protected override void Context()
{
_project = A.Fake <IPKSimProject>();
_entityTask = A.Fake <IEntityTask>();
_templateTaskQuery = A.Fake <ITemplateTaskQuery>();
_executionContext = A.Fake <IExecutionContext>();
A.CallTo(() => _executionContext.CurrentProject).Returns(_project);
_applicationController = A.Fake <IApplicationController>();
_buildingBlockInSimulationManager = A.Fake <IBuildingBlockInSimulationManager>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_clonePresenter = A.Fake <ICloneBuildingBlockPresenter>();
_renamePresenter = A.Fake <IRenameObjectPresenter>();
_dialogCreator = A.Fake <IDialogCreator>();
_singleStartPresenterTask = A.Fake <ISingleStartPresenterTask>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_presenterSettingsTask = A.Fake <IPresentationSettingsTask>();
_simulationReferenceUpdater = A.Fake <ISimulationReferenceUpdater>();
sut = new BuildingBlockTask(_executionContext, _applicationController, _dialogCreator, _buildingBlockInSimulationManager,
_entityTask, _templateTaskQuery, _singleStartPresenterTask, _buildingBlockRepository, _lazyLoadTask, _presenterSettingsTask, _simulationReferenceUpdater);
A.CallTo(() => _applicationController.Start <ICloneBuildingBlockPresenter>()).Returns(_clonePresenter);
A.CallTo(() => _applicationController.Start <IRenameObjectPresenter>()).Returns(_renamePresenter);
_buildingBlock = A.Fake <IPKSimBuildingBlock>();
}
protected override void Context()
{
_simulation = new IndividualSimulation();
_buildingBlockInSmulationManager = A.Fake <IBuildingBlockInSimulationManager>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
sut = new FormulationFromMappingRetriever(_buildingBlockInSmulationManager, _buildingBlockRepository);
}
protected override void Context()
{
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
sut = new BuildingBlockRetriever(_buildingBlockRepository);
_allBuildingBlocks = new List <IBuildingBlock>();
A.CallTo(() => _buildingBlockRepository.All()).Returns(_allBuildingBlocks);
}
protected override void Context()
{
_view = A.Fake <IExpressionProfileSelectionView>();
_moleculePropertiesMapper = A.Fake <IMoleculePropertiesMapper>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_expressionProfileTask = A.Fake <IExpressionProfileTask>();
sut = new ExpressionProfileSelectionPresenter(_view, _moleculePropertiesMapper, _buildingBlockRepository, _expressionProfileTask);
A.CallTo(() => _view.BindTo(A <ExpressionProfileSelectionDTO> ._))
.Invokes(x => _dto = x.GetArgument <ExpressionProfileSelectionDTO>(0));
_individual = DomainHelperForSpecs.CreateIndividual(speciesName: "Human");
_expressionProfile1 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(speciesName: "Human");
_expressionProfile2 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(speciesName: "Human");
_expressionProfile3 = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>(speciesName: "Human");
_expressionProfile4 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(speciesName: "Dog");
_expressionProfile5 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(speciesName: "Human");
_allExpressionProfiles = new List <ExpressionProfile> {
_expressionProfile1, _expressionProfile2
};
A.CallTo(() => _buildingBlockRepository.All(A <Func <ExpressionProfile, bool> > ._))
.Invokes(x => _predicate = x.GetArgument <Func <ExpressionProfile, bool> >(0))
.Returns(_allExpressionProfiles);
_individual.AddExpressionProfile(_expressionProfile5);
}
protected override void Context()
{
_allBuildingBlocks = new List <IPKSimBuildingBlock>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
A.CallTo(() => _buildingBlockRepository.All()).Returns(_allBuildingBlocks);
sut = new FormulationMappingDTOToFormulationMappingMapper(_buildingBlockRepository);
}
public CompoundTask(IExecutionContext executionContext, IBuildingBlockTask buildingBlockTask, IApplicationController applicationController,
IBuildingBlockRepository buildingBlockRepository, IDialogCreator dialogCreator)
