public override void GlobalContext()
{
base.GlobalContext();
_project = LoadProject("331_TestGI");
_spatialStructure = _project.SpatialStructureCollection.First();
_organism = _spatialStructure.TopContainers.FindByName(Constants.ORGANISM);
}
public void UpdateSpatialStructre(IMoBiSpatialStructure spatialStructure)
{
foreach (var topContainer in spatialStructure.TopContainers)
{
UpdateContainerTo3_1_3(topContainer);
}
}
protected override void Context()
{
base.Context();
_spatialStructure = A.Fake <IMoBiSpatialStructure>();
_topContainer = A.Fake <IContainer>();
A.CallTo(() => _spatialStructure.TopContainers).Returns(new[] { _topContainer });
}
private SpatialStructureDTO createSpatialStuctureDTOFrom(IMoBiSpatialStructure spatialStructure)
{
var dto = new SpatialStructureDTO();
dto.Id = spatialStructure.Id;
dto.Name = spatialStructure.Name;
dto.Icon = spatialStructure.Icon;
if (_localisation.Is(Localisations.ContainerOnly))
{
dto.TopContainer = spatialStructure.TopContainers.MapAllUsing(_dtoContainerMapper);
}
if (_localisation.Is(Localisations.NeighborhoodsOnly))
{
dto.Neighborhoods = _dtoContainerMapper.MapFrom(spatialStructure.NeighborhoodsContainer);
}
if (_localisation.Is(Localisations.Everywhere))
{
dto.TopContainer = spatialStructure.TopContainers.MapAllUsing(_dtoContainerMapper);
dto.Neighborhoods = _dtoContainerMapper.MapFrom(spatialStructure.NeighborhoodsContainer);
}
return(dto);
}
protected override void Context()
{
base.Context();
_parent = new Container().WithName("bla");
_distributedParameter = new DistributedParameter().WithName("Dis").WithParentContainer(_parent);
_spatialStructure = new MoBiSpatialStructure().WithTopContainer(_parent);
sut.Edit(_spatialStructure);
}
protected override void Context()
{
base.Context();
_cloneManager = A.Fake <ICloneManager>();
_diagramManager = A.Fake <ISpatialStructureDiagramManager>();
_spatialStructure = new MoBiSpatialStructure {
DiagramManager = _diagramManager
};
}
/// <summary>
/// Creates the Spatial Structure of the SBML Model with the TopContainer.
/// </summary>
internal void CreateSpatialStructureFromModel(IContainer topContainer, Model model)
{
SpatialStructure = _spatialStructureFactory.Create().DowncastTo <IMoBiSpatialStructure>()
.WithName(SBMLConstants.SBML_MODEL + model.getName())
.WithTopContainer(topContainer)
.WithDescription(SBMLConstants.SBML_NOTES + model.getNotesString() + SBMLConstants.SPACE +
SBMLConstants.SBML_METAID + model.getMetaId());
SpatialStructure.AddTopContainer(_eventsTopContainer);
}
protected SpatialStructureDTO CreateSpatialStuctureDTOFrom(IMoBiSpatialStructure spatialStructure)
{
return(new SpatialStructureDTO
{
Id = spatialStructure.Id,
Name = spatialStructure.Name,
Icon = spatialStructure.Icon,
TopContainer = spatialStructure.TopContainers.MapAllUsing(_containerDTOMapper),
Neighborhoods = _containerDTOMapper.MapFrom(spatialStructure.NeighborhoodsContainer)
});
}
protected override void Context()
{
base.Context();
_returnedBuildingBlocks = new List <IBuildingBlock>();
_childReactionBuilder = new ReactionBuilder().WithName("Test").WithId("FindME");
_reactionParameter = new Parameter().WithName("Para").WithId("ReactionPara");
_childReactionBuilder.AddParameter(_reactionParameter);
_reactionBuildingBlock = new MoBiReactionBuildingBlock()
{
_childReactionBuilder
};
_allBuildingBlocks.Add(_reactionBuildingBlock);
_moleculeBuilder = new MoleculeBuilder();
_moleculeParameter = new Parameter().WithName("para");
_moleculeBuilder.AddParameter(_moleculeParameter);
_moleculeBuildingBlock = new MoleculeBuildingBlock()
{
_moleculeBuilder
