protected SBMLImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, ASTHandler astHandler, IMoBiContext context) { ObjectPathFactory = objectPathFactory; ObjectBaseFactory = objectBaseFactory; _astHandler = astHandler; _context = context; }
protected override void Context() { _objectBaseFactory = A.Fake <IObjectBaseFactory>(); _rateObjectPathsRepository = A.Fake <IRateObjectPathsRepository>(); _rateFormulaRepository = A.Fake <IRateFormulaRepository>(); _distributionFactory = A.Fake <IDistributionFormulaFactory>(); _dimensionRepository = A.Fake <IDimensionRepository>(); _timeDimension = A.Fake <IDimension>(); _idGenerator = A.Fake <IIdGenerator>(); A.CallTo(() => _objectBaseFactory.Create <ExplicitFormula>()).Returns(new ExplicitFormula()); A.CallTo(() => _objectBaseFactory.Create <ConstantFormula>()).Returns(new ConstantFormula()); A.CallTo(() => _objectBaseFactory.Create <SumFormula>()).Returns(new SumFormula()); A.CallTo(() => _dimensionRepository.Time).Returns(_timeDimension); _objectPathFactory = new ObjectPathFactoryForSpecs(); _dynamicFormulaCriteriaRepo = A.Fake <IDynamicFormulaCriteriaRepository>(); _dynamicSumFormulaRateKey = new RateKey(CoreConstants.CalculationMethod.DynamicSumFormulas, "SomeFormula"); _sumFormulaCriteria = new DescriptorCriteria(); _sumFormulaCriteria.Add(new MatchTagCondition("xxx")); _sumFormulaCriteria.Add(new NotMatchTagCondition("yyy")); A.CallTo(() => _dynamicFormulaCriteriaRepo.CriteriaFor(_dynamicSumFormulaRateKey)).Returns(_sumFormulaCriteria); A.CallTo(() => _rateFormulaRepository.FormulaFor(_dynamicSumFormulaRateKey)).Returns("P_#i"); sut = new FormulaFactory(_objectBaseFactory, _rateObjectPathsRepository, _rateFormulaRepository, _distributionFactory, _objectPathFactory, _dimensionRepository, _idGenerator, _dynamicFormulaCriteriaRepo); }
/// <summary> /// Expands the dynamic formula using the list of available object that can be used in the formula /// </summary> public IFormula ExpandUsing(IReadOnlyList <IFormulaUsable> allFormulaUsable, IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory) { var explicitFormula = objectBaseFactory.Create <ExplicitFormula>().WithName(Name).WithFormulaString("0"); var allEntityToUse = allFormulaUsable.Where(Criteria.IsSatisfiedBy).ToList(); explicitFormula.Dimension = Dimension; //no entity to use in the dynamic formula? return if (allEntityToUse.Count == 0) { return(explicitFormula); } var stringBuilder = new StringBuilder(); for (int i = 0; i < allEntityToUse.Count; i++) { addDynamicVariablesToFormula(explicitFormula, stringBuilder, allEntityToUse[i], i, objectPathFactory); if (i < allEntityToUse.Count - 1) { stringBuilder.AppendFormat(" {0} ", Operation); } } explicitFormula.FormulaString = stringBuilder.ToString(); return(explicitFormula); }
public override void GlobalContext() { base.GlobalContext(); _objectPathFactory = IoC.Resolve <IObjectPathFactory>(); _modelCoreSimulation = IoC.Resolve <SimulationHelperForSpecs>().CreateSimulation(); var simModelExporter = IoC.Resolve <ISimModelExporter>(); var simModelSimulationFactory = A.Fake <ISimModelSimulationFactory>(); A.CallTo(() => simModelSimulationFactory.Create()).Returns(new Simulation()); _simModelManagerForSpecs = new SimModelManagerForSpecs(simModelExporter, simModelSimulationFactory); _simModelSimulation = _simModelManagerForSpecs.CreateSimulation(_modelCoreSimulation); _dataFactory = A.Fake <IDataFactory>(); _variableParameterPaths = new[] { _objectPathFactory.CreateObjectPathFrom(ConstantsForSpecs.Organism, ConstantsForSpecs.BW).PathAsString, _objectPathFactory.CreateObjectPathFrom(ConstantsForSpecs.Organism, ConstantsForSpecs.TableParameter1).PathAsString, }; _variableSpeciesPath = new [] { _objectPathFactory.CreateObjectPathFrom(ConstantsForSpecs.Organism, ConstantsForSpecs.ArterialBlood, ConstantsForSpecs.Plasma, "A").PathAsString, _objectPathFactory.CreateObjectPathFrom(ConstantsForSpecs.Organism, ConstantsForSpecs.VenousBlood, ConstantsForSpecs.Plasma, "B").PathAsString, }; sut = new SimModelBatch(simModelExporter, simModelSimulationFactory, _dataFactory); }
