protected override void Context()
{
_project = new PKSimProject();
_projectRetriever = A.Fake <IProjectRetriever>();
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
_compound1 = A.Fake <Compound>();
_compound1.IsLoaded = false;
_compound2 = new Compound {
IsLoaded = true
};
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "A", Name = "P1"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "C", Name = "P2"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "B", Name = "P3"
});
_individual1 = A.Fake <Individual>();
_individual1.IsLoaded = false;
_individual2 = new Individual {
IsLoaded = true
};
_individual2.AddMolecule(new IndividualEnzyme().WithName("B"));
_individual2.AddMolecule(new IndividualEnzyme().WithName("D"));
_project.AddBuildingBlock(_compound1);
_project.AddBuildingBlock(_compound2);
_project.AddBuildingBlock(_individual1);
_project.AddBuildingBlock(_individual2);
sut = new UsedMoleculeRepository(_projectRetriever);
}
protected override void ExecuteWith(IExecutionContext context)
{
IPKSimProject project = context.CurrentProject;
project.RemoveBuildingBlock(_buildingBlockToRemove);
Description = PKSimConstants.Command.RemoveEntityFromContainer(ObjectType, _buildingBlockToRemove.Name, context.TypeFor(project), project.Name);
//remove results for a simulation. This should be done before serialization
removeResultsForSimulation(_buildingBlockToRemove as Simulation);
SerializationStream = context.Serialize(_buildingBlockToRemove);
context.Unregister(_buildingBlockToRemove);
if (!_raiseEvent)
{
return;
}
context.PublishEvent(new BuildingBlockRemovedEvent(_buildingBlockToRemove, context.CurrentProject, _dueToSwap));
var simulation = _buildingBlockToRemove as ISimulation;
if (simulation != null)
{
context.PublishEvent(new SimulationRemovedEvent(simulation));
}
}
public CreateProjectCommand(IWorkspace workspace, IPKSimProject project)
{
_workspace = workspace;
_project = project;
ObjectType = ObjectTypes.Project;
CommandType = Command.CommandTypeAdd;
}
protected override void Context()
{
_executionContext = A.Fake <ISBSuiteExecutionContext>();
_entityTask = A.Fake <IEntityTask>();
_eventPublisher = A.Fake <IEventPublisher>();
_project = A.Fake <IPKSimProject>();
_parameterIdentification = new ParameterIdentification();
A.CallTo(() => _executionContext.Project).Returns(_project);
A.CallTo(() => _entityTask.NewNameFor(_parameterIdentification, A <IEnumerable <string> > ._, A <string> ._)).Returns("newName");
A.CallTo(() => _project.AllParameterIdentifications).Returns(new[]
{
new ParameterIdentification()
{
Name = "name1"
},
new ParameterIdentification()
{
Name = "name2"
}
});
sut = new RenameParameterIdentificationUICommand(_entityTask, _eventPublisher, _executionContext);
sut.For(_parameterIdentification);
}
protected override void Context()
{
_projectRetriever = A.Fake <IPKSimProjectRetriever>();
_registrationTask = A.Fake <IRegistrationTask>();
_eventPublisher = A.Fake <IEventPublisher>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_objectTypeResolver = A.Fake <IObjectTypeResolver>();
_buildingBlockRetriever = A.Fake <IBuildingBlockRetriever>();
_buildingBlockVersionUpdater = A.Fake <IBuildingBlockVersionUpdater>();
_projectChangedNotifier = A.Fake <IProjectChangedNotifier>();
_withIdRepository = A.Fake <IWithIdRepository>();
_stringSerializer = A.Fake <ICompressedSerializationManager>();
_cloneManager = A.Fake <ICloner>();
_reportGenerator = A.Fake <IReportGenerator>();
_fullPathDisplayResolver = A.Fake <IFullPathDisplayResolver>();
_project = A.Fake <IPKSimProject>();
