private ITreeNode addMoleculeBuilder(IMoleculeBuilder moleculeBuilder, IMoleculeBuildingBlock moleculeBuildingBlock)
{
var moleculeBuildingBlockNode = _view.NodeById(moleculeBuildingBlock.Id);
return(_view.AddNode(_treeNodeFactory.CreateFor(moleculeBuilder)
.Under(moleculeBuildingBlockNode)));
}
protected override void Context()
{
base.Context();
_newAlias = "new_Name";
_changedObject.Name = "Name really old";
_changedName = _changedObject.Name;
_oldAlias = "Name_really_old";
_theFormula = new ExplicitFormula(String.Format("k_{0}*{0}", _oldAlias));
_formulaUsablePathNotToChange = new FormulaUsablePath(new[] { ObjectPath.PARENT_CONTAINER, "BLA", String.Format("k_{0}", _oldAlias) })
{
Alias = String.Format("k_{0}", _oldAlias)
};
_theFormula.AddObjectPath(_formulaUsablePathNotToChange);
_formulaUsablePathToChange = new FormulaUsablePath(new[] { ObjectPath.PARENT_CONTAINER, _changedName })
{
Alias = _oldAlias
};
_theFormula.AddObjectPath(_formulaUsablePathToChange);
_theFormula.Name = "F1";
A.CallTo(() => _aliasCreator.CreateAliasFrom(_changedName)).Returns(_oldAlias);
A.CallTo(() => _aliasCreator.CreateAliasFrom(_newName)).Returns(_newAlias);
A.CallTo(() => _context.Get <IObjectBase>(A <string> ._)).Returns(_theFormula);
_moleculeBuildingBlock = new MoleculeBuildingBlock().WithName("M").WithId("M");
_moleculeBuildingBlock.AddFormula(_theFormula);
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = DomainFactoryForSpecs.CreateDefaultSimulation();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
var compoundProperties = _simulation.CompoundPropertiesList.First();
_compoundName = compoundProperties.Compound.Name;
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _compoundName, QuantityType = QuantityType.Drug
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Enzyme", QuantityType = QuantityType.Enzyme
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Metabolite", QuantityType = QuantityType.Metabolite
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Protein", QuantityType = QuantityType.OtherProtein
});
var specificBindingSelection = new ProcessSelection {
CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Specific Binding"
};
var metabolizationSelection = new EnzymaticProcessSelection {
CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Metabolism"
};
_complexProductName = specificBindingSelection.ProductName(CoreConstants.Molecule.Complex);
_metaboliteProductName = specificBindingSelection.ProductName(CoreConstants.Molecule.Metabolite);
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _complexProductName, QuantityType = QuantityType.Complex
});
compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(specificBindingSelection);
compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(metabolizationSelection);
}
protected override void Context()
{
_containerTask = A.Fake <IContainerTask>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_projectRetriever = A.Fake <IMoBiProjectRetriever>();
_eventPublisher = A.Fake <IEventPublisher>();
_cloneManagerForModel = A.Fake <ICloneManagerForModel>();
_formulaTask = A.Fake <IFormulaTask>();
sut = new PassiveTransportConverter(_objectBaseFactory, _projectRetriever, _containerTask, _eventPublisher, _cloneManagerForModel, _formulaTask);
A.CallTo(() => _containerTask.CreateUniqueName(A <IEnumerable <IWithName> > ._, A <string> ._, true))
.ReturnsLazily(x => x.Arguments[1].ToString());
_passiveTransportKinetic = new ExplicitFormula("1+2");
_moleculeWithPassiveTransport = new MoleculeBuilder().WithName("MOLECULE");
_passiveTransport = new TransportBuilder().WithName("PASSIVE TRANSPORT").WithFormula(_passiveTransportKinetic);
_moleculeWithPassiveTransport.Add(_passiveTransport);
_passiveTransports = new PassiveTransportBuildingBlock();
_molecules = new MoleculeBuildingBlock {
_moleculeWithPassiveTransport
}.WithName("MBB");
_project = new MoBiProject();
A.CallTo(() => _projectRetriever.Current).Returns(_project);
A.CallTo(() => _eventPublisher.PublishEvent(A <ShowNotificationsEvent> ._))
