public IBuildingBlock GetBuildingBlockFor(IObjectBase objectBase, IBuildingBlock buildingBlock)
{
try
{
var formula = objectBase as IFormula;
if (formula != null)
{
return(buildingBlockForFormula(formula, buildingBlock));
}
_entity = objectBase as IEntity;
var allBuildingBlocks = _buildingBlockRepository.All();
if (_entity == null)
{
throw new ArgumentException(AppConstants.Exceptions.BuildingBlockNotFoundFor(objectBase));
}
//looking for the first building block containing the root container or the entity itself if null
_entity = _entity.RootContainer ?? _entity;
_found = false;
return(allBuildingBlocks.FirstOrDefault(containsEntity));
}
finally
{
_entity = null;
}
}
public void CreateBuildingBlock()
{
var buildingBlockTask = _container.Resolve <IBuildingBlockTask <TBuildingBlock> >();
buildingBlockTask.AddToProject();
Edit(_buildingBlockRepository.All <TBuildingBlock>().LastOrDefault());
}
private void addPredefinedMoleculeValues(MetaDataCategory moleculeCategory)
{
addUndefinedValueTo(moleculeCategory);
foreach (var existingCompound in _buildingBlockRepository.All <Compound>())
{
addInfoToCategory(moleculeCategory, existingCompound);
}
}
public void UpdateMolWeightIn(DataRepository observedData)
{
var moleculeName = moleculeNameFrom(observedData);
var compound = _buildingBlockRepository.All <Compound>().FindByName(moleculeName);
updateMolWeight(observedData, compound);
}
protected override void Context()
{
_allBuildingBlocks = new List <IPKSimBuildingBlock>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
A.CallTo(() => _buildingBlockRepository.All()).Returns(_allBuildingBlocks);
sut = new FormulationMappingDTOToFormulationMappingMapper(_buildingBlockRepository);
}
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));
}
private void refreshExpressionProfilesForMolecule()
{
_allExpressionProfilesForMoleculeType = _buildingBlockRepository.All <ExpressionProfile>(canSelect);
_view.RefreshList();
//Pre selection
_expressionProfileSelectionDTO.ExpressionProfile = _allExpressionProfilesForMoleculeType.FirstOrDefault();
}
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);
}
private void bindToCompounds(IReadOnlyList <Compound> usedCompounds)
{
_compoundSelectionDTOs.Clear();
var availableCompounds = _buildingBlockRepository.All <Compound>().Union(usedCompounds).OrderBy(x => x.Name).ToList();
availableCompounds.Each(c => _compoundSelectionDTOs.Add(mapFrom(c, isSelected: shouldSelectCompoundByDefault(c, usedCompounds, availableCompounds))));
}
private IEnumerable <string> allPossibleMetabolites()
{
return(_buildingBlockRepository.All <Compound>()
.Where(x => !Equals(_process.ParentCompound, x))
.OrderBy(x => x.Name)
.Select(x => x.Name));
}
private MetaDataCategory compoundNameCategory(Compound compound, bool canEditName)
{
var nameCategory = new MetaDataCategory
{
Name = ObservedData.MOLECULE,
DisplayName = PKSimConstants.UI.Molecule,
Description = PKSimConstants.UI.MoleculeNameDescription,
MetaDataType = typeof(string),
IsListOfValuesFixed = !canEditName,
IsMandatory = true,
};
foreach (var existingCompound in _buildingBlockRepository.All <Compound>())
{
nameCategory.ListOfValues.Add(existingCompound.Name, existingCompound.Name);
}
if (canEditName)
{
nameCategory.ListOfValues.Add(PKSimConstants.UI.Undefined, PKSimConstants.UI.Undefined);
}
if (compound != null)
{
nameCategory.DefaultValue = compound.Name;
}
return(nameCategory);
}
protected override void Context()
{
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
sut = new BuildingBlockRetriever(_buildingBlockRepository);
_allBuildingBlocks = new List <IBuildingBlock>();
A.CallTo(() => _buildingBlockRepository.All()).Returns(_allBuildingBlocks);
}
private IReadOnlyList <Compound> retrieveAllMetabolitesFor(Compound compound)
{
_buildingBlockTask.Load(compound);
return(compound.AllProcesses <EnzymaticProcess>()
.Select(x => x.MetaboliteName).Distinct()
.Select(metaboliteName => _buildingBlockRepository.All <Compound>().FindByName(metaboliteName))
.Where(x => x != null).ToList());
}
private bool simulationsAreUsingAlternative(ParameterAlternative alternative)
{
var allCompoundGroupSelectionForAlternativeGroup = _buildingBlockRepository.All <Simulation>()
.SelectMany(x => x.CompoundPropertiesList)
.SelectMany(x => x.CompoundGroupSelections
.Where(groupSel => string.Equals(groupSel.GroupName, alternative.GroupName))
);
return(allCompoundGroupSelectionForAlternativeGroup.Any(x => string.Equals(x.AlternativeName, alternative.Name)));
}
public ObserverSetMappingDTO MapFrom(ObserverSetMapping observerSetMapping, Simulation simulation)
{
var observerSetMappingDTO = new ObserverSetMappingDTO(observerSetMapping);
var usedTemplateObserverSet = simulation.UsedBuildingBlockByTemplateId(observerSetMapping.TemplateObserverSetId);
//simulation was already using an event based on template. Retrieved the building block used
var templateObserverSet = _buildingBlockInSimulationManager.TemplateBuildingBlockUsedBy <ObserverSet>(usedTemplateObserverSet) ??