_idThatDoesNotExist = "tralalalal";
_parameter = A.Fake <IParameter>();
_parameterChangeUpdater = A.Fake <IParameterChangeUpdater>();
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
_idThatDoesExist = "toto";
_container = A.Fake <IContainer>();
A.CallTo(() => _withIdRepository.ContainsObjectWithId(_idThatDoesExist)).Returns(true);
A.CallTo(() => _withIdRepository.Get <IParameter>(_idThatDoesExist)).Returns(_parameter);
A.CallTo(() => _withIdRepository.Get(_idThatDoesExist)).Returns(_parameter);
A.CallTo(() => _withIdRepository.ContainsObjectWithId(_idThatDoesNotExist)).Returns(false);
A.CallTo(() => _withIdRepository.Get(_idThatDoesNotExist)).Throws(new Exception());
sut = new ExecutionContext(_projectRetriever, _withIdRepository, _lazyLoadTask, _registrationTask,
_eventPublisher, _objectTypeResolver, _buildingBlockRetriever,
_stringSerializer, _buildingBlockVersionUpdater, _projectChangedNotifier,
_cloneManager, _container, _reportGenerator, _fullPathDisplayResolver, _parameterChangeUpdater);
}
protected override void Context()
{
base.Context();
_project = A.Fake <IPKSimProject>();
sut.Project = _project;
sut.HistoryManager = A.Fake <IHistoryManager>();
}
protected override void Context()
{
base.Context();
_project = A.Fake <IPKSimProject>();
A.CallTo(() => _eventPublisher.PublishEvent(A <ProjectCreatedEvent> .Ignored)).Invokes(
x => _event = x.GetArgument <ProjectCreatedEvent>(0));
}
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>();
}
public void UpdateProjectAfterSave(IPKSimProject project)
{
foreach (var simulation in project.All <Simulation>())
{
simulation.ResultsHaveChanged = false;
}
}
protected override void Context()
{
_applicationController = A.Fake <IApplicationController>();
sut = new CloseSubjectPresenterInvoker(_applicationController);
_project = A.Fake <IPKSimProject>();
_buildingBlock = A.Fake <TBuildingBlock>();
}
protected override void Context()
{
_executionContext = A.Fake <IExecutionContext>();
_buildingBlock = A.Fake <IPKSimBuildingBlock>();
_project = A.Fake <IPKSimProject>();
A.CallTo(() => _executionContext.CurrentProject).Returns(_project);
sut = new RemoveBuildingBlockFromProjectCommand(_buildingBlock, _executionContext);
}
protected override void Context()
{
_context = A.Fake <IExecutionContext>();
_oldProtocol = A.Fake <PKSim.Core.Model.Protocol>();
_newProtocol = A.Fake <PKSim.Core.Model.Protocol>();
_project = A.Fake <IPKSimProject>();
A.CallTo(() => _context.CurrentProject).Returns(_project);
sut = new SwapProtocolCommand(_oldProtocol, _newProtocol, _context);
}
public void UnregisterProject(IPKSimProject project)
{
if (project == null)
{
return;
}
Unregister(project);
project.AllObservedData.Each(Unregister);
}
public void Visit(IPKSimProject project)
{
foreach (var observedData in project.AllObservedData)
{
var baseGrid = observedData.BaseGrid;
var baseGridName = baseGrid.Name.Replace(ObjectPath.PATH_DELIMITER, "\\");
baseGrid.QuantityInfo = new QuantityInfo(baseGrid.Name, new[] { observedData.Name, baseGridName }, QuantityType.Time);
}
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <Simulation>();
_templateBuildingBlock = A.Fake <IPKSimBuildingBlock>();
_project = A.Fake <IPKSimProject>();
A.CallTo(() => _executionContext.CurrentProject).Returns(_project);
_usedBuildingBlock = A.Fake <UsedBuildingBlock>();
A.CallTo(() => _simulationBuildingBlockUpdater.QuickUpdatePossibleFor(_templateBuildingBlock, _usedBuildingBlock)).Returns(false);
}
public void LoadProject(string projectFileName, bool isFullPath = false)
{