};
_allBuildingBlocks.Add(_moleculeBuildingBlock);
_passiveTranportBuilder = new TransportBuilder();
_passiveTransportParameter = new Parameter().WithName("PTParameter");
_passiveTranportBuilder.AddParameter(_passiveTransportParameter);
_passiveTranportBuildingBlock = new PassiveTransportBuildingBlock()
{
_passiveTranportBuilder
};
_allBuildingBlocks.Add(_passiveTranportBuildingBlock);
_applicationBuilder = new ApplicationBuilder();
_eventGroupBuildingBlock = new EventGroupBuildingBlock()
{
_applicationBuilder
};
_applicationBuilderParameter = new ApplicationBuilder().WithName("AppParameter");
_applicationBuilder.Add(_applicationBuilderParameter);
_allBuildingBlocks.Add(_eventGroupBuildingBlock);
_parameter = new Parameter().WithName("Para");
var container = new Container().WithName("Cont");
container.Add(_parameter);
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_parameterFactory = A.Fake <IParameterFactory>();
A.CallTo(() => _objectBaseFactory.Create <IContainer>()).Returns(new Container());
A.CallTo(() => _objectBaseFactory.Create <IMoBiSpatialStructure>()).Returns(new MoBiSpatialStructure());
var diagramManagerFactory = A.Fake <IDiagramManagerFactory>();
_spatialStructure = new MoBiSpatialStructureFactory(_objectBaseFactory, _parameterFactory, A.Fake <IIconRepository>(), diagramManagerFactory).Create() as IMoBiSpatialStructure;
_spatialStructure.AddTopContainer(container);
_allBuildingBlocks.Add(_spatialStructure);
_formula = new ExplicitFormula();
_moleculeBuildingBlock.AddFormula(_formula);
}
protected override void Context()
{
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_parameterFactory = A.Fake <IParameterFactory>();
_iconRepository = A.Fake <IIconRepository>();
_volumeParameter = A.Fake <IParameter>().WithName(Constants.Parameters.VOLUME);
A.CallTo(() => _parameterFactory.CreateVolumeParameter()).Returns(_volumeParameter);
_spatialStructure = new MoBiSpatialStructure();
A.CallTo(() => _objectBaseFactory.Create <IMoBiSpatialStructure>()).Returns(_spatialStructure);
A.CallTo(() => _objectBaseFactory.Create <IContainer>()).ReturnsLazily(x => new Container());
_diagramManagerFactory = A.Fake <IDiagramManagerFactory>();
sut = new MoBiSpatialStructureFactory(_objectBaseFactory, _parameterFactory, _iconRepository, _diagramManagerFactory);
}
protected override void Context()
{
base.Context();
_spatialStructure = new MoBiSpatialStructure()
{
Id = "1"
};
_project = new MoBiProject();
_project.AddBuildingBlock(new MoleculeStartValuesBuildingBlock {
SpatialStructureId = _spatialStructure.Id, MoleculeBuildingBlockId = ""
});
}
protected override void Context()
{
_view = A.Fake <IEditFavoritesView>();
_editParameterListPresenter = A.Fake <IEditParameterListPresenter>();
_favoriteRepository = A.Fake <IFavoriteRepository>();
_entityPathResolver = new EntityPathResolver(new ObjectPathFactory(A.Fake <IAliasCreator>()));
_favoriteTask = A.Fake <IFavoriteTask>();
sut = new EditFavoritesInSpatialStructurePresenter(_view, _favoriteRepository, _entityPathResolver, _editParameterListPresenter, _favoriteTask);
_spatialStructure = new MoBiSpatialStructure();
var cont = new Container().WithName("root");
_para = new Parameter().WithName("P").WithParentContainer(cont);
_fav = new Parameter().WithName("F").WithParentContainer(cont);
_spatialStructure.AddTopContainer(cont);
A.CallTo(() => _favoriteRepository.All()).Returns(new[] { _entityPathResolver.PathFor(_fav) });
}
protected override void Context()
{
_spatialStructureDiagramManager = A.Fake <ISpatialStructureDiagramManager>();
_spatialStructure = new MoBiSpatialStructure {