_buildingBlockRepository.All <ObserverSet>().FindById(observerSetMapping.TemplateObserverSetId);
observerSetMappingDTO.ObserverSet = templateObserverSet;
return(observerSetMappingDTO);
}
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 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());
}
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);
}
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);
}
protected override void Context()
{
_view = A.Fake <ISimulationSelectionForComparisonView>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_populationSimulationComparison = new PopulationSimulationComparison();
sut = new SimulationSelectionForComparisonPresenter(_view, _buildingBlockRepository, _lazyLoadTask);
A.CallTo(() => _view.BindTo(A <SimulationComparisonSelectionDTO> ._))
.Invokes(x => _dto = x.GetArgument <SimulationComparisonSelectionDTO>(0));
_sim1 = new PopulationSimulation().WithId("1").WithName("Sim1");
_sim2 = new PopulationSimulation().WithId("2").WithName("Sim2");
A.CallTo(() => _buildingBlockRepository.All <PopulationSimulation>()).Returns(new[] { _sim1, _sim2 });
}
private bool simulationsAreUsingAlternativeContaining(IParameter parameter)
{
var alternative = parameter.ParentContainer as ParameterAlternative;
if (alternative == null)
{
return(false);
}
var allCompoundGroupSelectionForAlternativeGroup = _buildingBlockRepository.All <Simulation>()
.SelectMany(x => x.CompoundPropertiesList)
.SelectMany(x => x.CompoundGroupSelections.Where(groupSel => string.Equals(groupSel.GroupName, alternative.GroupName)));
return(allCompoundGroupSelectionForAlternativeGroup.Any(x => string.Equals(x.AlternativeName, alternative.Name)));
}
protected override void Context()
{
_buildingBlockDTOFactory = A.Fake <IObjectBaseDTOFactory>();
_subPresenterManager = SubPresenterHelper.Create <IPopulationItemPresenter>();
_propertiesMapper = A.Fake <IBuildingBlockPropertiesMapper>();
_view = A.Fake <ICreateRandomPopulationView>();
_popSettingsPresenter = _subPresenterManager.CreateFake(RamdomPopulationItems.Settings);
_popAdvancedParameterPresenter = _subPresenterManager.CreateFake(RamdomPopulationItems.AdvancedParameters);
_popDistributionPresenter = _subPresenterManager.CreateFake(RamdomPopulationItems.ParameterDistribution);
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_dialogCreator = A.Fake <IDialogCreator>();
_allIndividuals = new List <Individual>();
A.CallTo(() => _buildingBlockRepository.All <Individual>()).Returns(_allIndividuals);
sut = new CreateRandomPopulationPresenter(_view, _subPresenterManager, _dialogCreator, _propertiesMapper, _buildingBlockDTOFactory, _buildingBlockRepository);
sut.Initialize();
}
public IEventMapping MapFrom(EventMappingDTO eventMappingDTO, PKSim.Core.Model.Simulation simulation)
{
var templateEventId = eventMappingDTO.Event.Id;
var templateEvent = _buildingBlockRepository.All().FindById(templateEventId);
//in that case, event is a simulation event, we need to retrieve the template event
if (templateEvent == null)
{
var usedEvent = simulation.UsedBuildingBlockById(templateEventId);
templateEventId = usedEvent.TemplateId;
}
var eventMapping = eventMappingDTO.EventMapping;
eventMapping.TemplateEventId = templateEventId;
return(eventMapping);
}
public EventMappingDTO MapFrom(IEventMapping eventMapping, PKSim.Core.Model.Simulation simulation)
{
var eventMappingDTO = new EventMappingDTO(eventMapping);
eventMappingDTO.StartTimeParameter = _parameterDTOMapper.MapFrom(eventMapping.StartTime, eventMappingDTO, x => x.StartTime, x => x.StartTimeParameter);
var templateEvent = _buildingBlockRepository.All <PKSim.Core.Model.PKSimEvent>().FindById(eventMapping.TemplateEventId);
var usedEvent = simulation.UsedBuildingBlockByTemplateId(eventMapping.TemplateEventId);
//simulation was already using an event based on template. Retrieved the building block used
if (usedEvent != null)
{
templateEvent = _buildingBlockInSimulationManager.TemplateBuildingBlockUsedBy <PKSim.Core.Model.PKSimEvent>(usedEvent);
}
eventMappingDTO.Event = templateEvent;
