private void addLiverZoneCompartmentObserver(IObserverBuilder observerBuilder, string compartment, IObserverBuildingBlock observerBuildingBlock, Compound compound) { var observerName = CoreConstants.CompositeNameFor(observerBuilder.Name, CoreConstants.Organ.Liver, compartment); if (observerBuildingBlock.ExistsByName(observerName)) { return; } var observer = _objectBaseFactory.Create <IContainerObserverBuilder>() .WithName(observerName) .WithDimension(_dimensionRepository.Fraction); observer.ForAll = false; observerBuilder.MoleculeNames().Each(observer.AddMoleculeName); observer.ContainerCriteria = Create.Criteria(x => x.With(CoreConstants.Organ.Liver) .And.With(compartment) .And.Not(CoreConstants.Compartment.Pericentral) .And.Not(CoreConstants.Compartment.Periportal)); var formula = _objectBaseFactory.Create <ExplicitFormula>() .WithName(observerName) .WithFormulaString("(M_periportal + M_pericentral)/" + TOTAL_DRUG_MASS_ALIAS) .WithDimension(_dimensionRepository.Fraction); formula.AddObjectPath(createZoneAmoutPath(compartment, CoreConstants.Compartment.Periportal, "M_periportal")); formula.AddObjectPath(createZoneAmoutPath(compartment, CoreConstants.Compartment.Pericentral, "M_pericentral")); formula.AddObjectPath(createTotalDrugMassObjectPath(compound.Name)); observer.Formula = formula; observerBuildingBlock.Add(observer); observerBuildingBlock.AddFormula(formula); }
protected override void Context() { _context = A.Fake <IMoBiContext>(); _buildingBlock = A.Fake <IBuildingBlock>(); _observerBuilder = new ContainerObserverBuilder(); sut = new TagTask(_context); }
protected override void Context() { base.Context(); _observer = new ObserverBuilder().WithName("NNNNNN"); _observer.ContainerCriteria.Add(new MatchTagCondition(_changedName)); _observerBuildingBlock = new ObserverBuildingBlock().WithName("Observer").WithId("Observer"); _observerBuildingBlock.Add(_observer); }
private IObserver addObserverInContainer(IObserverBuilder observerBuilder, IContainer observerContainer, QuantityType moleculeType) { var observer = _observerMapper.MapFrom(observerBuilder, _buildConfiguration); observer.QuantityType = QuantityType.Observer | moleculeType; observerContainer.Add(observer); return(observer); }
protected override void Context() { base.Context(); _simulationFactory = IoC.Resolve <ISimulationFactory>(); _buildConfigurationFactory = IoC.Resolve <IBuildConfigurationFactory>(); _modelConstructor = IoC.Resolve <IModelConstructor>(); _simulationSettingsFactory = IoC.Resolve <ISimulationSettingsFactory>(); _observerBuilder = IoC.Resolve <IObserverBuilder>(); _fileName = Helper.TestFileFullPath("tiny_example_12.xml"); }
protected override void Context() { base.Context(); _buildConfiguration = A.Fake <IBuildConfiguration>(); _observerBuilder = A.Fake <IObserverBuilder>().WithName("toto").WithDimension(A.Fake <IDimension>()); _observerBuilder.Formula = A.Fake <IFormula>(); _mappedFormula = A.Fake <IFormula>(); A.CallTo(() => _objectBaseFactory.Create <IObserver>()).Returns(A.Fake <IObserver>()); A.CallTo(() => _formulaMapper.MapFrom(_observerBuilder.Formula, _buildConfiguration)).Returns(_mappedFormula); }
protected override void SelectObserver(IObserverBuilder selectedObserver) { var containerObserver = selectedObserver as ContainerObserverBuilder; if (containerObserver == null) { return; } Select(_containerObserverBuilderToDTOContainerObserverBuilderMapper.MapFrom(containerObserver)); }
protected override void SelectObserver(IObserverBuilder selectedObserver) { var amountObserver = (IAmountObserverBuilder)selectedObserver; if (amountObserver == null) { return; } Select(_amountObserverBuilderToDTOAmountObserverBuilderMapper.MapFrom(amountObserver)); }