public FormulaTask(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IAliasCreator aliasCreator, IDimensionFactory dimensionFactory) { _objectPathFactory = objectPathFactory; _objectBaseFactory = objectBaseFactory; _aliasCreator = aliasCreator; _dimensionFactory = dimensionFactory; }
protected override void Context() { _dimensionFactory = A.Fake <IMoBiDimensionFactory>(); _eventPublisher = A.Fake <IEventPublisher>(); _objectBaseFactory = A.Fake <IObjectBaseFactory>(); _registerTask = A.Fake <IRegisterTask>(); _objectBaseRepository = A.Fake <IWithIdRepository>(); _moBiHistoryManagerFactory = A.Fake <IHistoryManagerFactory>(); _serializationService = A.Fake <IXmlSerializationService>(); _objectPathFactory = A.Fake <IObjectPathFactory>(); _unregisterTask = A.Fake <IUnregisterTask>(); _clipboardManager = A.Fake <IClipboardManager>(); _container = A.Fake <IContainer>(); _objectTypeResolver = A.Fake <IObjectTypeResolver>(); _cloneManager = A.Fake <ICloneManagerForBuildingBlock>(); _journalSession = A.Fake <IJournalSession>(); _fileLocker = A.Fake <IFileLocker>(); _lazyLoadTask = A.Fake <ILazyLoadTask>(); sut = new MoBiContext(_objectBaseFactory, _dimensionFactory, _eventPublisher, _serializationService, _objectPathFactory, _objectBaseRepository, _moBiHistoryManagerFactory, _registerTask, _unregisterTask, _clipboardManager, _container, _objectTypeResolver, _cloneManager, _journalSession, _fileLocker, _lazyLoadTask); A.CallTo(() => _moBiHistoryManagerFactory.Create()).Returns(A.Fake <MoBiHistoryManager>()); }
public ParameterImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, ASTHandler astHandler, IMoBiContext context, IUnitDefinitionImporter unitDefinitionImporter, IFormulaFactory formulaFactory) : base(objectPathFactory, objectBaseFactory, astHandler, context) { _paramList = new List <IEntity>(); _unitDefinitionImporter = unitDefinitionImporter; _formulaFactory = formulaFactory; }
protected override void Context() { _formulaUsablePathMapper = new FormulaUsablePathToFormulaUsablePathDTOMapper(); _objectPathFactory = new ObjectPathFactory(new AliasCreator()); _entityPathResolver = new EntityPathResolver(_objectPathFactory); sut = new ExplicitFormulaToExplicitFormulaDTOMapper(_formulaUsablePathMapper, _objectPathFactory, _entityPathResolver); _explicitFormula = new ExplicitFormula(); _explicitFormula.AddObjectPath( new FormulaUsablePath(ObjectPath.PARENT_CONTAINER, "P2") .WithDimension(DimensionFactoryForSpecs.MassDimension) .WithAlias(AppConstants.Param) ); _explicitFormula.FormulaString = "Param*2"; _topContainer = new Container().WithName("TOP"); _parentContainer = new Container().WithName("Parent"); _topContainer.Add(_parentContainer); _parameter = new Parameter().WithName("P").WithFormula(_explicitFormula); _parameter2 = new Parameter().WithName("P2").WithFormula(new ConstantFormula(2)); _parentContainer.Add(_parameter); _parentContainer.Add(_parameter2); }
