public SBMLTask(IMoBiContext moBiContext,
SBMLImporterRepository importerRepository, IMoBiDimensionFactory moBiDimensionFactory)
{
_mobiContext = moBiContext;
_importerRepository = importerRepository;
_moBiDimensionFactory = moBiDimensionFactory;
}
protected void CreateDimensionFactory()
{
BaseDimensionRepresentation baseRepresentation = new BaseDimensionRepresentation();
_concentrationDimension = new Dimension(baseRepresentation, "Concentration", "mol");
_volumeDimension = new Dimension(baseRepresentation, "Volume", "l");
_volumeDimension.AddUnit("ml", 0.001, 0);
_timeDimension = new Dimension(baseRepresentation, "Time", "min");
_timeDimension.AddUnit("s", 1 / 60.0, 0);
_inversedTime = new Dimension(baseRepresentation, "Inversed time", "1/min");
_becquerel = new Dimension(baseRepresentation, "Becquerel", "1/min");
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
A.CallTo(() => _dimensionFactory.DimensionForUnit("mol")).Returns(_concentrationDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("ml")).Returns(_volumeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("s")).Returns(_timeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("1/min")).Returns(_inversedTime);
A.CallTo(() => _dimensionFactory.Has(_inversedTime.Name)).Returns(true);
A.CallTo(() => _dimensionFactory.Has(_becquerel.Name)).Returns(true);
A.CallTo(() => _dimensionFactory.DimensionForUnit("r/h")).Returns(null);
A.CallTo(() => _dimensionFactory.DimensionForUnit("")).Throws <Exception>();
A.CallTo(() => _dimensionFactory.Dimension(_becquerel.Name)).Returns(_becquerel);
A.CallTo(() => _dimensionFactory.Dimension(_inversedTime.Name)).Returns(_inversedTime);
}
protected override void Because()
{
_dimensionFactoy = IoC.Resolve <IMoBiDimensionFactory>();
sut = new UnitDefinitionImporter(IoC.Resolve <IObjectPathFactory>(), IoC.Resolve <IObjectBaseFactory>(), _dimensionFactoy, IoC.Resolve <ASTHandler>(), A.Fake <IMoBiContext>());
//create unit "substance"
_unit = new Unit(3, 1);
_unit.setExponent(1);
_unit.setMultiplier(1.0);
_unit.setScale(0);
_unit.setKind(libsbml.UNIT_KIND_MOLE);
//create unitdef "substance"
_unitDef = _sbmlModel.createUnitDefinition();
_unitDef.setId("substance");
_unitDef.setName("substance");
_unitDef.addUnit(_unit);
//create unit "volume"
_unit2 = _sbmlModel.createUnit();
_unit2.setExponent(1);
_unit2.setMultiplier(1.0);
_unit2.setScale(0);
_unit2.setKind(libsbml.UnitKind_forName("volume"));
//create unitdef "volume"
_unitDef2 = _sbmlModel.createUnitDefinition();
_unitDef2.setId("volume");
_unitDef2.setName("volume");
_unitDef2.addUnit(_unit2);
_sbmlModel.addUnitDefinition(_unitDef);
sut.DoImport(_sbmlModel, new MoBiProject(), A.Fake <SBMLInformation>(), new MoBiMacroCommand());
_substanceDimension = _dimensionFactoy.Dimension("SBML_substance");
_volumeDimension = _dimensionFactoy.Dimension("Volume");
}
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 InteractionTasksForDistributedParameter(IInteractionTaskContext interactionTaskContext, IEditTaskFor <IDistributedParameter> editTasks,
IMoBiDimensionFactory dimensionFactory, IParameterFactory parameterFactory, IDistributionFormulaFactory distributionFormulaFactory)
: base(interactionTaskContext, editTasks)
{
_dimensionFactory = dimensionFactory;
_parameterFactory = parameterFactory;
_distributionFormulaFactory = distributionFormulaFactory;
}
protected ObserverBuilderListPresenterBase(IObserverListView view, IFormulaToFormulaBuilderDTOMapper formulaToDTOFormulaMapper,
IMoBiDimensionFactory dimensionFactory, IViewItemContextMenuFactory viewItemContextMenuFactory, IMoBiContext context) : base(view)
{
_context = context;
_viewItemContextMenuFactory = viewItemContextMenuFactory;
_formulaToDTOFormulaMapper = formulaToDTOFormulaMapper;
_dimensionFactory = dimensionFactory;
}
protected override void Context()
{
_context = A.Fake <IInteractionTaskContext>();
_editTask = A.Fake <IEditTaskFor <IDistributedParameter> >();
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
_parameterFactory = A.Fake <IParameterFactory>();
_distributionFactory = A.Fake <IDistributionFormulaFactory>();