: base(executionContext, buildingBlockTask, applicationController, PKSimBuildingBlockType.Compound)
{
_buildingBlockRepository = buildingBlockRepository;
_dialogCreator = dialogCreator;
}
public ObservedDataFolderContextMenu(
ITreeNode <RootNodeType> treeNode,
IMenuBarItemRepository repository,
IBuildingBlockRepository buildingBlockRepository,
IBuildingBlockExplorerPresenter presenter,
IUserSettings userSettings)
{
var allCompounds = buildingBlockRepository.All <Compound>().ToList();
//create sub menu containing all compounds
var addObservedDataFor = CreateSubMenu.WithCaption(PKSimConstants.MenuNames.AddObservedDataFor)
.WithIcon(ApplicationIcons.ObservedDataForMolecule);
foreach (var compound in allCompounds)
{
addObservedDataFor.AddItem(CreateMenuButton.WithCaption(compound.Name)
.WithCommandFor <AddObservedDataForCompoundUICommand, Compound>(compound));
}
_view.AddMenuItem(repository[MenuBarItemIds.AddObservedData]);
if (allCompounds.Any())
{
_view.AddMenuItem(addObservedDataFor);
}
if (treeNode.HasChildren)
{
_view.AddMenuItem(ObservedDataClassificationCommonContextMenuItems.ColorGroupObservedData(userSettings));
}
_view.AddMenuItem(CreateMenuButton.WithCaption(PKSimConstants.MenuNames.LoadFromTemplate)
.WithCommand <LoadObservedDataFromTemplateUICommand>()
.WithIcon(ApplicationIcons.LoadFromTemplate)
.AsGroupStarter());
_view.AddMenuItem(CreateMenuButton.WithCaption(PKSimConstants.MenuNames.AsDeveloperOnly("Load from Snapshot"))
.WithCommand <LoadObservedDataFromSnapshotUICommand>()
.WithIcon(ApplicationIcons.SnapshotImport)
.ForDeveloper());
if (treeNode.AllLeafNodes.OfType <ObservedDataNode>().Any())
{
_view.AddMenuItem(ObservedDataClassificationCommonContextMenuItems.EditMultipleMetaData(treeNode).AsGroupStarter());
}
_view.AddMenuItem(ClassificationCommonContextMenuItems.CreateClassificationUnderMenu(treeNode, presenter));
var groupMenu = createGroupingSubMenu(treeNode, presenter);
if (groupMenu.AllItems().Any())
{
_view.AddMenuItem(groupMenu);
}
_view.AddMenuItem(createDeleteSubMenu(treeNode, presenter));
}
public EventMappingToEventMappingDTOMapper(IBuildingBlockRepository buildingBlockRepository,
IParameterToParameterDTOInContainerMapper <EventMappingDTO> parameterDTOMapper,
IBuildingBlockInSimulationManager buildingBlockInSimulationManager)
{
_buildingBlockRepository = buildingBlockRepository;
_parameterDTOMapper = parameterDTOMapper;
_buildingBlockInSimulationManager = buildingBlockInSimulationManager;
}
public IndividualExtractor(IExecutionContext executionContext, IEntityPathResolver entityPathResolver, IIndividualTask individualTask, IContainerTask containerTask, IBuildingBlockRepository buildingBlockRepository)
{
_executionContext = executionContext;
_entityPathResolver = entityPathResolver;
_individualTask = individualTask;
_containerTask = containerTask;
_buildingBlockRepository = buildingBlockRepository;
}
public BuildingBlockSelectionPresenter(IBuildingBlockSelectionView view, IBuildingBlockRepository buildingBlockRepository,
IInteractionTasksForBuildingBlock <TBuildingBlock> interactionTasks, IMoBiContext context)
: base(view)
{
_buildingBlockRepository = buildingBlockRepository;
_interactionTasks = interactionTasks;
_context = context;
_buildingBlockSelectionDTO = new BuildingBlockSelectionDTO();
}
public SimulationSelectionForComparisonPresenter(ISimulationSelectionForComparisonView view, IBuildingBlockRepository buildingBlockRepository, ILazyLoadTask lazyLoadTask) : base(view)
{
_buildingBlockRepository = buildingBlockRepository;
_lazyLoadTask = lazyLoadTask;
_selectionDTO = new SimulationComparisonSelectionDTO();
_nullSimulation = new NullSimulation();
_selectionDTO.Reference = _nullSimulation;
_selectionDTO.GroupingItem.Color = PKSimColors.StartGroupingColor;
}
protected CreatePopulationPresenter(TView view, ISubPresenterItemManager <IPopulationItemPresenter> subPresenterItemManager,