public UpdateDimensionInObserverBuilderCommand(IObserverBuilder observerBuilder, IDimension newDimension, IBuildingBlock observerBuildingBlock) : base(observerBuildingBlock) { _newDimension = newDimension; _oldDimension = observerBuilder.Dimension; _observerBuilder = observerBuilder; _observerBuilderId = observerBuilder.Id; ObjectType = ObjectTypes.ObserverBuilder; CommandType = AppConstants.Commands.EditCommand; Description = AppConstants.Commands.UpdateDimensions(observerBuilder.Name, ObjectType, _oldDimension, newDimension, observerBuildingBlock.Name); }
public void Edit(IObserverBuilder observer) { if (observer == null) { _view.Clear(); } else { _view.BindTo(_observerMapper.MapFrom(observer)); } }
protected T MapObserverBuilder <T>(T dto, IObserverBuilder observerBuilder) where T : ObserverBuilderDTO, new() { MapProperties(observerBuilder, dto); dto.Dimension = observerBuilder.Dimension; if (observerBuilder.Formula != null) { dto.Monitor = _formulaToDTOFormulaMapper.MapFrom(observerBuilder.Formula); dto.MonitorString = observerBuilder.Formula.ToString(); } return(dto); }
protected override void Context() { _observerLoader = A.Fake <IObserverLoader>(); _executionContext = A.Fake <IExecutionContext>(); _objectIdResetter = A.Fake <IObjectIdResetter>(); sut = new ObserverTask(_executionContext, _observerLoader, _objectIdResetter); _observer1 = new AmountObserverBuilder().WithName("OBS1"); _observer2 = new AmountObserverBuilder().WithName("OBS2"); _observerSet = new ObserverSet(); }
public IObserver MapFrom(IObserverBuilder observerBuilder, IBuildConfiguration buildConfiguration) { var observer = _objectBaseFactory.Create <IObserver>() .WithName(observerBuilder.Name) .WithIcon(observerBuilder.Icon) .WithDescription(observerBuilder.Description) .WithDimension(observerBuilder.Dimension) .WithFormula(_formulaMapper.MapFrom(observerBuilder.Formula, buildConfiguration)); buildConfiguration.AddBuilderReference(observer, observerBuilder); return(observer); }
public ObjectBaseSummaryDTO MapFrom(IObserverBuilder observerBuilder) { var dto = new ObjectBaseSummaryDTO { ApplicationIcon = ApplicationIcons.Observer, EntityName = observerBuilder.Name }; dto.AddToDictionary(AppConstants.Captions.Type, _objectTypeResolver.TypeFor(observerBuilder)); return(dto); }
public void TestSerializationObserverBuilderWithoutFormula() { ContainerObserverBuilder x1 = CreateObject <ContainerObserverBuilder>().WithName("Oberon.Builder"); x1.MoleculeList.ForAll = true; x1.AddMoleculeName("H2O"); x1.AddMoleculeName("CO2"); x1.AddMoleculeNameToExclude("NO2"); IObserverBuilder x2 = SerializeAndDeserialize(x1); AssertForSpecs.AreEqualObserverBuilder(x2, x1); }
protected override void Context() { _context = A.Fake <IMoBiContext>(); _buildingBlock = A.Fake <IBuildingBlock>(); _observerBuilder = new ContainerObserverBuilder(); sut = new TagTask(_context); _commandParameters = new TagConditionCommandParameters <IObserverBuilder> { BuildingBlock = _buildingBlock, DescriptorCriteriaRetriever = x => x.ContainerCriteria, TaggedObject = _observerBuilder }; }
protected override async Task Context() { await base.Context(); _snapshot = await sut.MapToSnapshot(_observerSet); A.CallTo(() => _observerSetFactory.Create()).Returns(new ObserverSet()); _snapshot.Name = "New Observer Set"; _snapshot.Description = "The description that will be deserialized"; _newObserverBuilder = new ContainerObserverBuilder(); A.CallTo(() => _observerMapper.MapToModel(_observerSnapshot)).Returns(_newObserverBuilder); }