.Invokes(x => _showNotificationEvent = x.GetArgument <ShowNotificationsEvent>(0));
}
protected override void Context()
{
_view = A.Fake <ISelectEventAssignmentTargetView>();
_context = A.Fake <IMoBiContext>();
_objectBaseDTOMapper = A.Fake <IObjectBaseToObjectBaseDTOMapper>();
_containerDTOMapper = A.Fake <IContainerToContainerDTOMapper>();
_reactionMapper = A.Fake <IReactionBuilderToDummyReactionDTOMapper>();
_moleculeMapper = A.Fake <IMoleculeBuilderToDummyMoleculeDTOMapper>();
_objectPathFactory = A.Fake <IObjectPathFactory>();
_parameterMapper = A.Fake <IParameterToDummyParameterDTOMapper>();
_dimensionRetriever = A.Fake <IReactionDimensionRetriever>();
sut = new SelectEventAssingmentTargetPresenter(_view, _context, _objectBaseDTOMapper, _containerDTOMapper, _reactionMapper,
_moleculeMapper, _objectPathFactory, _parameterMapper, _dimensionRetriever);
_mobiProject = A.Fake <IMoBiProject>();
_rootContainer = new Container();
_moleculeBuilder = new MoleculeBuilder().WithName("M");
_reaction = new ReactionBuilder().WithName("R");
_localParameter = new Parameter().WithMode(ParameterBuildMode.Local).WithName("LocalParam");
_globalParameter = new Parameter().WithMode(ParameterBuildMode.Global).WithName("GlobalParam");
_reaction.Add(_localParameter);
_reaction.Add(_globalParameter);
_reactionBB = new MoBiReactionBuildingBlock()
{
_reaction
};
_moleculeBB = new MoleculeBuildingBlock {
_moleculeBuilder
};
A.CallTo(() => _mobiProject.ReactionBlockCollection).Returns(new [] { _reactionBB });
A.CallTo(() => _mobiProject.MoleculeBlockCollection).Returns(new [] { _moleculeBB });
sut.Init(_mobiProject, _rootContainer);
}
public IObserverBuildingBlock AllObserversFor(IMoleculeBuildingBlock moleculeBuildingBlock, Simulation simulation)
{
var observerBuildingBlock = _objectBaseFactory.Create <IObserverBuildingBlock>().WithName(simulation.Name);
addStandardObserversTo(simulation, observerBuildingBlock, moleculeBuildingBlock);
//now add dynamic observers for molecules needing one
createFractionExcretedToUrineObserver(simulation, observerBuildingBlock);
createFractionOfDoseExcretedToBileObserver(simulation, observerBuildingBlock);
createFractionOfDoseExcretedToFecesObserver(simulation, observerBuildingBlock);
//add fraction observers for metabolite and complex
createFractionOfDoseObserver(simulation, observerBuildingBlock);
foreach (var compound in simulation.Compounds)
{
foreach (var specificBinding in simulation.CompoundPropertiesFor(compound).Processes.SpecificBindingSelection.AllEnabledProcesses())
{
var complexName = specificBinding.ProductName(CoreConstants.Molecule.Complex);
var protein = moleculeBuildingBlock[specificBinding.MoleculeName];
var complex = moleculeBuildingBlock[complexName];
createReceptorOccupancyObserver(observerBuildingBlock, protein, complex);
}
}
return(observerBuildingBlock);
}
public void Visit(IMoleculeBuildingBlock moleculeBuildingBlock)
{
var command = synchronizeInParameters(moleculeBuildingBlock);
if (!command.IsEmpty())
{
return;
}
var transporterMoleculeContainers = moleculeBuildingBlock.SelectMany(m => m.TransporterMoleculeContainerCollection).ToList();
if (!transporterMoleculeContainers.Any())
{
return;
}
var parameterTransporterName = _parameter.ParentContainer.Name;
var parameterMoleculeName = _parameter.ParentContainer.ParentContainer?.Name;
var transporterMoleculeContainer = findTransporterMoleculeContainerFor(transporterMoleculeContainers, parameterTransporterName, parameterMoleculeName);
if (transporterMoleculeContainer == null)
{
return;
}
var buildingBlockParameter = transporterMoleculeContainer.Parameter(_parameter.Name);
setSynchronizeCommand(buildingBlockParameter);
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
_moleculeBuildingBlock.Add(new MoleculeBuilder().WithName("Drug"));
_moleculeBuildingBlock.Add(new MoleculeBuilder().WithName("Transporter"));
}
/// <summary>
/// Adds event group to all model containers with defined criteria
/// </summary>
