protected override void Context()
{
_msvCreator = A.Fake <IMoleculeStartValuesCreator>();
A.CallTo(() => _msvCreator.CreateMoleculeStartValue(A <IObjectPath> .Ignored, A <string> .Ignored, A <IDimension> .Ignored, A <Unit> ._, A <ValueOrigin> ._))
.ReturnsLazily((IObjectPath path, string moleculeName, IDimension dimension) => new MoleculeStartValue {
ContainerPath = path, Name = moleculeName, Dimension = dimension
});
_concentrationDimension = new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.MOLAR_CONCENTRATION, "mol/l");
_amountDimension = new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.AMOUNT, "mol");
_amountDimension.AddUnit("mmol", 0.001, 0);
_timeDimension = new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.TIME, "s");
_timeDimension.Unit("s").Factor = 1.0 / 60;
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
_startValuesBuildingBlock = A.Fake <IMoleculeStartValuesBuildingBlock>();
_reactionDimensionRetriever = A.Fake <IReactionDimensionRetriever>();
A.CallTo(() => _dimensionFactory.DimensionForUnit("mol")).Returns(_amountDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("mmol")).Returns(_amountDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("mol/l")).Returns(_concentrationDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("s")).Returns(_timeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("")).Throws <Exception>();
A.CallTo(() => _dimensionFactory.Dimension(Constants.Dimension.AMOUNT)).Returns(_amountDimension);
A.CallTo(() => _dimensionFactory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION)).Returns(_concentrationDimension);
A.CallTo(() => _reactionDimensionRetriever.SelectedDimensionMode).Returns(ReactionDimensionMode.AmountBased);
sut = new DataTableToImportQuantityDTOMapperForMolecules(_dimensionFactory, _reactionDimensionRetriever);
}
public CreateMoleculeStartValuesPresenter(ICreateStartValuesView view, IMoBiContext context, IMoleculeStartValuesCreator startValuesCreator) : base(view, context)
{
_startValuesCreator = startValuesCreator;
_unallowedNames.AddRange(_context.CurrentProject.MoleculeStartValueBlockCollection.Select(x => x.Name));
view.ApplicationIcon = ApplicationIcons.MoleculeStartValues;
view.Caption = AppConstants.Captions.NewMolculeStartValues;
}
public SpeciesImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoleculeBuilderFactory moleculeBuilderFactory, IMoleculeStartValuesCreator moleculeStartValuesCreator, IMoBiDimensionFactory moBiDimensionFactory, ASTHandler astHandler, IMoBiContext context)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_moleculeBuilderFactory = moleculeBuilderFactory;
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_moBiDimensionFactory = moBiDimensionFactory;
_counter = 1;
_dimensionDictionary = new Dictionary <string, Dimension>();
}
protected override void Context()
{
_context = A.Fake <IInteractionTaskContext>();
_editTask = A.Fake <IEditTasksForBuildingBlock <IMoleculeStartValuesBuildingBlock> >();
_moleculeStartValuesCreator = A.Fake <IMoleculeStartValuesCreator>();
_cloneManagerForBuildingBlock = A.Fake <ICloneManagerForBuildingBlock>();
_moleculeStartValueBuildingBlock = new MoleculeStartValuesBuildingBlock();
_reactionDimensionRetriever = A.Fake <IReactionDimensionRetriever>();
_moleculeResolver = A.Fake <IMoleculeResolver>();
sut = new MoleculeStartValuesTask(_context, _editTask, _moleculeStartValuesCreator,
new ImportedQuantityToMoleculeStartValueMapper(_moleculeStartValuesCreator), A.Fake <IMoleculeStartValueBuildingBlockMergeManager>(), _cloneManagerForBuildingBlock, _reactionDimensionRetriever, A.Fake <IMoBiFormulaTask>(), A.Fake <IMoBiSpatialStructureFactory>(), new MoleculeStartValuePathTask(A.Fake <IFormulaTask>(), _context.Context), _moleculeResolver);