sut = new InteractionTasksForDistributedParameter(_context, _editTask, _dimensionFactory, _parameterFactory, _distributionFactory);
}
public SpeciesImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoleculeBuilderFactory moleculeBuilderFactory, IMoleculeStartValuesCreator moleculeStartValuesCreator, IMoBiDimensionFactory moBiDimensionFactory, ASTHandler astHandler, IMoBiContext context)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_moleculeBuilderFactory = moleculeBuilderFactory;
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_moBiDimensionFactory = moBiDimensionFactory;
_counter = 1;
_dimensionDictionary = new Dictionary <string, Dimension>();
}
protected override void Context()
{
_context = A.Fake <IInteractionTaskContext>();
_editTasks = A.Fake <IEditTaskFor <IParameter> >();
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
_formulaTask = A.Fake <IMoBiFormulaTask>();
_quantityTask = A.Fake <IQuantityTask>();
sut = new InteractionTasksForParameter(_context, _editTasks, _dimensionFactory, _formulaTask, _quantityTask);
}
protected override void Context()
{
_dimensionConverter = A.Fake <IDimensionConverter>();
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_formulaMapper = A.Fake <IFormulaMapper>();
_dimensionMapper = A.Fake <IDimensionMapper>();
_eventPublisher = A.Fake <IEventPublisher>();
sut = new Converter313To32(_dimensionConverter, _dimensionFactory, _objectBaseFactory, _formulaMapper, _dimensionMapper, _eventPublisher);
}
public Converter313To32(IDimensionConverter dimensionConverter, IMoBiDimensionFactory dimensionFactory,
IObjectBaseFactory objectBaseFactory, IFormulaMapper formulaMapper, IDimensionMapper dimensionMapper, IEventPublisher eventPublisher)
{
_dimensionConverter = dimensionConverter;
_dimensionFactory = dimensionFactory;
_objectBaseFactory = objectBaseFactory;
_formulaMapper = formulaMapper;
_dimensionMapper = dimensionMapper;
_eventPublisher = eventPublisher;
_objectTypeResolver = new ObjectTypeResolver();
_suspendWarning = false;
}
public InteractionTasksForParameter(
IInteractionTaskContext interactionTaskContext,
IEditTaskFor <IParameter> editTasks,
IMoBiDimensionFactory dimensionFactory,
IMoBiFormulaTask formulaTask,
IQuantityTask quantityTask) :
base(interactionTaskContext, editTasks)
{
_dimensionFactory = dimensionFactory;
_formulaTask = formulaTask;
_quantityTask = quantityTask;
}
public ASTHandler(IObjectBaseFactory obf, IObjectPathFactory objectPathFactory, IAliasCreator aliasCreator,
IMoBiDimensionFactory moBiDimensionFactory)
{
_objectBaseFactory = obf;
_objectPathFactory = objectPathFactory;
_objectPaths = new List <IFormulaUsablePath>();
_functionDefDictionary = new Dictionary <string, string>();
_aliasCreator = aliasCreator;
_moBiDimensionFactory = moBiDimensionFactory;
_counter = 0;
NeedAbsolutePath = false;
}
protected void CreateDimensionFactory()
{
_concentrationDimension = new Dimension();
_concentrationDimension.AddUnit("mol", 1.0, 0);
_volumeDimension = new Dimension();
_volumeDimension.AddUnit("ml", 0.001, 0);
_timeDimension = new Dimension();
_timeDimension.AddUnit("s", 1 / 60.0, 0);
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
A.CallTo(() => _dimensionFactory.DimensionForUnit("mol")).Returns(_concentrationDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("ml")).Returns(_volumeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("s")).Returns(_timeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("r/h")).Returns(null);
A.CallTo(() => _dimensionFactory.DimensionForUnit("")).Throws <Exception>();
}
public MoBiContext(IObjectBaseFactory objectBaseFactory, IMoBiDimensionFactory dimensionFactory, IEventPublisher eventPublisher,
IXmlSerializationService serializationService, IObjectPathFactory objectPathFactory, IWithIdRepository objectBaseRepository,
IHistoryManagerFactory historyManagerFactory, IRegisterTask registerTask, IUnregisterTask unregisterTask,
IClipboardManager clipboardManager, IContainer container, IObjectTypeResolver objectTypeResolver,
