.Invokes(x => _mappedParameters = x.GetArgument <IEnumerable <IParameter> >(0).ToList())
.Returns(new[] { _localizedParameterKidney });
return(_completed);
}
protected override void Context()
{
base.Context();
var originData = new OriginData
{
Species = CoreConstants.Species.HUMAN,
Population = CoreConstants.Population.PRETERM,
};
originData.AddCalculationMethods("SurfaceAreaPlsInt_VAR1");
_settings = new PopulationSettings
{
Individual = new Individual
{
OriginData = originData
},
Age = new ParameterRange
{
Min = 0,
Max = 80,
Unit = "year(s)",
},
Weight = new ParameterRange
{
Min = 70,
Unit = "kg",
},
GestationalAge = new ParameterRange
{
Min = 30,
Max = 35,
Unit = "week(s)",
},
NumberOfIndividuals = 10,
ProportionOfFemales = 70
};
}