protected override Task Context() { _descriptorConditionMapper = A.Fake <DescriptorConditionMapper>(); _explicitFormulaMapper = A.Fake <ExplicitFormulaMapper>(); _moleculeListMapper = A.Fake <MoleculeListMapper>(); _objectBaseFactory = A.Fake <IObjectBaseFactory>(); _dimensionRepository = A.Fake <IDimensionRepository>(); _logger = A.Fake <ILogger>(); _dimension = DomainHelperForSpecs.TimeDimensionForSpecs(); _amountObserver = new AmountObserverBuilder { Dimension = _dimension }; _containerObserver = new ContainerObserverBuilder { Dimension = _dimension }; _formula = new OSPSuite.Core.Domain.Formulas.ExplicitFormula("1+2"); _amountObserver.Formula = _formula; _containerObserver.Formula = _formula; _moleculeListSnapshot = new MoleculeList(); _snapshotFormula = new ExplicitFormula(); _newMoleculeList = new OSPSuite.Core.Domain.Builder.MoleculeList(); _newMoleculeList.AddMoleculeNameToExclude("A"); _newMoleculeList.AddMoleculeName("B"); _newMoleculeList.ForAll = false; _newFormula = new OSPSuite.Core.Domain.Formulas.ExplicitFormula("New"); sut = new ObserverMapper( _descriptorConditionMapper, _explicitFormulaMapper, _moleculeListMapper, _objectBaseFactory, _dimensionRepository, _logger); A.CallTo(() => _explicitFormulaMapper.MapToSnapshot(_formula)).Returns(_snapshotFormula); A.CallTo(() => _explicitFormulaMapper.MapToModel(_snapshotFormula)).Returns(_newFormula); A.CallTo(() => _moleculeListMapper.MapToSnapshot(_amountObserver.MoleculeList)).Returns(_moleculeListSnapshot); A.CallTo(() => _moleculeListMapper.MapToSnapshot(_containerObserver.MoleculeList)).Returns(_moleculeListSnapshot); A.CallTo(() => _moleculeListMapper.MapToModel(_moleculeListSnapshot)).Returns(_newMoleculeList); A.CallTo(() => _dimensionRepository.DimensionByName(_dimension.Name)).Returns(_dimension); A.CallTo(() => _objectBaseFactory.Create <AmountObserverBuilder>()).Returns(new AmountObserverBuilder()); A.CallTo(() => _objectBaseFactory.Create <ContainerObserverBuilder>()).Returns(new ContainerObserverBuilder()); return(_completed); }
protected override Task Context() { _observerMapper = A.Fake <ObserverMapper>(); _observerSetFactory = A.Fake <IObserverSetFactory>(); _observer = new AmountObserverBuilder(); _observerSet = new ObserverSet { _observer }; _observerSet.Name = "OBS_SET"; _observerSet.Description = "OBS_SET_DESCRIPTION"; sut = new ObserverSetMapper(_observerMapper, _observerSetFactory); _observerSnapshot = new Observer(); A.CallTo(() => _observerMapper.MapToSnapshot(_observer)).Returns(_observerSnapshot); return(_completed); }
public void TestSerializationObserverBuilderWithConstantFormula() { ContainerObserverBuilder x1 = CreateObject <ContainerObserverBuilder>() .WithName("Obasi.Builder").WithDimension(DimensionLength); x1.MoleculeList.ForAll = false; x1.AddMoleculeName("H2O"); x1.AddMoleculeName("CO2"); x1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4); IObserverBuilder x2 = SerializeAndDeserialize(x1); AssertForSpecs.AreEqualObserverBuilder(x2, x1); }
protected override void Context() { _buildingBlock = new ObserverBuildingBlock(); _context = A.Fake <IMoBiContext>(); _newDimension = DimensionFactoryForSpecs.Factory.Dimension(DimensionFactoryForSpecs.DimensionNames.Mass); _oldDimension = DimensionFactoryForSpecs.Factory.Dimension(DimensionFactoryForSpecs.DimensionNames.Concentration); _observedBuilder = new ObserverBuilder { Dimension = _oldDimension, Formula = new ConstantFormula(5).WithDimension(_oldDimension) }.WithId("5"); sut = new UpdateDimensionInObserverBuilderCommand(_observedBuilder, _newDimension, _buildingBlock); }
public override void GlobalContext() { base.GlobalContext(); _simulation = DomainFactoryForSpecs.CreateDefaultSimulation(); _moleculeBuildingBlock = new MoleculeBuildingBlock(); var compoundProperties = _simulation.CompoundPropertiesList.First(); _compoundName = compoundProperties.Compound.Name; _moleculeBuildingBlock.Add(new MoleculeBuilder { Name = _compoundName, QuantityType = QuantityType.Drug }); _moleculeBuildingBlock.Add(new MoleculeBuilder { Name = "Enzyme", QuantityType = QuantityType.Enzyme }); _moleculeBuildingBlock.Add(new MoleculeBuilder { Name = "Metabolite", QuantityType = QuantityType.Metabolite }); _moleculeBuildingBlock.Add(new MoleculeBuilder { Name = "Protein", QuantityType = QuantityType.OtherProtein }); var specificBindingSelection = new ProcessSelection { CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Specific Binding" }; var metabolizationSelection = new EnzymaticProcessSelection { CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Metabolism" }; _complexProductName = specificBindingSelection.ProductName(CoreConstants.Molecule.Complex); _metaboliteProductName = metabolizationSelection.ProductName(CoreConstants.Molecule.Metabolite); _moleculeBuildingBlock.Add(new MoleculeBuilder { Name = _complexProductName, QuantityType = QuantityType.Complex }); compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(specificBindingSelection); compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(metabolizationSelection); var observerSet = new ObserverSet(); var observerSetBuildingBlock = new UsedBuildingBlock("OBS_ID", PKSimBuildingBlockType.ObserverSet) { BuildingBlock = observerSet }; _observer = new AmountObserverBuilder().WithName("Test"); observerSet.Add(_observer); _simulation.AddUsedBuildingBlock(observerSetBuildingBlock); }
protected override void Context() { _view = A.Fake <IImportObserverSetView>(); _observerInfoPresenter = A.Fake <IObserverInfoPresenter>(); _dialogCreator = A.Fake <IDialogCreator>(); _observerTask = A.Fake <IObserverTask>(); _commandCollector = A.Fake <ICommandCollector>(); _observer1 = new ContainerObserverBuilder().WithName("OBS1"); _observer2 = new ContainerObserverBuilder().WithName("OBS2"); _observerSet = new ObserverSet { _observer1, _observer2 }; _entityTask = A.Fake <IEntityTask>(); A.CallTo(() => _view.BindTo(A <IReadOnlyList <ImportObserverDTO> > ._)) .Invokes(x => _allImportObserverDTO = x.GetArgument <IReadOnlyList <ImportObserverDTO> >(0)); sut = new ImportObserverSetPresenter(_view, _observerInfoPresenter, _dialogCreator, _observerTask, _entityTask); sut.InitializeWith(_commandCollector); }
public void TestSerializationObserverBuilderWithExplicitFormula() { ContainerObserverBuilder x1 = CreateObject <ContainerObserverBuilder>().WithName("Oberon.Builder"); x1.ForAll = false; x1.AddMoleculeName("H2O"); x1.AddMoleculeName("CO2"); ExplicitFormula f1 = CreateObject <ExplicitFormula>().WithName("Fortunato").WithDimension(DimensionLength); IFormulaUsablePath fup = new FormulaUsablePath(new string[] { "aa", "bb" }).WithAlias("b").WithDimension(DimensionLength); f1.AddObjectPath(fup); IFormulaCache formulaCache = new FormulaCache(); formulaCache.Add(f1); x1.Formula = formulaCache[f1.Id]; //SerializeAndDeserializeGeneral(formulaCache); IObserverBuilder x2 = SerializeAndDeserialize(x1); AssertForSpecs.AreEqualObserverBuilder(x2, x1); }
public IPKSimCommand RemoveObserver(IObserverBuilder observer, ObserverSet observerSet) { return(new RemoveObserverFromObserverSetCommand(observer, observerSet, _executionContext).Run(_executionContext)); }
public IPKSimCommand AddObserver(IObserverBuilder observer, ObserverSet observerSet) { return(new AddObserverToObserverSetCommand(observer, observerSet, _executionContext).Run(_executionContext)); }
public void Visit(IObserverBuilder observerBuilder) { checkMoleculeDependentBuilder(observerBuilder, ObjectTypes.ObserverBuilder); checkDescriptorCriteria(observerBuilder, x => x.ContainerCriteria); }
public static bool IsConcentration(this IObserverBuilder observerBuilder) { return(string.Equals(observerBuilder.Name, CoreConstants.Observer.CONCENTRATION_IN_CONTAINER)); }
private void addLiverZoneObserversBasedOn(IObserverBuilder observerBuilder, IObserverBuildingBlock observerBuildingBlock, Compound compound) { CoreConstants.Compartment.LiverCompartments.Each(compartment => addLiverZoneCompartmentObserver(observerBuilder, compartment, observerBuildingBlock, compound)); }
protected override async Task Because() { _result = await sut.MapToModel(_snapshot); }