}
public PKSimMoleculeStartValuesCreator(
IMoleculeStartValuesCreator moleculeStartValuesCreator,
IMoleculeStartFormulaRepository moleculeStartFormulaRepository,
IFormulaFactory formulaFactory,
IModelContainerMoleculeRepository modelContainerMoleculeRepository,
IEntityPathResolver entityPathResolver)
{
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_moleculeStartFormulaRepository = moleculeStartFormulaRepository;
_formulaFactory = formulaFactory;
_modelContainerMoleculeRepository = modelContainerMoleculeRepository;
_entityPathResolver = entityPathResolver;
}
protected virtual void InitializeSimulation()
{
_objectPathFactory = IoC.Resolve <IObjectPathFactory>();
_moleculeStartValuesCreator = IoC.Resolve <IMoleculeStartValuesCreator>();
_buildConfiguration = IoC.Resolve <ModelHelperForSpecs>().CreateBuildConfiguration();
_modelConstructor = IoC.Resolve <IModelConstructor>();
_result = _modelConstructor.CreateModelFrom(_buildConfiguration, "MyModel");
_model = _result.Model;
_simulation = new ModelCoreSimulation
{
BuildConfiguration = _buildConfiguration,
Model = _model
};
}
public PKSimMoleculeStartValuesCreator(IMoleculeStartValuesCreator moleculeStartValuesCreator,
IObjectPathFactory objectPathFactory,
IExpressionContainersRetriever expressionContainersRetriever,
IMoleculeStartFormulaRepository moleculeStartFormulaRepository,
IFormulaFactory formulaFactory,
IModelContainerMoleculeRepository modelContainerMoleculeRepository)
{
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_objectPathFactory = objectPathFactory;
_expressionContainersRetriever = expressionContainersRetriever;
_moleculeStartFormulaRepository = moleculeStartFormulaRepository;
_formulaFactory = formulaFactory;
_modelContainerMoleculeRepository = modelContainerMoleculeRepository;
}
public MoleculeStartValuesTask(
IInteractionTaskContext interactionTaskContext,
IEditTasksForBuildingBlock <IMoleculeStartValuesBuildingBlock> editTask,
IMoleculeStartValuesCreator startValuesCreator,
IImportedQuantityToMoleculeStartValueMapper dtoMapper,
IMoleculeStartValueBuildingBlockMergeManager startValueBuildingBlockMergeManager,
ICloneManagerForBuildingBlock cloneManagerForBuildingBlock,
IReactionDimensionRetriever dimensionRetriever,
IMoBiFormulaTask moBiFormulaTask,
IMoBiSpatialStructureFactory spatialStructureFactory, IMoleculeStartValuePathTask moleculeStartValuePathTask, IMoleculeResolver moleculeResolver)
: base(interactionTaskContext, editTask, startValueBuildingBlockMergeManager, cloneManagerForBuildingBlock, moBiFormulaTask, spatialStructureFactory, dtoMapper, moleculeStartValuePathTask)
{
_startValuesCreator = startValuesCreator;
_dimensionRetriever = dimensionRetriever;
_moleculeResolver = moleculeResolver;
}
public ConcentrationBaseModelHelperForSpecs(IObjectBaseFactory objectBaseFactory, IParameterStartValuesCreator parameterStartValuesCreator, IMoleculeStartValuesCreator moleculeStartValuesCreator,
IObjectPathFactory objectPathFactory, IDimensionFactory dimensionFactory, ISpatialStructureFactory spatialStructureFactory,
IOutputSchemaFactory outputSchemaFactory, IMoleculeBuilderFactory moleculeBuilderFactory,
IReactionDimensionRetriever reactionDimensionRetriever, IModelConstructor modelConstructor, ISolverSettingsFactory solverSettingsFactory)
{
_objectBaseFactory = objectBaseFactory;
_outputSchemaFactory = outputSchemaFactory;
_moleculeBuilderFactory = moleculeBuilderFactory;
_modelConstructor = modelConstructor;
_solverSettingsFactory = solverSettingsFactory;
_reactionDimensionRetriever = reactionDimensionRetriever.DowncastTo <ReactionDimensionRetrieverForSpecs>();
