protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_expressionProfileEnzyme);
_newExpressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
A.CallTo(() => _expressionProfileFactory.Create(_snapshot.Type, _snapshot.Species, _snapshot.Molecule))
.Returns(_newExpressionProfile);
_snapshot.Localization = null;
_snapshot.IntracellularVascularEndoLocation = IntracellularVascularEndoLocation.Interstitial;
_snapshot.MembraneLocation = MembraneLocation.BloodBrainBarrier;
_snapshot.TissueLocation = TissueLocation.Interstitial;
//Add expression container to simulate v9 format
_snapshot.Expression = new[] { _relativeExpressionContainerSnapshot1, _relativeExpressionContainerSnapshot2, };
_relativeExpressionParameter1.Value = 0;
_relativeExpressionContainerSnapshot1.Value = 1000;
A.CallTo(() => _expressionContainerMapper.MapToModel(_relativeExpressionContainerSnapshot1, A <ExpressionContainerMapperContext> ._))
.Invokes(x => _relativeExpressionParameter1.Value = _relativeExpressionContainerSnapshot1.Value.Value);
_newExpressionProfile.Molecule.Ontogeny = null;
A.CallTo(() => _ontogenyMapper.MapToModel(_snapshot.Ontogeny, A <SnapshotContextWithSubject> .That.Matches(x => x.SimulationSubject == _newExpressionProfile.Individual))).Returns(_ontogeny);
var enzyme = _newExpressionProfile.Molecule.DowncastTo <IndividualEnzyme>();
//Localization is now set in task. We override behavior here and pretend that command was executed
A.CallTo(() => _moleculeExpressionTask.SetExpressionLocalizationFor(enzyme, A <Localization> ._, _newExpressionProfile.Individual))
.Invokes(x => enzyme.Localization = x.GetArgument <Localization>(1));
//Ensure that the parameter is at the right location so that it will be normalized
enzyme.Add(_relativeExpressionParameter1);
}
protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_expressionProfileOtherProtein);
_newOtherProteinExpressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualOtherProtein>();
A.CallTo(() => _expressionProfileFactory.Create(_snapshot.Type, _snapshot.Species, _snapshot.Molecule))
.Returns(_newOtherProteinExpressionProfile);
}
protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_expressionProfileTransporter);
_newTransporterExpressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>();
A.CallTo(() => _expressionProfileFactory.Create(_snapshot.Type, _snapshot.Species, _snapshot.Molecule))
.Returns(_newTransporterExpressionProfile);
_snapshot.TransportType = TransportType.PgpLike;
}
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 Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionContainerMapper = A.Fake <ExpressionContainerMapper>();
_expressionProfileFactory = A.Fake <IExpressionProfileFactory>();
_ontogenyMapper = A.Fake <OntogenyMapper>();
_ontogenyTask = A.Fake <IOntogenyTask>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_moleculeParameterTask = A.Fake <IMoleculeParameterTask>();
sut = new ExpressionProfileMapper(
_parameterMapper,
_expressionContainerMapper,
_ontogenyMapper,
_ontogenyTask,
_moleculeExpressionTask,
_expressionProfileFactory,
_moleculeParameterTask);
_ontogeny = new DatabaseOntogeny
{
Name = "Ontogeny"
};
_expressionProfileEnzyme = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>("Enzyme");
_expressionProfileEnzyme.Molecule.Ontogeny = _ontogeny;
_expressionProfileEnzyme.Description = "Help";
_expressionProfileTransporter = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>("Transporter");
_expressionProfileTransporter.Description = "Help";
_expressionProfileOtherProtein = DomainHelperForSpecs.CreateExpressionProfile <IndividualOtherProtein>("OtherProtein");
_enzymeGlobalParameter = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: true)
.WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_enzymeGlobalParameterSnapshot = new Parameter();
A.CallTo(() => _parameterMapper.MapToSnapshot(_enzymeGlobalParameter)).Returns(_enzymeGlobalParameterSnapshot);
_expressionContainer1 = new MoleculeExpressionContainer {
Name = "Exp Container1"
};
_expressionContainer2 = new MoleculeExpressionContainer {
Name = "Exp Container2"
};
_expressionProfileEnzyme.Individual.AddChildren(_expressionContainer1, _expressionContainer2, _enzymeGlobalParameter);
_expressionProfileEnzyme.Molecule.DowncastTo <IndividualEnzyme>().Localization = Localization.Intracellular | Localization.BloodCellsMembrane;
_relativeExpressionParameter1 = DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameters.REL_EXP);
_expressionContainer1.Add(_relativeExpressionParameter1);
_relativeExpressionParameterNotSet = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP);
_expressionContainer2.Add(_relativeExpressionParameterNotSet);
_relativeExpressionContainerSnapshot1 = new ExpressionContainer();
_relativeExpressionContainerSnapshot2 = new ExpressionContainer();
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer1)).Returns(_relativeExpressionContainerSnapshot1);
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer2)).Returns(_relativeExpressionContainerSnapshot2);
_snapshotOntogeny = new Snapshots.Ontogeny();
A.CallTo(() => _ontogenyMapper.MapToSnapshot(_ontogeny)).Returns(_snapshotOntogeny);
_individual = new Individual();
return(_completed);
}
protected override async Task Because()
{
_newOtherProteinExpressionProfile = await sut.MapToModel(_snapshot, new SnapshotContext());
}
protected override async Task Because()
{
_newExpressionProfile = await sut.MapToModel(_snapshot, new SnapshotContext(new PKSimProject(), ProjectVersions.V9));
}