protected override void Context() { _view = A.Fake <ISelectEventAssignmentTargetView>(); _context = A.Fake <IMoBiContext>(); _objectBaseDTOMapper = A.Fake <IObjectBaseToObjectBaseDTOMapper>(); _containerDTOMapper = A.Fake <IContainerToContainerDTOMapper>(); _reactionMapper = A.Fake <IReactionBuilderToDummyReactionDTOMapper>(); _moleculeMapper = A.Fake <IMoleculeBuilderToDummyMoleculeDTOMapper>(); _objectPathFactory = A.Fake <IObjectPathFactory>(); _parameterMapper = A.Fake <IParameterToDummyParameterDTOMapper>(); _dimensionRetriever = A.Fake <IReactionDimensionRetriever>(); sut = new SelectEventAssingmentTargetPresenter(_view, _context, _objectBaseDTOMapper, _containerDTOMapper, _reactionMapper, _moleculeMapper, _objectPathFactory, _parameterMapper, _dimensionRetriever); _mobiProject = A.Fake <IMoBiProject>(); _rootContainer = new Container(); _moleculeBuilder = new MoleculeBuilder().WithName("M"); _reaction = new ReactionBuilder().WithName("R"); _localParameter = new Parameter().WithMode(ParameterBuildMode.Local).WithName("LocalParam"); _globalParameter = new Parameter().WithMode(ParameterBuildMode.Global).WithName("GlobalParam"); _reaction.Add(_localParameter); _reaction.Add(_globalParameter); _reactionBB = new MoBiReactionBuildingBlock() { _reaction }; _moleculeBB = new MoleculeBuildingBlock { _moleculeBuilder }; A.CallTo(() => _mobiProject.ReactionBlockCollection).Returns(new [] { _reactionBB }); A.CallTo(() => _mobiProject.MoleculeBlockCollection).Returns(new [] { _moleculeBB }); sut.Init(_mobiProject, _rootContainer); }
public QuantityPathToQuantityDisplayPathMapper(IObjectPathFactory objectPathFactory, IPathToPathElementsMapper pathToPathElementsMapper, IDataColumnToPathElementsMapper dataColumnToPathElementsMapper) { _objectPathFactory = objectPathFactory; _pathToPathElementsMapper = pathToPathElementsMapper; _dataColumnToPathElementsMapper = dataColumnToPathElementsMapper; }
public CreateExportModelVisitor(IObjectPathFactory objectPathFactory, ITableFormulaToTableFormulaExportMapper tableFormulaExportMapper, IConcentrationBasedFormulaUpdater concentrationBasedFormulaUpdater) { _objectPathFactory = objectPathFactory; _tableFormulaExportMapper = tableFormulaExportMapper; _concentrationBasedFormulaUpdater = concentrationBasedFormulaUpdater; }
protected override void Context() { _objectPathFactory = new ObjectPathFactory(new AliasCreator()); _buildConfiguration = A.Fake <IBuildConfiguration>(); _validFormula = new ExplicitFormula("5*PAR1"); _validFormula.AddObjectPath(_objectPathFactory.CreateFormulaUsablePathFrom("ROOT", "VALID", "PARA1").WithAlias("PAR1")); _invalidFormula = new ExplicitFormula("toto"); _invalidFormula.AddObjectPath(_objectPathFactory.CreateFormulaUsablePathFrom("ROOT", "INVALID", "PARA5").WithAlias("PAR1")); _rootContainer = new Container().WithName("ROOT"); _validContainer = new Container().WithName("VALID"); _validContainer.Add(new Parameter().WithName("PARA1").WithFormula(new ConstantFormula(1))); _validContainer.Add(new Parameter().WithName("PARA2").WithFormula(_validFormula)); _validContainer.Add(new Reaction().WithName("REACTION").WithFormula(_validFormula)); _validContainer.Add(new Transport().WithName("TRANSPORT").WithFormula(_validFormula)); _invalidContainer = new Container().WithName("INVALID"); _invalidContainer.Add(new Parameter().WithName("PARA1").WithFormula(new ConstantFormula(1))); _invalidContainer.Add(new Parameter().WithName("PARA2").WithFormula(_invalidFormula)); _invalidContainer.Add(new Reaction().WithName("REACTION").WithFormula(_invalidFormula)); _invalidContainer.Add(new Transport().WithName("TRANSPORT").WithFormula(_invalidFormula)); _rootContainer.Add(_validContainer); _rootContainer.Add(_invalidContainer); _objectTypeResolver = A.Fake <IObjectTypeResolver>(); }
