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 void Context()
{
base.Context();
_expressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.AddExpressionProfile(_expressionProfile);
_usedBuildingBlock = new UsedBuildingBlock(_expressionProfile.Id, _expressionProfile.BuildingBlockType);
_simulation1.AddUsedBuildingBlock(_usedBuildingBlock);
A.CallTo(() => _buildingBlockRepository.All(A <Func <ISimulationSubject, bool> > ._))
.Returns(new[] { _individual });
}
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 void Context()
{
_context = A.Fake <IExecutionContext>();
var expressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
(_molecule, _) = expressionProfile;
_protein = _molecule.DowncastTo <IndividualProtein>();
_result = new QueryExpressionResults(_expressionResults);
_simulationSubject = A.Fake <ISimulationSubject>();
sut = new EditIndividualMoleculeExpressionInSimulationSubjectFromQueryCommand(_molecule, _result, _simulationSubject);
A.CallTo(() => _simulationSubject.AllExpressionParametersFor(_molecule)).Returns(_allExpressionParameters);
}
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 Task Context()
{
_classificationMapper = A.Fake <ClassificationMapper>();
_snapshotMapper = A.Fake <ISnapshotMapper>();
_executionContext = A.Fake <IExecutionContext>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_simulationMapper = A.Fake <SimulationMapper>();
_simulationComparisonMapper = A.Fake <SimulationComparisonMapper>();
_parameterIdentificationMapper = A.Fake <ParameterIdentificationMapper>();
_classificationSnapshotTask = A.Fake <IClassificationSnapshotTask>();
_qualificationPlanMapper = A.Fake <QualificationPlanMapper>();
_creationMetaDataFactory = A.Fake <ICreationMetaDataFactory>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new ProjectMapper(
_simulationMapper,
_simulationComparisonMapper,
_parameterIdentificationMapper,
_qualificationPlanMapper,
_executionContext,
_classificationSnapshotTask,
_lazyLoadTask,
_creationMetaDataFactory,
_logger);
A.CallTo(() => _executionContext.Resolve <ISnapshotMapper>()).Returns(_snapshotMapper);
_individual = new Individual().WithName("IND");
_compound = new Compound().WithName("COMP");
_event = new PKSimEvent().WithName("EVENT");
_formulation = new Formulation().WithName("FORM");
_protocol = new SimpleProtocol().WithName("PROTO");
_population = new RandomPopulation().WithName("POP");
_observerSet = new ObserverSet().WithName("OBS_SET");
_observedData = new DataRepository().WithName("OD");
_expressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
_parameterIdentification = new OSPSuite.Core.Domain.ParameterIdentifications.ParameterIdentification().WithName("PI").WithId("PI_ID");
_classifiableObservedData = new ClassifiableObservedData {
Subject = _observedData
};
_classification = new Classification {
ClassificationType = ClassificationType.ObservedData
}.WithName("OD Classification");
_simulationComparison = new IndividualSimulationComparison().WithName("COMP").WithId("SimComp");
_simulation = new IndividualSimulation().WithName("IND_SIM").WithId("IndSim");
_qualificationPlan = new QualificationPlan().WithName("QP").WithId("QP_ID");
_project = new PKSimProject();
_project.AddBuildingBlock(_individual);
_project.AddBuildingBlock(_compound);
_project.AddBuildingBlock(_event);
_project.AddBuildingBlock(_formulation);
_project.AddBuildingBlock(_protocol);
_project.AddBuildingBlock(_population);
_project.AddBuildingBlock(_observerSet);
_project.AddObservedData(_observedData);
_project.AddBuildingBlock(_simulation);
_project.AddBuildingBlock(_expressionProfile);
_project.AddClassifiable(_classifiableObservedData);
_project.AddClassification(_classification);
_project.AddSimulationComparison(_simulationComparison);
_project.AddParameterIdentification(_parameterIdentification);
_project.AddQualificationPlan(_qualificationPlan);
_compoundSnapshot = new Snapshots.Compound();
_individualSnapshot = new Snapshots.Individual();
_eventSnapshot = new Event();
_observerSetSnapshot = new Snapshots.ObserverSet();
_formulationSnapshot = new Snapshots.Formulation();
_protocolSnapshot = new Snapshots.Protocol();
_populationSnapshot = new Snapshots.Population();
_observedDataSnapshot = new Snapshots.DataRepository();
_parameterIdentificationSnapshot = new ParameterIdentification();
_observedDataClassificationSnapshot = new Snapshots.Classification();
_simulationComparisonSnapshot = new SimulationComparison();
_simulationClassificationSnapshot = new Snapshots.Classification();
_comparisonClassificationSnapshot = new Snapshots.Classification();
_parameterIdentificationClassificationSnapshot = new Snapshots.Classification();
_qualificationPlanClassificationSnapshot = new Snapshots.Classification();
_qualificationPlanSnapshot = new Snapshots.QualificationPlan();
_expressionProfileSnapshot = new Snapshots.ExpressionProfile();
_simulationSnapshot = new Simulation();
A.CallTo(() => _snapshotMapper.MapToSnapshot(_compound)).Returns(_compoundSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_individual)).Returns(_individualSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_event)).Returns(_eventSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_formulation)).Returns(_formulationSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_protocol)).Returns(_protocolSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_population)).Returns(_populationSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_observedData)).Returns(_observedDataSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_observerSet)).Returns(_observerSetSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_expressionProfile)).Returns(_expressionProfileSnapshot);
A.CallTo(() => _simulationMapper.MapToSnapshot(_simulation, _project)).Returns(_simulationSnapshot);
A.CallTo(() => _simulationComparisonMapper.MapToSnapshot(_simulationComparison)).Returns(_simulationComparisonSnapshot);
A.CallTo(() => _parameterIdentificationMapper.MapToSnapshot(_parameterIdentification)).Returns(_parameterIdentificationSnapshot);
A.CallTo(() => _qualificationPlanMapper.MapToSnapshot(_qualificationPlan)).Returns(_qualificationPlanSnapshot);
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableObservedData>(_project)).Returns(new[] { _observedDataClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableSimulation>(_project)).Returns(new[] { _simulationClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableComparison>(_project)).Returns(new[] { _comparisonClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableParameterIdentification>(_project)).Returns(new[] { _parameterIdentificationClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableQualificationPlan>(_project)).Returns(new[] { _qualificationPlanClassificationSnapshot });
return(_completed);
}