return(eventMappingDTO);
}
protected override void Context()
{
_compoundTask = A.Fake <ICompoundTask>();
_view = A.Fake <ISimulationCompoundsSelectionView>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_buildingBlockInSimulationManager = A.Fake <IBuildingBlockInSimulationManager>();
_buildingBlockSelectionDisplayer = A.Fake <IBuildingBlockSelectionDisplayer>();
A.CallTo(() => _buildingBlockRepository.All <Compound>()).Returns(_allCompoundTemplates);
A.CallTo(() => _view.BindTo(A <NotifyList <CompoundSelectionDTO> > ._))
.Invokes(x => _compoundDTOList = x.GetArgument <NotifyList <CompoundSelectionDTO> >(0));
sut = new SimulationCompoundsSelectionPresenter(_view, _buildingBlockRepository, _buildingBlockInSimulationManager, _compoundTask, _buildingBlockSelectionDisplayer);
sut.Initialize();
CompoundSelectionDTOFor(_compound1).Selected = true;
}
public FormulationMapping MapFrom(FormulationMappingDTO formulationMappingDTO, Simulation simulation)
{
var templateFormulationId = formulationMappingDTO.Formulation.Id;
var templateFormulation = _buildingBlockRepository.All().FindById(templateFormulationId);
//in that case, formulation is a simulation formulation, we need to retrieve the template formulation
if (templateFormulation == null)
{
var usedFormulation = simulation.UsedBuildingBlockById(templateFormulationId);
templateFormulationId = usedFormulation.TemplateId;
}
return(new FormulationMapping
{
TemplateFormulationId = templateFormulationId,
FormulationKey = formulationMappingDTO.FormulationKey,
Formulation = formulationMappingDTO.Formulation
});
}
protected override void Context()
{
_individualList = new List <Individual>();
_individualBuildingBlockTask = A.Fake <IBuildingBlockTask <Individual> >();
_container = A.Fake <IContainer>();
A.CallTo(() => _container.Resolve <IBuildingBlockTask <Individual> >()).Returns(_individualBuildingBlockTask);
_view = A.Fake <IBuildingBlockSelectionView>();
_objectTypeResolver = A.Fake <IObjectTypeResolver>();
_individualRepository = A.Fake <IBuildingBlockRepository>();
A.CallTo(() => _individualRepository.All <Individual>()).Returns(_individualList);
_buildingBlockType = "Tralal";
A.CallTo(() => _objectTypeResolver.TypeFor <Individual>()).Returns(_buildingBlockType);
_toolTipCreator = A.Fake <IToolTipPartCreator>();
_buildingBlockSelection = A.Fake <IBuildingBlockSelectionDisplayer>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_emptySelection = new Individual().WithId("TOTO");
A.CallTo(() => _objectBaseFactory.Create <Individual>()).Returns(_emptySelection);
sut = new BuildingBlockSelectionPresenter <Individual>(_view, _objectTypeResolver, _individualRepository, _container, _objectBaseFactory, _buildingBlockSelection);
}
protected override void Context()
{
_context = A.Fake <IMoBiContext>();
_view = A.Fake <IBuildingBlockSelectionView>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_interactionTask = A.Fake <IInteractionTasksForBuildingBlock <IMoBiReactionBuildingBlock> >();
sut = new BuildingBlockSelectionPresenter <IMoBiReactionBuildingBlock>(_view, _buildingBlockRepository, _interactionTask, _context);
_buildingBlockInfo = new ReactionBuildingBlockInfo();
_templateBuildingBlock1 = A.Fake <IMoBiReactionBuildingBlock>().WithName("BB1");
_templateBuildingBlock2 = A.Fake <IMoBiReactionBuildingBlock>().WithName("BB2");
_simulationBuildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithName("BBSIM");
_allBuildingBlocks = new List <IMoBiReactionBuildingBlock> {
_templateBuildingBlock1, _templateBuildingBlock2
};
A.CallTo(() => _buildingBlockRepository.All <IMoBiReactionBuildingBlock>()).Returns(_allBuildingBlocks);
A.CallTo(() => _view.BindTo(A <BuildingBlockSelectionDTO> ._))
.Invokes(x => _buildingBlockSelectionDTO = x.GetArgument <BuildingBlockSelectionDTO>(0));
}
private List <IBuildingBlock> getAllAvailableBuildingBlocks <TBuildingBlock>() where TBuildingBlock : class, IBuildingBlock
{
var allAvailableBuildingBlocks = new List <IBuildingBlock>(_buildingBlockRepository.All <TBuildingBlock>());
return(allAvailableBuildingBlocks);
}