public ModelReportCreator(IObjectPathFactory objectPathFactory) { _objectPathFactory = objectPathFactory; _reportFormulaReferences = false; _reportFormulaObjectPaths = false; _reportDescriptions = false; }
protected override void Context() { var organism = new Container().WithName("Organism"); _objectPathFactory = new ObjectPathFactory(new AliasCreator()); _fuParameter = new Parameter().WithName("fu").WithValue(0.5); organism.Add(_fuParameter); var liver = new Container().WithName("Liver").WithParentContainer(organism); var liverVolume = new Parameter().WithName("Volume").WithValue(10).WithParentContainer(liver); var f_vas_liver = new Parameter().WithName("f_vas").WithValue(0.1); liver.Add(f_vas_liver); var kidney = new Container().WithName("Kidney").WithParentContainer(organism); var kidneyVolume = new Parameter().WithName("Volume").WithValue(20).WithParentContainer(kidney); kidney.Add(new Parameter().WithName("f_vas").WithValue(0.2)); sut = new SumFormula(); sut.Criteria = Create.Criteria(x => x.With("Volume")); sut.Variable = "V"; sut.FormulaString = "fu * V_#i * f_vas_#i"; sut.AddObjectPath(_objectPathFactory.CreateRelativeFormulaUsablePath(liverVolume, f_vas_liver).WithAlias("f_vas_#i")); sut.AddObjectPath(_objectPathFactory.CreateAbsoluteFormulaUsablePath(_fuParameter).WithAlias("fu")); sut.Dimension = new Dimension(new BaseDimensionRepresentation(), "dim1", "unit1"); _allFormulaUsable = organism.GetAllChildren <IFormulaUsable>().ToEntityDescriptorMapList(); _objectBaseFactory = A.Fake <IObjectBaseFactory>(); A.CallTo(() => _objectBaseFactory.Create <ExplicitFormula>()).Returns(new ExplicitFormula()); }
public FormulaUsablePathToFormulaUsablePathDTOMapper( IEntityPathResolver entityPathResolver, IObjectPathFactory objectPathFactory) { _entityPathResolver = entityPathResolver; _objectPathFactory = objectPathFactory; }
protected SelectReferencePresenterBase(ISelectReferenceView view, IObjectBaseToObjectBaseDTOMapper objectBaseDTOMapper, IMoBiContext context, IUserSettings userSettings, IObjectBaseToDummyMoleculeDTOMapper objectBaseToDummyMoleculeDTOMapper, IParameterToDummyParameterDTOMapper dummyParameterDTOMapper, IObjectBaseDTOToReferenceNodeMapper referenceMapper, IObjectPathCreator objectPathCreator, Localisations localisation) : base(view) { _objectPathCreator = objectPathCreator; _localisation = localisation; _dummyParameterDTOMapper = dummyParameterDTOMapper; _referenceMapper = referenceMapper; _dummyMoleculeDTOMapper = objectBaseToDummyMoleculeDTOMapper; _userSettings = userSettings; _context = context; _objectBaseDTOMapper = objectBaseDTOMapper; _objectPathFactory = _context.ObjectPathFactory; _view.ObjectPathType = _userSettings.ObjectPathType; _referenceMapper.Initialize(GetChildObjects); SelectionPredicate = parameter => true; }
public DataFactory(IDimensionFactory dimensionFactory, IDataNamingService dataNamingService, IObjectPathFactory objectPathFactory, IDisplayUnitRetriever displayUnitRetriever) { _dimensionFactory = dimensionFactory; _dataNamingService = dataNamingService; _objectPathFactory = objectPathFactory; _displayUnitRetriever = displayUnitRetriever; }