var projectFile = isFullPath ? projectFileName : DomainHelperForSpecs.DataFilePathFor($"{projectFileName}.pksim5");
var workspacePersistor = IoC.Resolve <IWorkspacePersistor>();
_workspace = IoC.Resolve <IWorkspace>();
_lazyLoadTask = IoC.Resolve <ILazyLoadTask>();
workspacePersistor.LoadSession(_workspace, projectFile);
_project = _workspace.Project;
}
protected override void Context()
{
_projectRetriever = A.Fake <IProjectRetriever>();
_project = A.Fake <IPKSimProject>();
_individual1 = new Individual();
_individual2 = new Individual();
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
A.CallTo(() => _project.All <Individual>()).Returns(new[] { _individual1, _individual2 });
sut = new BuildingBlockRepository(_projectRetriever);
}
protected override void Context()
{
base.Context();
_project = A.Fake <IPKSimProject>();
_templateSettings = A.Fake <OutputSelections>();
A.CallTo(() => _editedSettings.Clone()).Returns(_templateSettings);
sut.CreateSettings(_populationSimulation);
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
}
protected override void Context()
{
_populationSimulationSettingsPresenter = A.Fake <IPopulationSimulationSettingsPresenter>();
_applicationController = A.Fake <IApplicationController>();
_projectRetriever = A.Fake <IProjectRetriever>();
_project = A.Fake <IPKSimProject>();
_compound1 = A.Fake <Compound>();
_individual = A.Fake <Individual>();
_human = new Species().WithName(CoreConstants.Species.Human);
_rat = new Species().WithName(CoreConstants.Species.Rat);
_mouse = new Species().WithName(CoreConstants.Species.Mouse);
A.CallTo(() => _individual.Species).Returns(_human);
_populationSimulation = A.Fake <PopulationSimulation>();
A.CallTo(() => _populationSimulation.Compounds).Returns(new[] { _compound1 });
A.CallTo(() => _populationSimulation.Individual).Returns(_individual);
_keyPathMapper = A.Fake <IKeyPathMapper>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_userSettings = A.Fake <ICoreUserSettings>();
_originalSettings = new OutputSelections();
A.CallTo(() => _populationSimulation.OutputSelections).Returns(_originalSettings);
_populationSimulation.Model = new Model();
_populationSimulation.Model.Root = new Container();
_compound1.Name = "DRUG";
var organism = new Organism();
var peripheralVenousBlood = new Container().WithName(CoreConstants.Organ.PeripheralVenousBlood);
var venousBlood = new Container().WithName(CoreConstants.Organ.VenousBlood);
var venousBloodPlasma = new Container().WithName(CoreConstants.Compartment.Plasma).WithParentContainer(venousBlood);
var drugPeripheralBlood = new Container().WithName(_compound1.Name);
var drugVenousBlood = new Container().WithName(_compound1.Name);
var periperhalVenousBloodObserver = new Observer {
Name = CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD
};
drugPeripheralBlood.Add(periperhalVenousBloodObserver);
var venousBloodObserver = new Observer {
Name = CoreConstants.Observer.CONCENTRATION
};
drugVenousBlood.Add(venousBloodObserver);
peripheralVenousBlood.Add(drugPeripheralBlood);
venousBloodPlasma.Add(drugVenousBlood);
organism.Add(peripheralVenousBlood);
organism.Add(venousBlood);
_populationSimulation.Model.Root.Add(organism);
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
A.CallTo(() => _applicationController.Start <ISimulationOutputSelectionPresenter <PopulationSimulation> >()).Returns(_populationSimulationSettingsPresenter);
sut = new SimulationSettingsRetriever(_applicationController, _projectRetriever, _entityPathResolver, _keyPathMapper, _userSettings);
A.CallTo(() => _entityPathResolver.PathFor(periperhalVenousBloodObserver)).Returns("PERIPHERAL_OBSERVER");