DiagramManager = _spatialStructureDiagramManager
}.WithName("SpSt");
_spatialStructure.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_parent = new Container().WithName("Top").WithMode(ContainerMode.Logical).WithId(_parentId);
_containerToRemove = new Container().WithName("A").WithMode(ContainerMode.Physical).WithParentContainer(_parent);
_otherContainer = new Container().WithName("B").WithMode(ContainerMode.Physical).WithParentContainer(_parent);
_spatialStructure.AddTopContainer(_parent);
_neighborhood = new NeighborhoodBuilder().WithFirstNeighbor(_containerToRemove).WithSecondNeighbor(_otherContainer).WithName("A2B");
_spatialStructure.AddNeighborhood(_neighborhood);
_context = A.Fake <IMoBiContext>();
sut = new RemoveContainerFromSpatialStructureCommand(_parent, _containerToRemove, _spatialStructure);
}
protected override void Context()
{
_buildConfiguration = new MoBiBuildConfiguration();
_moleculeBuidingBlock = new MoleculeBuildingBlock().WithName("M");
_buildConfiguration.Molecules = _moleculeBuidingBlock;
_reactionBuildingBlock = new MoBiReactionBuildingBlock().WithName("R");
_reactionBuildingBlock.Add(new ReactionBuilder().WithName("R1"));
_buildConfiguration.Reactions = _reactionBuildingBlock;
_passiveTransportBuildingBlock = new PassiveTransportBuildingBlock().WithName("PT");
_passiveTransportBuildingBlock.Add(new TransportBuilder().WithName("PT2"));
_passiveTransportBuildingBlock.Add(new TransportBuilder().WithName("PT1"));
_buildConfiguration.PassiveTransports = _passiveTransportBuildingBlock;
_eventGroupBuildingBlock = new EventGroupBuildingBlock().WithName("EG");
_buildConfiguration.EventGroups = _eventGroupBuildingBlock;
_msvBuildingBlock = new MoleculeStartValuesBuildingBlock().WithName("MSV");
_buildConfiguration.MoleculeStartValues = _msvBuildingBlock;
_psvBuildingBlock = new ParameterStartValuesBuildingBlock().WithName("PSV");
_buildConfiguration.ParameterStartValues = _psvBuildingBlock;
_spatialStructure = new MoBiSpatialStructure().WithName("SPST");
_buildConfiguration.SpatialStructure = _spatialStructure;
_observerBuildingBlock = new ObserverBuildingBlock().WithName("O");
_buildConfiguration.Observers = _observerBuildingBlock;
_objectPathFactory = new ObjectPathFactory(new AliasCreator());
_entityPathResolver = new EntityPathResolver(_objectPathFactory);
sut = new AffectedBuildingBlockRetriever(_entityPathResolver);
//common setup
_simulation = new MoBiSimulation {
BuildConfiguration = _buildConfiguration
};
}
protected override void Context()
{
base.Context();
_project = A.Fake <IMoBiProject>();
_objectBaseRepository = A.Fake <IWithIdRepository>();
_spatialStructure = A.Fake <IMoBiSpatialStructure>();
_simulationSettings = A.Fake <ISimulationSettings>();
_moBiReactionBuildingBlock = A.Fake <IMoBiReactionBuildingBlock>();
_moleculeBuildingBlock = A.Fake <IMoleculeBuildingBlock>();
A.CallTo(() => _context.CurrentProject).Returns(_project);
A.CallTo(() => _context.Create <IMoleculeBuildingBlock>()).Returns(_moleculeBuildingBlock);
A.CallTo(() => _context.Create <IMoBiReactionBuildingBlock>()).Returns(_moBiReactionBuildingBlock);
A.CallTo(() => _spatialStructureFactory.CreateDefault(AppConstants.DefaultNames.SpatialStructure)).Returns(_spatialStructure);
A.CallTo(() => _simulationSettingsFactory.CreateDefault()).Returns(_simulationSettings);
_topContainer = A.Fake <IContainer>();
A.CallTo(() => _context.Create <IContainer>()).Returns(_topContainer);
_passiveTransportBuildingBlock = A.Fake <IPassiveTransportBuildingBlock>();