ICloneManagerForBuildingBlock cloneManager, IJournalSession journalSession, IFileLocker fileLocker, ILazyLoadTask lazyLoadTask) : base(eventPublisher, journalSession, fileLocker)
{
ObjectBaseFactory = objectBaseFactory;
ObjectRepository = objectBaseRepository;
EventPublisher = eventPublisher;
DimensionFactory = dimensionFactory;
ObjectPathFactory = objectPathFactory;
_serializationService = serializationService;
_container = container;
_objectTypeResolver = objectTypeResolver;
_cloneManager = cloneManager;
_lazyLoadTask = lazyLoadTask;
_historyManagerFactory = historyManagerFactory;
_registerTask = registerTask;
_unregisterTask = unregisterTask;
_clipboardManager = clipboardManager;
}
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 DataTableToImportQuantityDTOMapperForSimulations(IMoBiDimensionFactory dimensionFactory) : base(dimensionFactory)
{
}
protected DataTableToImportParameterQuantityDTOMapper(IMoBiDimensionFactory dimensionFactory)
: base(dimensionFactory)
{
}
protected AbstractDataTableProviderToQuantityDTOMapper(IMoBiDimensionFactory dimensionFactory)
{
_dimensionFactory = dimensionFactory;
}
public ReactionImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoBiDimensionFactory moBiDimensionFactory, ASTHandler astHandler, IMoBiContext context, IReactionBuildingBlockFactory reactionBuildingBlockFactory)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_dimensionFactory = moBiDimensionFactory;
ReactionBuilderList = new List <IReactionBuilder>();
_passiveTransportList = new List <ITransportBuilder>();
_reactionBuildingBlock = reactionBuildingBlockFactory.Create().WithName(SBMLConstants.SBML_REACTION_BB);
_passiveTransportBuildingBlock = ObjectBaseFactory.Create <IPassiveTransportBuildingBlock>()
.WithName(SBMLConstants.SBML_PASSIVETRANSPORTS_BB);
}
private void initialiseDimensionFactory()
{
_moBiDimensionFactory = new MoBiDimensionFactory();
_mobiContext.DimensionFactory.Dimensions.Each(_moBiDimensionFactory.AddDimension);
}
public CompartmentImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory,
IMoBiSpatialStructureFactory spatialStructureFactory, IMoBiDimensionFactory moBiDimensionFactory,
ASTHandler astHandler, IMoBiContext context, IFormulaFactory formulaFactory, IUnitDefinitionImporter unitDefinitionImporter)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_objectBaseFactory = objectBaseFactory;
_spatialStructureFactory = spatialStructureFactory;
_dimensionFactory = moBiDimensionFactory;
_formulaFactory = formulaFactory;
_unitDefinitionImporter = unitDefinitionImporter;
}
private void initialiseDimensionFactory(IMoBiProject project)
{
_moBiDimensionFactory = new MoBiDimensionFactory();
_mobiContext.DimensionFactory.BaseFactory.Dimensions.Each(_moBiDimensionFactory.BaseFactory.AddDimension);
project.DimensionFactory.Dimensions.Each(_moBiDimensionFactory.ProjectFactory.AddDimension);
}
public DataTableToImportQuantityDTOMapperForMolecules(IMoBiDimensionFactory dimensionFactory, IReactionDimensionRetriever reactionDimensionRetriever) : base(dimensionFactory)
{
_reactionDimensionRetriever = reactionDimensionRetriever;
}
public ContainerObserverBuilderListPresenter(IObserverListView view, IFormulaToFormulaBuilderDTOMapper formulaToDTOFormulaMapper, IMoBiDimensionFactory dimensionFactory, IObserverBuilderToDTOObserverBuilderMapper containerObserverBuilderToDTOContainerObserverBuilderMapper, IViewItemContextMenuFactory viewItemContextMenuFactory, IMoBiContext context)
: base(view, formulaToDTOFormulaMapper, dimensionFactory, viewItemContextMenuFactory, context)
{
_containerObserverBuilderToDTOContainerObserverBuilderMapper = containerObserverBuilderToDTOContainerObserverBuilderMapper;
}
public UnitDefinitionImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoBiDimensionFactory mobiDimensionFactory, ASTHandler astHandler, IMoBiContext context) : base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_moBiDimensionFactory = mobiDimensionFactory;
_baseUnitsDictionary = new Dictionary <int, Unit>();
InitBaseUnitsDictionary();
}
public DataTableToImportQuantityDTOMapperForParameters(IMoBiDimensionFactory dimensionFactory)
: base(dimensionFactory)
{
}