IReadOnlyList <ISubPresenterItem> subPresenterItems, IDialogCreator dialogCreator,
IBuildingBlockPropertiesMapper propertiesMapper, IObjectBaseDTOFactory buildingBlockDTOFactory, IBuildingBlockRepository buildingBlockRepository)
: base(view, subPresenterItemManager, subPresenterItems, dialogCreator)
{
_propertiesMapper = propertiesMapper;
_buildingBlockDTOFactory = buildingBlockDTOFactory;
_buildingBlockRepository = buildingBlockRepository;
}
protected override void Context()
{
_toolTipPartCreator = A.Fake <IToolTipPartCreator>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
sut = new BuildingBlockSelectionDisplayer(_buildingBlockRepository, _toolTipPartCreator);
_templateCompound = new Compound().WithName("A").WithId("A");
_nonTemplateCompound = new Compound().WithName("B").WithId("B");
A.CallTo(() => _buildingBlockRepository.ById(_templateCompound.Id)).Returns(_templateCompound);
A.CallTo(() => _buildingBlockRepository.ById(_nonTemplateCompound.Id)).Returns(null);
}
public SimulationCompoundsSelectionPresenter(ISimulationCompoundsSelectionView view, IBuildingBlockRepository buildingBlockRepository,
IBuildingBlockInSimulationManager buildingBlockInSimulationManager, ICompoundTask compoundTask, IBuildingBlockSelectionDisplayer buildingBlockSelectionDisplayer)
: base(view)
{
_buildingBlockRepository = buildingBlockRepository;
_buildingBlockInSimulationManager = buildingBlockInSimulationManager;
_compoundTask = compoundTask;
_buildingBlockSelectionDisplayer = buildingBlockSelectionDisplayer;
_compoundSelectionDTOs = new NotifyList <CompoundSelectionDTO>();
_view.BindTo(_compoundSelectionDTOs);
_compoundSelectionDTOs.CollectionChanged += onCollectionChanged;
}
public EnzymaticCompoundProcessPresenter(
IEnzymaticCompoundProcessView view,
IParametersByGroupPresenter parametersPresenter,
IEntityTask entityTask, ISpeciesRepository speciesRepository,
IRepresentationInfoRepository representationInfoRepository,
IEnzymaticProcessToEnzymaticProcessDTOMapper mapper,
IBuildingBlockRepository buildingBlockRepository,
ICompoundProcessTask processTask)
: base(view, parametersPresenter, entityTask, speciesRepository, representationInfoRepository, mapper, processTask)
{
_buildingBlockRepository = buildingBlockRepository;
}
public ExpressionProfileSelectionPresenter(
IExpressionProfileSelectionView view,
IMoleculePropertiesMapper moleculePropertiesMapper,
IBuildingBlockRepository buildingBlockRepository,
IExpressionProfileTask expressionProfileTask)
: base(view)
{
_moleculePropertiesMapper = moleculePropertiesMapper;
_buildingBlockRepository = buildingBlockRepository;
_expressionProfileTask = expressionProfileTask;
_expressionProfileSelectionDTO = new ExpressionProfileSelectionDTO();
}
protected override void Context()
{
base.Context();
_view = A.Fake <ICreateEnzymaticProcessView>();
_compoundProcessTask = A.Fake <ICompoundProcessTask>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_processMapper = A.Fake <ICompoundProcessToCompoundProcessDTOMapper>();
_partialProcessMapper = A.Fake <IPartialProcessToPartialProcessDTOMapper>();
_parameterPresenter = A.Fake <IParametersByGroupPresenter>();
_usedMOleculeRepository = A.Fake <IUsedMoleculeRepository>();
_speciesRepository = A.Fake <ISpeciesRepository>();
sut = new CreateEnzymaticProcessPresenter(_view, _compoundProcessTask, _processMapper, _partialProcessMapper, _parameterPresenter, _usedMOleculeRepository, _speciesRepository, _buildingBlockRepository);
}
protected override void Context()
{
_executionContext = A.Fake <IExecutionContext>();
_buildingBlockTask = A.Fake <IBuildingBlockTask>();
_applicationController = A.Fake <IApplicationController>();
_compound = new Compound().WithId("Drug").WithName("Drug");
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_dialogCreator = A.Fake <IDialogCreator>();
sut = new CompoundTask(_executionContext, _buildingBlockTask, _applicationController, _buildingBlockRepository, _dialogCreator);