A.CallTo(() => _entityPathResolver.PathFor(venousBloodObserver)).Returns("VENOUS_BLOOD_OBSERVER");
}
protected override void Context()
{
base.Context();
_fileName = "toto";
_project = A.Fake <IPKSimProject>();
sut.Project = _project;
A.CallTo(() => _eventPublisher.PublishEvent(A <ProjectSavingEvent> .Ignored)).Invokes(
x => _savingEvent = x.GetArgument <ProjectSavingEvent>(0));
A.CallTo(() => _eventPublisher.PublishEvent(A <ProjectSavedEvent> .Ignored)).Invokes(
x => _savedEvent = x.GetArgument <ProjectSavedEvent>(0));
}
protected override void Context()
{
var workspace = A.Fake <IWorkspace>();
_project = A.Fake <IPKSimProject>();
workspace.Project = _project;
A.CallTo(() => _project.AllObservedData).Returns(new List <DataRepository>());
A.CallTo(() => _project.All(PKSimBuildingBlockType.Template)).Returns(_allBuildingBlocks);
A.CallTo(() => _project.All <Simulation>()).Returns(new[] { _simulation });
sut = IoC.Resolve <SimulationsReporter>();
}
protected override void Context()
{
_dialogCreator = A.Fake <IDialogCreator>();
_applicationController = A.Fake <IApplicationController>();
_workspace = A.Fake <IWorkspace>();
_project = A.Fake <IPKSimProject>();
_registrationTask = A.Fake <IRegistrationTask>();
A.CallTo(() => _workspace.Project).Returns(_project);
_eventPublisher = A.Fake <IEventPublisher>();
sut = new DeleteSimulationComparisonsUICommand(_applicationController, _workspace, _eventPublisher, _dialogCreator, _registrationTask);
_individualSimulationComparison = new IndividualSimulationComparison().WithName("chart");
sut.For(new [] { _individualSimulationComparison });
}
public void Save(IPKSimProject projectToSave, ISession session)
{
var projectMetaData = projectMetaDataFrom(projectToSave);
var projectFromDb = projectFromDatabase(session);
if (projectFromDb == null)
{
saveProject(session, projectMetaData);
}
else
{
projectFromDb.UpdateFrom(projectMetaData, session);
}
}
protected override void Context()
{
_chartFactory = A.Fake <IPKSimChartFactory>();
_containerTask = A.Fake <IContainerTask>();
_applicationController = A.Fake <IApplicationController>();
_project = new PKSimProject();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_singleStartPresenterTask = A.Fake <ISingleStartPresenterTask>();
_executionContext = A.Fake <IExecutionContext>();
_simulationAnalysisCreator = A.Fake <ISimulationAnalysisCreator>();
A.CallTo(() => _executionContext.CurrentProject).Returns(_project);
sut = new SimulationComparisonCreator(_chartFactory, _containerTask, _objectBaseFactory,
_applicationController, _singleStartPresenterTask, _executionContext, _simulationAnalysisCreator);
}
protected override void Context()
{
_buildingBlockTask = A.Fake <IBuildingBlockTask>();
_executionContext = A.Fake <IExecutionContext>();
_project = A.Fake <IPKSimProject>();
_population = A.Fake <RandomPopulation>();
_randomPopulationPresenter = A.Fake <ICreateRandomPopulationPresenter>();
_applicationController = A.Fake <IApplicationController>();
A.CallTo(() => _applicationController.Start <ICreateRandomPopulationPresenter>()).Returns(_randomPopulationPresenter);
A.CallTo(() => _randomPopulationPresenter.BuildingBlock).Returns(_population);
A.CallTo(() => _buildingBlockTask.TypeFor(_population)).Returns("pop");
A.CallTo(() => _executionContext.CurrentProject).Returns(_project);
sut = new PopulationTask(_executionContext, _buildingBlockTask, _applicationController);
}
public void UpdateCompoundInObservedDataFor(IPKSimProject project)
{
var allProjectCompound = project.All <PKSim.Core.Model.Compound>();