A.CallTo(() => _context.Create <IPassiveTransportBuildingBlock>()).Returns(_passiveTransportBuildingBlock);
_observerBuildingBlock = A.Fake <IObserverBuildingBlock>();
A.CallTo(() => _context.Create <IObserverBuildingBlock>()).Returns(_observerBuildingBlock);
_eventGroupBuildingBlock = A.Fake <IEventGroupBuildingBlock>();
A.CallTo(() => _context.Create <IEventGroupBuildingBlock>()).Returns(_eventGroupBuildingBlock);
A.CallTo(() => _context.ObjectRepository).Returns(_objectBaseRepository);
}
private StartValuesDTO createDto(string name, IMoleculeBuildingBlock moleculeBuildingBlock, IMoBiSpatialStructure spatialStructure)
{
var dto = new StartValuesDTO {
Name = name, Molecules = moleculeBuildingBlock, SpatialStructrue = spatialStructure
};
dto.AddUsedNames(AppConstants.UnallowedNames);
dto.AddUsedNames(_unallowedNames);
return(dto);
}
private static IParameter searchParameterInContainers(IObjectPath parameterPath, IMoBiSpatialStructure spatialStructure)
{
if (spatialStructure == null)
{
return(null);
}
IParameter parameter = null;
foreach (var top in spatialStructure.TopContainers)
{
parameter = parameterPath.Resolve <IParameter>(top);
if (parameter != null)
{
break;
}
}
if (parameter == null)
{
parameter = parameterPath.Resolve <IParameter>(spatialStructure.NeighborhoodsContainer);
}
return(parameter);
}
public void Visit(IMoBiSpatialStructure objToVisit)
{
retrieveTask(objToVisit);
}
public override void RestoreExecutionData(IMoBiContext context)
{
base.RestoreExecutionData(context);
_spatialStructure = context.Get <IMoBiSpatialStructure>(SpatialStructureId);
}
protected override void ClearReferences()
{
base.ClearReferences();
_spatialStructure = null;
// Keep references to neighborhoods to execute the reverse command.
}
protected override void ClearReferences()
{
base.ClearReferences();
_spatialStructure = null;
}
public RemoveContainerFromSpatialStructureCommand(IContainer parent, IContainer childToRemove, IMoBiSpatialStructure spatialStructure)
: base(parent, childToRemove, spatialStructure)
{
_spatialStructure = spatialStructure;
SpatialStructureId = _spatialStructure.Id;
}
protected override void Context()
{
base.Context();
_returnedBuildingBlocks = new List <IBuildingBlock>();
_childReactionBuilder = new ReactionBuilder().WithName("Test").WithId("FindME");
_reactionBuildingBlock = new MoBiReactionBuildingBlock()
{
_childReactionBuilder
};
_allBuildingBlocks.Add(_reactionBuildingBlock);
_moleculeBuilder = new MoleculeBuilder();
_moleculeBuildingBlock = new MoleculeBuildingBlock()
{
_moleculeBuilder
};
_allBuildingBlocks.Add(_moleculeBuildingBlock);
_obseverBuilder = new ObserverBuilder();
_observerBuildingBlock = new ObserverBuildingBlock()
{
_obseverBuilder
};
_allBuildingBlocks.Add(_observerBuildingBlock);
_passiveTranportBuilder = new TransportBuilder();
_passiveTranportBuildingBlock = new PassiveTransportBuildingBlock()
{
_passiveTranportBuilder
};
_allBuildingBlocks.Add(_passiveTranportBuildingBlock);
_applicationBuilder = new ApplicationBuilder();
_eventGroupBuildingBlock = new EventGroupBuildingBlock()
{
_applicationBuilder
};
_allBuildingBlocks.Add(_eventGroupBuildingBlock);
_parameter = new Parameter().WithName("Para");
var container = new Container().WithName("Cont");
container.Add(_parameter);
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_parmaeterFactory = A.Fake <IParameterFactory>();
A.CallTo(() => _objectBaseFactory.Create <IContainer>()).Returns(A.Fake <IContainer>());
A.CallTo(() => _objectBaseFactory.Create <IMoBiSpatialStructure>()).Returns(new MoBiSpatialStructure());
var diagramManagerFactory = A.Fake <IDiagramManagerFactory>();