A.CallTo(() => _buildingBlockTask.SaveAsTemplate(A <ICache <IPKSimBuildingBlock, IReadOnlyList <IPKSimBuildingBlock> > > ._, TemplateDatabaseType.User))
.Invokes(x => _cache = x.GetArgument <ICache <IPKSimBuildingBlock, IReadOnlyList <IPKSimBuildingBlock> > >(0));
}
protected override void Context()
{
_parameterAlternativeFactory = A.Fake <IParameterAlternativeFactory>();
_applicationController = A.Fake <IApplicationController>();
_executionContext = A.Fake <IExecutionContext>();
_entityTask = A.Fake <IEntityTask>();
_formulaFactory = A.Fake <IFormulaFactory>();
_parameterTask = A.Fake <IParameterTask>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_compoundFactory = new CompoundFactoryForSpecs();
sut = new CompoundAlternativeTask(_parameterAlternativeFactory, _applicationController,
_executionContext, _compoundFactory, _entityTask, _formulaFactory, _parameterTask, _buildingBlockRepository);
}
protected BuildingBlockFolderContextMenu(IMenuBarItemRepository repository, IBuildingBlockRepository buildingBlockRepository, params MenuBarItemId[] staticMenus)
{
staticMenus.Each(menu => _view.AddMenuItem(repository[menu]));
var allBuildingBlocks = buildingBlockRepository.All <TBuildingBlock>();
if (!allBuildingBlocks.Any())
{
return;
}
_view.AddMenuItem(GenericMenu.ExportCollectionToPDFMenuFor <TBuildingBlock>().AsGroupStarter());
}
public CompoundAlternativeTask(IParameterAlternativeFactory parameterAlternativeFactory, IApplicationController applicationController,
IExecutionContext executionContext, ICompoundFactory compoundFactory, IEntityTask entityTask,
IFormulaFactory formulaFactory, IParameterTask parameterTask, IBuildingBlockRepository buildingBlockRepository)
{
_parameterAlternativeFactory = parameterAlternativeFactory;
_applicationController = applicationController;
_executionContext = executionContext;
_compoundFactory = compoundFactory;
_entityTask = entityTask;
_formulaFactory = formulaFactory;
_parameterTask = parameterTask;
_buildingBlockRepository = buildingBlockRepository;
}
protected override void Context()
{
_enzymaticProcessToEnzymaticProcessDTOMapper = A.Fake <IEnzymaticProcessToEnzymaticProcessDTOMapper>();
_view = A.Fake <IEnzymaticCompoundProcessView>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_compoundProcessTask = A.Fake <ICompoundProcessTask>();
sut = new EnzymaticCompoundProcessPresenter(
_view, A.Fake <IParametersByGroupPresenter>(), A.Fake <IEntityTask>(), A.Fake <ISpeciesRepository>(), A.Fake <IRepresentationInfoRepository>(),
_enzymaticProcessToEnzymaticProcessDTOMapper,
_buildingBlockRepository,
_compoundProcessTask);
}
protected override void Context()
{
_executionContext = A.Fake <IExecutionContext>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_individualTask = A.Fake <IIndividualTask>();
_containerTask = new ContainerTaskForSpecs();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
sut = new IndividualExtractor(_executionContext, _entityPathResolver, _individualTask, _containerTask, _buildingBlockRepository);
_templateIndividual1 = new Individual();
A.CallTo(() => _buildingBlockRepository.All <Individual>()).Returns(new[] { _templateIndividual1 });
}
protected BuildingBlockFolderContextMenu(IMenuBarItemRepository repository, IBuildingBlockRepository buildingBlockRepository, params MenuBarItemId[] staticMenus)
{
staticMenus.Each(menu => _view.AddMenuItem(repository[menu]));
_view.AddMenuItem(GenericMenu.LoadBuildingBlockFromSnapshot <TBuildingBlock>());
var allBuildingBlocks = buildingBlockRepository.All <TBuildingBlock>();
if (!allBuildingBlocks.Any())
{
return;
}
}
protected override void Context()
{
_parameterAlternativeFactory = A.Fake <IParameterAlternativeFactory>();
_executionContext = A.Fake <IExecutionContext>();
_formulaFactory = A.Fake <IFormulaFactory>();
_parameterTask = A.Fake <IParameterTask>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_dataImporter = A.Fake <IDataImporter>();