_spatialStructureFactory = spatialStructureFactory;
_parameterStartValuesCreator = parameterStartValuesCreator;
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_objectPathFactory = objectPathFactory;
_concentrationDimension = dimensionFactory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION);
_concentrationPerTimeDimension = dimensionFactory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION_PER_TIME);
_volumeDimension = dimensionFactory.Dimension(Constants.Dimension.VOLUME);
}
public MoleculeStartValuesPresenter(
IMoleculeStartValuesView view,
IMoleculeStartValueToMoleculeStartValueDTOMapper startValueMapper,
IMoleculeIsPresentSelectionPresenter isPresentSelectionPresenter,
IRefreshStartValueFromOriginalBuildingBlockPresenter refreshStartValuesPresenter,
IMoleculeNegativeValuesAllowedSelectionPresenter negativeStartValuesAllowedSelectionPresenter,
IMoleculeStartValuesTask moleculeStartValuesTask,
IMoleculeStartValuesCreator msvCreator,
IMoBiContext context,
ILegendPresenter legendPresenter,
IDeleteStartValuePresenter deleteStartValuePresenter)
: base(view, startValueMapper, refreshStartValuesPresenter, moleculeStartValuesTask, msvCreator, context, legendPresenter, deleteStartValuePresenter)
{
_moleculeStartValuesTask = moleculeStartValuesTask;
isPresentSelectionPresenter.ApplySelectionAction = performIsPresentAction;
negativeStartValuesAllowedSelectionPresenter.ApplySelectionAction = performNegativeValuesAllowedAction;
_view.AddIsPresentSelectionView(isPresentSelectionPresenter.BaseView);
_view.AddNegativeValuesAllowedSelectionView(negativeStartValuesAllowedSelectionPresenter.BaseView);
}
protected override void Context()
{
_view = A.Fake <IMoleculeStartValuesView>();
_mapper = A.Fake <IMoleculeStartValueToMoleculeStartValueDTOMapper>();
_context = A.Fake <IMoBiContext>();
_isPresentSelectionPresenter = A.Fake <IMoleculeIsPresentSelectionPresenter>();
_refreshStartValuesPresenter = A.Fake <IRefreshStartValueFromOriginalBuildingBlockPresenter>();
_negativeStartValuesAllowedSelectionPresenter = A.Fake <IMoleculeNegativeValuesAllowedSelectionPresenter>();
_moleculeStartValueTask = A.Fake <IMoleculeStartValuesTask>();
_commandCollector = A.Fake <ICommandCollector>();
_deleteStartValuePresenter = A.Fake <IDeleteStartValuePresenter>();
_legendPresenter = A.Fake <ILegendPresenter>();
_moleculeStartValuesCreator = A.Fake <IMoleculeStartValuesCreator>();
sut = new MoleculeStartValuesPresenter(
_view, _mapper, _isPresentSelectionPresenter, _refreshStartValuesPresenter, _negativeStartValuesAllowedSelectionPresenter, _moleculeStartValueTask,
_moleculeStartValuesCreator, _context, _legendPresenter, _deleteStartValuePresenter);
_moleculeStartValueBuildingBlock = new MoleculeStartValuesBuildingBlock();
sut.InitializeWith(_commandCollector);
}
public ImportedQuantityToMoleculeStartValueMapper(IMoleculeStartValuesCreator msvCreator)
{
_msvCreator = msvCreator;
}
public SimulationHelperForSpecs(IObjectBaseFactory objectBaseFactory, IParameterStartValuesCreator parameterStartValuesCreator, IMoleculeStartValuesCreator moleculeStartValuesCreator, IObjectPathFactory objectPathFactory, IDimensionFactory dimensionFactory, IModelConstructor modelConstructor, ISpatialStructureFactory spatialStructureFactory, INeighborhoodBuilderFactory neighborhoodFactory, IOutputSchemaFactory outputSchemaFactory, IMoleculeBuilderFactory moleculeBuilderFactory, ISolverSettingsFactory solverSettingsFactory)
: base(objectBaseFactory, parameterStartValuesCreator, moleculeStartValuesCreator, objectPathFactory,
dimensionFactory, spatialStructureFactory, neighborhoodFactory, outputSchemaFactory, moleculeBuilderFactory, solverSettingsFactory)
{
_modelConstructor = modelConstructor;
}