private void createEventGroupFrom(IEventGroupBuilder eventGroupBuilder, IMoleculeBuildingBlock molecules)
{
foreach (var sourceContainer in _sourceCriteriaTargetContainerCache[eventGroupBuilder.SourceCriteria])
{
createEventGroupInContainer(eventGroupBuilder, sourceContainer);
}
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
sut.Edit(_moleculeBuildingBlock);
_moleculeBuilder = new MoleculeBuilder();
_moleculeBuildingBlock.Add(_moleculeBuilder);
}
protected override void Context()
{
base.Context();
_projectItem = new MoleculeBuildingBlock();
_editPresenter = A.Fake <IEditMoleculeBuildingBlockPresenter>();
_commandCollector = A.Fake <ICommandCollector>();
A.CallTo(() => _container.Resolve <IEditMoleculeBuildingBlockPresenter>()).Returns(_editPresenter);
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = A.Fake <IMoleculeBuildingBlock>();
_moleculeBuilderToAdd = new MoleculeBuilder();
A.CallTo(() => _interactionTask.CorrectName(_moleculeBuilderToAdd, A <IEnumerable <string> > ._)).Returns(false);
A.CallTo(() => _context.PublishEvent(A <AddedEvent <IMoleculeBuilder> > ._))
.Invokes(x => _addEvent = x.GetArgument <AddedEvent <IMoleculeBuilder> >(0));
}
private void addMolecules(IMoleculeBuildingBlock moleculeBuilders, IList <DTOMoleculeSelection> dtos)
{
moleculeBuilders.Each(x => dtos.Add(new DTOMoleculeSelection
{
BuildingBlock = moleculeBuilders.Name,
Molecule = x.Name,
MoleculeBuilder = x
}));
}
protected override void Context()
{
sut = new ParameterResolver();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
_spatialStructure = new SpatialStructure {
GlobalMoleculeDependentProperties = new Container()
};
_containerPath = new ObjectPath();
}
protected override void Context()
{
sut = new FormulaUsageChecker();
_formula = new ExplicitFormula("1").WithName("Test Formula");
_buildingBlock = new MoleculeBuildingBlock();
_moleculeBuilder = new MoleculeBuilder().WithName("Container");
_moleculeBuilder.DefaultStartFormula = A.Fake <IFormula>();
_buildingBlock.Add(_moleculeBuilder);
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock {
Id = "1"
};
_moleculeBuildingBlock.Add(A.Fake <IMoleculeBuilder>().WithId("2"));
_moleculeBuildingBlock.Add(A.Fake <IMoleculeBuilder>().WithId("3"));
}
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);
}
public void Visit(IMoleculeBuildingBlock moleculeBuildingBlock)
{
foreach (var moleculeBuilder in moleculeBuildingBlock.Where(x => !x.ContainsName(Constants.Parameters.CONCENTRATION)).ToList())
{
var concentrationParameter = _parameterFactory.CreateConcentrationParameter(moleculeBuildingBlock.FormulaCache);
moleculeBuilder.AddParameter(concentrationParameter);
}
convertFormulaReferencingAeffIn(moleculeBuildingBlock);
}
public void TestComplexMoleculeBB()
{
MoleculeBuildingBlock x1 = _buildConfiguration.Molecules as MoleculeBuildingBlock;
Assert.IsNotNull(x1);
IMoleculeBuildingBlock x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualBuildingBlock(x2, x1);
}
public ITreeNode CreateFor(IMoleculeBuildingBlock moleculeBuildingBlock)
{
var moleculeBuildingBlockNode = createFor(moleculeBuildingBlock);
foreach (var molecule in moleculeBuildingBlock)
{
var moleculeNode = CreateFor(molecule);
moleculeBuildingBlockNode.AddChild(moleculeNode);
}
return(moleculeBuildingBlockNode);
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock {
Id = "1"
};
_project = new MoBiProject();
_project.AddBuildingBlock(new MoleculeStartValuesBuildingBlock {
MoleculeBuildingBlockId = _moleculeBuildingBlock.Id, SpatialStructureId = ""
});
}
protected override void Context()
{
base.Context();
_moleculeNode = A.Fake <ITreeNode>();
_moleculeBuildingBlockNode = A.Fake <ITreeNode>();
_moleculeBuildingBlock = A.Fake <IMoleculeBuildingBlock>().WithId("Id");
_moleculeBuilder = A.Fake <IMoleculeBuilder>();
A.CallTo(() => _view.TreeView.NodeById(_moleculeBuildingBlock.Id)).Returns(_moleculeBuildingBlockNode);
A.CallTo(() => _treeNodeFactory.CreateFor(_moleculeBuilder)).Returns(_moleculeNode);
}
protected override void Context()
{
base.Context();