_compoundFactory = new CompoundFactoryForSpecs();
sut = new CompoundAlternativeTask(_parameterAlternativeFactory,
_executionContext, _compoundFactory, _formulaFactory, _parameterTask,
_buildingBlockRepository, _dimensionRepository, _dataImporter);
}
public BuildingBlockMergePresenter(IBuildingBlockMergeView view, IDialogCreator dialogCreator,
IMergeTask mergeTask, IBuildingBlockRepository buildingBlockRepository,
IIconRepository iconRepository, ISerializationTask serializationTask) : base(view)
{
_cancellationTokenSource = new CancellationTokenSource();
_dialogCreator = dialogCreator;
_mergeTask = mergeTask;
_buildingBlockRepository = buildingBlockRepository;
_allBuildingBlockMappings = new List <BuildingBlockMappingDTO>();
_noneBuildingBlock = new NullBuildingBlock(AppConstants.None);
_importAsNewBuildingBlock = new NullBuildingBlock(AppConstants.Captions.ImportAsNew);
_iconRepository = iconRepository;
_serializationTask = serializationTask;
}
protected override void Context()
{
_eventPublisher = A.Fake <IEventPublisher>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_simulation1 = new IndividualSimulation();
_simulation2 = new IndividualSimulation();
_simulation3 = new IndividualSimulation();
A.CallTo(() => _buildingBlockRepository.All <Simulation>()).Returns(new[] { _simulation1, _simulation2, _simulation3 });
_id = "tralala";
_templateBuildingBlock = A.Fake <IPKSimBuildingBlock>().WithId(_id);
_usedBuildingBlock = new UsedBuildingBlock(_templateBuildingBlock.Id, _templateBuildingBlock.BuildingBlockType);
A.CallTo(() => _buildingBlockRepository.ById(_templateBuildingBlock.Id)).Returns(_templateBuildingBlock);
sut = new BuildingBlockInProjectManager(_buildingBlockRepository, _eventPublisher);
}
public BuildingBlockSelectionPresenter(IBuildingBlockSelectionView view, IObjectTypeResolver objectTypeResolver,
IBuildingBlockRepository buildingBlockRepository, IContainer container,
IObjectBaseFactory objectBaseFactory, IBuildingBlockSelectionDisplayer buildingBlockSelectionDisplayer)
: base(view)
{
_buildingBlockRepository = buildingBlockRepository;
_container = container;
_buildingBlockSelectionDisplayer = buildingBlockSelectionDisplayer;
BuildingBlockType = objectTypeResolver.TypeFor <TBuildingBlock>();
_buildingBlockDTO = new BuildingBlockSelectionDTO {
BuildingBockType = BuildingBlockType
};
_view.DisplayIcons = true;
_emptySelection = objectBaseFactory.Create <TBuildingBlock>().WithName(PKSimConstants.UI.None);
}
public ImportObservedDataTask(IDataImporter dataImporter, IExecutionContext executionContext,
IDimensionRepository dimensionRepository, IBuildingBlockRepository buildingBlockRepository, ISpeciesRepository speciesRepository,
IDefaultIndividualRetriever defaultIndividualRetriever, IRepresentationInfoRepository representationInfoRepository,
IObservedDataTask observedDataTask, IParameterChangeUpdater parameterChangeUpdater)
{
_dataImporter = dataImporter;
_executionContext = executionContext;
_dimensionRepository = dimensionRepository;
_buildingBlockRepository = buildingBlockRepository;
_speciesRepository = speciesRepository;
_defaultIndividualRetriever = defaultIndividualRetriever;
_representationInfoRepository = representationInfoRepository;
_observedDataTask = observedDataTask;
_parameterChangeUpdater = parameterChangeUpdater;
}
protected override void Context()
{
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_buildingBockRetriever = A.Fake <IBuildingBlockRetriever>();
_observedDataRepository = A.Fake <IObservedDataRepository>();
sut = new ParameterChangeUpdater(_buildingBockRetriever, _observedDataRepository, _buildingBlockRepository);
_compounds = new List <Compound>();
A.CallTo(() => _buildingBlockRepository.All <Compound>()).Returns(_compounds);
_observedDataList = new List <DataRepository>();
A.CallTo(() => _observedDataRepository.All()).Returns(_observedDataList);
_compound = A.Fake <Compound>().WithName("C");
A.CallTo(() => _compound.MolWeight).Returns(200);
}