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); }