_spatialStructure = new MoBiSpatialStructureFactory(_objectBaseFactory, _parmaeterFactory, A.Fake <IconRepository>(), diagramManagerFactory).Create().DowncastTo <IMoBiSpatialStructure>();
_spatialStructure.AddTopContainer(container);
_allBuildingBlocks.Add(_spatialStructure);
_formula = new ExplicitFormula();
_moleculeBuildingBlock.AddFormula(_formula);
_parameterStartValue = new ParameterStartValue {
Path = new ObjectPath {
"test"
}, StartValue = 1, Dimension = A.Fake <IDimension>()
};
_parameterStartValueBuildingBlock = new ParameterStartValuesBuildingBlock()
{
_parameterStartValue
};
_allBuildingBlocks.Add(_parameterStartValueBuildingBlock);
_moleculeStartValue = new MoleculeStartValue {
ContainerPath = new ObjectPath {
"test"
}, Name = "drug"
};
_moleculeStartValuesBuildingBlock = new MoleculeStartValuesBuildingBlock()
{
_moleculeStartValue
};
_allBuildingBlocks.Add(_moleculeStartValuesBuildingBlock);
}
public AddContainerToSpatialStructureCommand(IContainer parent, IContainer child, IMoBiSpatialStructure spatialStructure) : base(parent, child, spatialStructure)
{
_spatialStructure = spatialStructure;
SpatialStructureId = spatialStructure.Id;
}
private bool addNeighborhood(INeighborhoodBuilder neighborhoodBuilder, MoBiMacroCommand command, IMoBiSpatialStructure spatialStructure)
{
var forbiddenNames = spatialStructure.NeighborhoodsContainer.Children.Select(x => x.Name).Union(AppConstants.UnallowedNames).ToList();
if (forbiddenNames.Contains(neighborhoodBuilder.Name))
{
string newName = _dialogCreator.AskForInput(AppConstants.Dialog.AskForChangedName(neighborhoodBuilder.Name, ObjectTypes.NeighborhoodBuilder), AppConstants.Captions.NewName, neighborhoodBuilder.Name, forbiddenNames);
if (string.IsNullOrEmpty(newName))
{
return(false);
}
neighborhoodBuilder.Name = newName;
}
command.AddCommand(new AddContainerToSpatialStructureCommand(spatialStructure.NeighborhoodsContainer, neighborhoodBuilder, spatialStructure).Run(Context));
return(true);
}
protected override void Context()
{
base.Context();
_spSt = A.Fake <IMoBiSpatialStructure>();
sut.Edit(_spSt);
}
protected override void Because()
{
_result = sut.CreateDefault(AppConstants.DefaultNames.SpatialStructure);
}
private void removeNeighborhoods(IContainer entityToRemove, Cache <string, INeighborhoodBuilder> removedIds, IMoBiSpatialStructure spatialStructure, IMoBiContext context)
{
var containerTask = context.Resolve <IContainerTask>();
var neighborhoodsToDelete = containerTask.AllNeighborhoodBuildersConnectedWith(spatialStructure, entityToRemove).ToList();
foreach (var neighborhoodBuilder in neighborhoodsToDelete)
{
if (!removedIds.Contains(neighborhoodBuilder.Id))
{
spatialStructure.RemoveNeighborhood(neighborhoodBuilder);
spatialStructure.DiagramManager.RemoveObjectBase(neighborhoodBuilder);
removedIds.Add(neighborhoodBuilder);
}
}
}
private IMoBiCommand addNeighborhoodsToProject(IList <INeighborhoodBuilder> neighborhoods, IMoBiSpatialStructure spatialStructure)
{
if (neighborhoods == null || !neighborhoods.Any())
{
return(new MoBiEmptyCommand());
}
var command = new MoBiMacroCommand
{
CommandType = AppConstants.Commands.AddCommand,
ObjectType = ObjectTypes.NeighborhoodBuilder,
Description = AppConstants.Commands.AddDependentDescription(spatialStructure, ObjectTypes.NeighborhoodBuilder, ObjectTypes.SpatialStructure)
};
return(neighborhoods.Any(existingItem => !addNeighborhood(existingItem, command, spatialStructure)) ? CancelCommand(command) : command);
}
public void Visit(IMoBiSpatialStructure spatialStructure)
{
_found = spatialStructure.Contains(_entity);
}