public DistributedParameterToTableParameterConverter( IFormulaFactory formulaFactory, IEntityPathResolver entityPathResolver, IParameterFactory parameterFactory, ICloneManager cloneManager, IParameterQuery parameterQuery, IDimensionRepository dimensionRepository, IOntogenyRepository ontogenyRepository, IFullPathDisplayResolver fullPathDisplayResolver, IInterpolation interpolation, IParameterStartValuesCreator parameterStartValuesCreator, IObjectPathFactory objectPathFactory, IGenderRepository genderRepository) { _formulaFactory = formulaFactory; _entityPathResolver = entityPathResolver; _parameterFactory = parameterFactory; _cloneManager = cloneManager; _parameterQuery = parameterQuery; _dimensionRepository = dimensionRepository; _ontogenyRepository = ontogenyRepository; _fullPathDisplayResolver = fullPathDisplayResolver; _interpolation = interpolation; _parameterStartValuesCreator = parameterStartValuesCreator; _objectPathFactory = objectPathFactory; _genderRepository = genderRepository; _timeDimension = dimensionRepository.Time; _yearUnit = _timeDimension.Unit(dimensionRepository.AgeInYears.BaseUnit.Name); }
protected IndividualMoleculeFactory(IObjectBaseFactory objectBaseFactory, IParameterFactory parameterFactory, IObjectPathFactory objectPathFactory, IEntityPathResolver entityPathResolver) { _objectBaseFactory = objectBaseFactory; _parameterFactory = parameterFactory; _objectPathFactory = objectPathFactory; _entityPathResolver = entityPathResolver; }
protected override void Context() { _randomGenerator = new RandomGenerator(); sut = new PKSimDistributedParameter().WithName("P"); _minValue = 5; _maxValue = 10; sut.Info.MinValue = _minValue; sut.Info.MaxValue = _maxValue; _pathFactory = new ObjectPathFactoryForSpecs(); _minimumParameter = new PKSimParameter { Name = Constants.Distribution.MINIMUM }.WithFormula(new ExplicitFormula("0")); _maximumParameter = new PKSimParameter { Name = Constants.Distribution.MAXIMUM }.WithFormula(new ExplicitFormula("1")); _percentileParameter = new PKSimParameter { Name = Constants.Distribution.PERCENTILE }.WithFormula(new ExplicitFormula("0.5")); sut.Add(_minimumParameter); sut.Add(_maximumParameter); sut.Add(_percentileParameter); _distributedFormula = new UniformDistributionFormula(); _distributedFormula.AddObjectPath(_pathFactory.CreateRelativeFormulaUsablePath(sut, _minimumParameter).WithAlias(Constants.Distribution.MINIMUM)); _distributedFormula.AddObjectPath(_pathFactory.CreateRelativeFormulaUsablePath(sut, _maximumParameter).WithAlias(Constants.Distribution.MAXIMUM)); sut.Formula = _distributedFormula; }
public ExplicitFormulaToExplicitFormulaDTOMapper(IFormulaUsablePathToFormulaUsablePathDTOMapper formulaUsablePathDTOMapper, IObjectPathFactory objectPathFactory, IEntityPathResolver entityPathResolver) { _formulaUsablePathDTOMapper = formulaUsablePathDTOMapper; _objectPathFactory = objectPathFactory; _entityPathResolver = entityPathResolver; }
protected override void Context() { _applicationController = A.Fake <IApplicationController>(); _buildingBlockTask = A.Fake <IBuildingBlockTask>(); _buildingBlockInSimulationManager = A.Fake <IBuildingBlockInSimulationManager>(); _lazyloadTask = A.Fake <ILazyLoadTask>(); _heavyWorkManager = A.Fake <IHeavyWorkManager>(); _containerTask = A.Fake <IContainerTask>(); _objectReferencingRetriever = A.Fake <IObjectReferencingRetriever>(); _projectRetriever = A.Fake <IProjectRetriever>(); _renameAbsolutePathVisitor = new RenameAbsolutePathVisitor(); _objectPathFactory = new ObjectPathFactoryForSpecs(); _parameterIdentificationSimulationPathUpdater = A.Fake <IParameterIdentificationSimulationPathUpdater>(); _dataRepositoryNamer = A.Fake <IDataRepositoryNamer>(); _curveNamer = A.Fake <ICurveNamer>(); sut = new RenameBuildingBlockTask(_buildingBlockTask, _buildingBlockInSimulationManager, _applicationController, _lazyloadTask, _containerTask, _heavyWorkManager, _renameAbsolutePathVisitor, _objectReferencingRetriever, _projectRetriever, _parameterIdentificationSimulationPathUpdater, _dataRepositoryNamer, _curveNamer); _initialSimulationName = "S"; _individualSimulation = new IndividualSimulation().WithName(_initialSimulationName); _individualSimulation.Model = new Model().WithName(_initialSimulationName); _simulation = _individualSimulation; _root = new Container().WithName(_initialSimulationName); _individualSimulation.Model.Root = _root; }