_moleculeBuilder = A.Fake <IMoleculeBuilder>();
_moleculeBuildingBlock = A.Fake <IMoleculeBuildingBlock>();
var moleculeBuildingBlockNode = A.Fake <ITreeNode>();
A.CallTo(() => moleculeBuildingBlockNode.TagAsObject).Returns(_moleculeBuildingBlock);
_node = A.Fake <ITreeNode>();
_node.ParentNode = moleculeBuildingBlockNode;
A.CallTo(() => _node.TagAsObject).Returns(_moleculeBuilder);
}
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);
}
private void updateForPKSimChanges(IMoleculeBuildingBlock moleculeBuildingBlock)
{
var calculatedSpecificIntestinalPermeabilityTranscellularFormula =
moleculeBuildingBlock.FormulaCache.FindByName("PARAM_P_int_InVitro");
if (calculatedSpecificIntestinalPermeabilityTranscellularFormula == null)
{
return;
}
var velocity = _dimensionFactory.Dimension(AppConstants.DimensionNames.VELOCITY);
moleculeBuildingBlock.Each(mb => addCalculatedSpecificIntestinalPermeabilityTranscellularParameterTo(mb, calculatedSpecificIntestinalPermeabilityTranscellularFormula, velocity));
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = A.Fake <IMoleculeBuildingBlock>();
_moleculeBuilderToAdd = new MoleculeBuilder();
A.CallTo(() => _interactionTask.CorrectName(_moleculeBuilderToAdd, A <IEnumerable <string> > ._)).Returns(true);
A.CallTo(() => _interactionTask.AdjustFormula(_moleculeBuilderToAdd, _moleculeBuildingBlock, A <IMoBiMacroCommand> ._)).Returns(false);
A.CallTo(() => _context.PublishEvent(A <AddedEvent <IMoleculeBuilder> > ._))
.Invokes(x => _addEvent = x.GetArgument <AddedEvent <IMoleculeBuilder> >(0));
_cancelCommand = A.Fake <IMoBiCommand>();
A.CallTo(() => _interactionTaskContext.CancelCommand(A <IMoBiCommand> ._)).Returns(_cancelCommand);
}
protected override void Context()
{
_view = A.Fake <ICreatePKSimMoleculeView>();
_configuration = A.Fake <IMoBiConfiguration>();
_parameterDTOMapper = A.Fake <IParameterToParameterDTOMapper>();
_moleculeBuilderMapper = A.Fake <IMoleculeBuilderToMoleculeBuilderDTOMapper>();
_quantityTask = A.Fake <IQuantityTask>();
_serializationTask = A.Fake <ISerializationTask>();
_moleculeBuildingBlock = A.Fake <IMoleculeBuildingBlock>();
_editTask = A.Fake <IEditTaskFor <IMoleculeBuilder> >();
sut = new CreatePKSimMoleculePresenter(_view, _configuration, _parameterDTOMapper, _moleculeBuilderMapper, _serializationTask, _quantityTask, _editTask);
}
public ValidationResult Validate(IMoleculeBuildingBlock moleculeBuildingBlock)
{
var validationResults = new ValidationResult();
foreach (var molecule in moleculeBuildingBlock.Where(m => m.IsFloating))
{
foreach (var parameter in molecule.Parameters.Where(parameterIsInvalid))
{
validationResults.AddMessage(NotificationType.Error, parameter, Error.FloatingMoleculeParameterNotDefined(molecule.Name, parameter.Name, parameter.Value), moleculeBuildingBlock);
}
}
return(validationResults);
}
public void Visit(IMoleculeBuildingBlock moleculeBuildingBlock)
{
var amountDimension = _context.DimensionFactory.Dimension(Constants.Dimension.AMOUNT);
var formula = createTotalDrugMassFormula(amountDimension);
foreach (var moleculeBuilder in moleculeBuildingBlock)
{
moleculeBuilder.Add(
createTotalDrugMassParameter(formula, amountDimension));
}
updateAllParameters(moleculeBuildingBlock.SelectMany(mb => mb.GetAllChildren <IParameter>()));
moleculeBuildingBlock.AddFormula(formula);
_converted = true;
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
_createMoleculePresenter = A.Fake <ICreatePKSimMoleculePresenter>();
_molecule = new MoleculeBuilder();
_molecule.DefaultStartFormula = A.Fake <IFormula>();
A.CallTo(() => _createMoleculePresenter.CreateMolecule(_moleculeBuildingBlock)).Returns(_molecule);
A.CallTo(() => _interactionTaskContext.ApplicationController.Start <ICreatePKSimMoleculePresenter>()).Returns(_createMoleculePresenter);
_defaultStartFormula = new ConstantFormula();
A.CallTo(_formulaTask).WithReturnType <ConstantFormula>().Returns(_defaultStartFormula);
A.CallTo(() => _context.AddToHistory(A <ICommand> ._))
.Invokes(x => _command = x.GetArgument <ICommand>(0));
}