_allAvailableCompounds.AddRange(allProjectCompound);
_mapping = new List <ObservedDataToCompoundMappingDTO>();
project.AllObservedData.Each(data => _mapping.Add(mapFrom(data, allProjectCompound)));
_view.BindTo(_mapping);
_view.Display();
updateMolWeight();
}
protected override void Context()
{
base.Context();
_project = A.Fake <IPKSimProject>();
_command = A.Fake <IPKSimCommand>();
_simulationToClone = A.Fake <Simulation>().WithName("OLD");
_clonedSimulation = A.Fake <Simulation>().WithName("NEW");
_cloneSimulationPresenter = A.Fake <ICloneSimulationPresenter>();
A.CallTo(() => _applicationController.Start <ICloneSimulationPresenter>()).Returns(_cloneSimulationPresenter);
A.CallTo(() => _executionContext.CurrentProject).Returns(_project);
A.CallTo(() => _cloneSimulationPresenter.CloneSimulation(_simulationToClone)).Returns(_command);
A.CallTo(() => _cloneSimulationPresenter.Simulation).Returns(_clonedSimulation);
A.CallTo(() => _buildingBlockInSimulationManager.StatusFor(_simulationToClone)).Returns(BuildingBlockStatus.Green);
}
public ProjectMetaData MapFrom(IPKSimProject project)
{
var projectMetaData = new ProjectMetaData();
project.All <IPKSimBuildingBlock>().Each(x => projectMetaData.AddBuildingBlock(mapFrom(x)));
project.AllSimulationComparisons.Each(x => projectMetaData.AddSimulationComparison(mapFrom(x)));
project.AllParameterIdentifications.Each(x => projectMetaData.AddParameterIdentification(mapFrom(x)));
project.AllSensitivityAnalyses.Each(x => projectMetaData.AddSensitivityAnalysis(mapFrom(x)));
project.AllObservedData.Each(x => projectMetaData.AddObservedData(mapFrom(x)));
projectMetaData.Name = project.Name;
projectMetaData.Description = project.Description;
projectMetaData.Content.Data = _serializationManager.Serialize(project);
_metaData = null;
return(projectMetaData);
}
protected override void Context()
{
_pkmlFile = "file";
_project = new PKSimProject();
_dimensionFactory = A.Fake <IDimensionFactory>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_simulationPersister = A.Fake <ISimulationPersistor>();
_projectRetriever = A.Fake <IProjectRetriever>();
_dialogCreator = A.Fake <IDialogCreator>();
_journalTask = A.Fake <IJournalTask>();
_cloneManagerForModel = A.Fake <ICloneManagerForModel>();
sut = new SimulationTransferLoader(_dimensionFactory, _objectBaseFactory, _simulationPersister, _projectRetriever, _dialogCreator, _journalTask, _cloneManagerForModel);
_simulationTransfer = new SimulationTransfer();
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
A.CallTo(() => _simulationPersister.Load(_pkmlFile, _dimensionFactory, _objectBaseFactory, A <IWithIdRepository> ._, _cloneManagerForModel)).Returns(_simulationTransfer);
}
protected override void Context()
{
_context = A.Fake <IExecutionContext>();
_oldSimulation = A.Fake <Simulation>();
_newSimulation = A.Fake <Simulation>();
_project = A.Fake <IPKSimProject>();
_simulationDifferenceBuilder = A.Fake <ISimulationCommandDescriptionBuilder>();
_simulationReferenceUpdater = A.Fake <ISimulationReferenceUpdater>();
A.CallTo(() => _context.CurrentProject).Returns(_project);
A.CallTo(() => _context.Resolve <ISimulationCommandDescriptionBuilder>()).Returns(_simulationDifferenceBuilder);
A.CallTo(() => _context.Resolve <ISimulationReferenceUpdater>()).Returns(_simulationReferenceUpdater);
var reportPart = new ReportPart();
reportPart.AddToContent("toto");
A.CallTo(() => _simulationDifferenceBuilder.BuildDifferenceBetween(_oldSimulation, _newSimulation)).Returns(reportPart);
sut = new SwapSimulationCommand(_oldSimulation, _newSimulation, _context);
}