public FlatRateObjectToFormulaUsablePathMapper(IFlatObjectPathToObjectPathMapper objectPathMapper, IObjectPathFactory objectPathFactory, IDimensionRepository dimensionRepository) { _objectPathMapper = objectPathMapper; _objectPathFactory = objectPathFactory; _dimensionRepository = dimensionRepository; }
protected override void Context() { _objectBaseFactory = A.Fake <IObjectBaseFactory>(); _objectPathFactory = new ObjectPathFactory(new AliasCreator()); _aliasCreator = new AliasCreator(); _dimensionFactory = A.Fake <IDimensionFactory>(); sut = new FormulaTask(_objectPathFactory, _objectBaseFactory, _aliasCreator, _dimensionFactory); }
public NeighborhoodCollectionToContainerMapper(IObjectBaseFactory objectBaseFactory, INeighborhoodBuilderToNeighborhoodMapper neighborhoodMapper, IObjectPathFactory objectPathFactory) { _objectBaseFactory = objectBaseFactory; _neighborhoodMapper = neighborhoodMapper; _objectPathFactory = objectPathFactory; }
protected override void Context() { _objectPathFactory = A.Fake <IObjectPathFactory>(); _pathToPathElementMapper = A.Fake <IPathToPathElementsMapper>(); _dataColumnToPathElementsMapper = A.Fake <IDataColumnToPathElementsMapper>(); sut = new QuantityPathToQuantityDisplayPathMapper(_objectPathFactory, _pathToPathElementMapper, _dataColumnToPathElementsMapper); }
public CompartmentImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoBiSpatialStructureFactory spatialStructureFactory, IMoBiDimensionFactory moBiDimensionFactory, ASTHandler astHandler, IMoBiContext context) : base(objectPathFactory, objectBaseFactory, astHandler, context) { _objectBaseFactory = objectBaseFactory; _spatialStructureFactory = spatialStructureFactory; _dimensionFactory = moBiDimensionFactory; }
public MixedInhibitionKineticUpdaterSpecification(IObjectPathFactory objectPathFactory, IDimensionRepository dimensionRepository, IInteractionTask interactionTask) : base(objectPathFactory, dimensionRepository, interactionTask, InteractionType.MixedInhibition, kiNumeratorAlias: CoreConstants.Alias.MIXED_COMPETITIVE_INHIBITION_KI, kiNumeratorParameter: CoreConstants.Parameter.KI_C, kiDenominatorAlias: CoreConstants.Alias.MIXED_UNCOMPETITIVE_INHIBITION_KI, kiDenominatorParameter: CoreConstants.Parameter.KI_U, inhibitorAlias: CoreConstants.Alias.MIXED_COMPETIVE_INHIBITION_I) { }
protected override void Context() { _objectPathFactory = IoC.Resolve <IObjectPathFactory>(); var solverSettingsFactory = IoC.Resolve <ISolverSettingsFactory>(); _solverSettings = solverSettingsFactory.CreateCVODE(); _simulationExporterCreatorFactory = IoC.Resolve <ISimulationExportCreatorFactory>(); sut = new SimModelExporter(_simulationExporterCreatorFactory, new ExportSerializer(_simModelXmlSerializerRepository)); }
public DataRepositoryFromResultsCreator( IDimensionRepository dimensionRepository, IObjectPathFactory objectPathFactory, IDataRepositoryTask dataRepositoryTask) { _dimensionRepository = dimensionRepository; _objectPathFactory = objectPathFactory; _dataRepositoryTask = dataRepositoryTask; }