protected override void Context()
{
base.Context();
_templateMoleculeStartValues = new MoleculeStartValuesBuildingBlock();
A.CallTo(_context.Context.ObjectRepository).WithReturnType <bool>().Returns(true);
var moleculeBuildingBlock = new MoleculeBuildingBlock();
A.CallTo(_context.Context).WithReturnType <IMoleculeBuildingBlock>().Returns(moleculeBuildingBlock);
var spatialStructure = new SpatialStructure();
A.CallTo(_context.Context).WithReturnType <ISpatialStructure>().Returns(spatialStructure);
A.CallTo(() => _moleculeStartValuesCreator.CreateFrom(spatialStructure, moleculeBuildingBlock)).Returns(_templateMoleculeStartValues);
_newEndogenousValue = new MoleculeStartValue {
ContainerPath = new ObjectPath("Organism", AppConstants.Organs.ENDOGENOUS_IGG, "Plasma"), Name = "M", IsPresent = true
};
_existingEndogenousValue = new MoleculeStartValue {
ContainerPath = new ObjectPath("Organism", AppConstants.Organs.ENDOGENOUS_IGG, "Cell"), Name = "M", IsPresent = true
};
_existingTemplateEndogenousValue = new MoleculeStartValue {
ContainerPath = new ObjectPath("Organism", AppConstants.Organs.ENDOGENOUS_IGG, "Cell"), Name = "M", IsPresent = true
};
_templateMoleculeStartValues.Add(_newEndogenousValue);
_templateMoleculeStartValues.Add(_existingTemplateEndogenousValue);
_moleculeStartValueBuildingBlock.Add(_existingEndogenousValue);
}
protected override void Context()
{
base.Context();
_context = A.Fake <IMoBiContext>();
A.CallTo(() => _context.HistoryManager).Returns(A.Fake <IMoBiHistoryManager>());
_startValuesTask = A.Fake <IMoleculeStartValuesTask>();
_view = A.Fake <IImportQuantityView>();
_dialogCreator = A.Fake <IDialogCreator>();
_dataTableToImportQuantityDTOMapperForMolecules = A.Fake <IDataTableToImportQuantityDTOMapperForMolecules>();
_buildingBlock = new MoleculeStartValuesBuildingBlock();
_excelTask = A.Fake <IImportFromExcelTask>();
sut = new ImportMoleculeStartValuePresenter(_view, _dialogCreator, _context, _excelTask, _startValuesTask, _dataTableToImportQuantityDTOMapperForMolecules);
sut.Initialize();
_quantityImporterDTO = new QuantityImporterDTO();
new List <ImportedQuantityDTO>
{
new ImportedQuantityDTO {
Name = "drug", ContainerPath = new ObjectPath("First")
},
new ImportedQuantityDTO {
Name = "drug", ContainerPath = new ObjectPath("Second")
},
}.Each(_quantityImporterDTO.QuantitDTOs.Add);
A.CallTo(() => _dataTableToImportQuantityDTOMapperForMolecules.MapFrom(A <DataTable> ._, _buildingBlock)).Returns(_quantityImporterDTO);
A.CallTo(() => _view.Display()).Invokes(() =>
{
sut.StartImport();
sut.TransferImportedQuantities();
});
}
protected override void Context()
{
base.Context();
_buildConfiguration = A.Fake <IMoBiBuildConfiguration>();
_templateStartValuesBuildingBlock = new MoleculeStartValuesBuildingBlock();
_newMoleculeStartValues = new MoleculeStartValuesBuildingBlock();
_buildConfiguration.MoleculeStartValuesInfo = new MoleculeStartValuesBuildingBlockInfo {
BuildingBlock = _templateStartValuesBuildingBlock, TemplateBuildingBlock = _templateStartValuesBuildingBlock
};
A.CallTo(_moleculeStartValuesCreator).WithReturnType <IMoleculeStartValuesBuildingBlock>().Returns(_newMoleculeStartValues);
_newEndogenousValue = new MoleculeStartValue {
ContainerPath = new ObjectPath("Organism", AppConstants.Organs.ENDOGENOUS_IGG, "Plasma"), Name = "M", IsPresent = true
};
_existingEndogenousValue = new MoleculeStartValue {
ContainerPath = new ObjectPath("Organism", AppConstants.Organs.ENDOGENOUS_IGG, "Cell"), Name = "M", IsPresent = true
};
_otherStartValues = new MoleculeStartValue {
ContainerPath = new ObjectPath("Organism", "Liver", "Cell"), Name = "M", IsPresent = true
};
_existingTemplateEndogenousValue = new MoleculeStartValue {
ContainerPath = new ObjectPath("Organism", AppConstants.Organs.ENDOGENOUS_IGG, "Cell"), Name = "M", IsPresent = true
};
_templateStartValuesBuildingBlock.Add(_existingTemplateEndogenousValue);
_newMoleculeStartValues.Add(_newEndogenousValue);
_newMoleculeStartValues.Add(_existingEndogenousValue);
_newMoleculeStartValues.Add(_otherStartValues);
}
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);
}
private void CreateMoleculeStartValueBuildingBlock(Model model)
{
_moleculeStartValuesBuildingBlock = _moleculeStartValuesCreator.CreateFrom(GetMainSpatialStructure(model),
MoleculeBuildingBlock)
.WithId(SBMLConstants.SBML_MOLECULESTARTVALUES_BB)
.WithName(SBMLConstants.SBML_MOLECULESTARTVALUES_BB)
.WithDescription(SBMLConstants.SBML_MOLECULESTARTVALUES_DESCRIPTION);
}
public void Visit(IMoleculeStartValuesBuildingBlock moleculeStartValuesBuilding)
{
foreach (var moleculeStartValue in moleculeStartValuesBuilding)
{
moleculeStartValue.ScaleDivisor = Constants.DEFAULT_SCALE_DIVISOR;
updateToAmountDimension(moleculeStartValue);
}
}
public IEnumerable <IMoleculeBuilder> AllPresentFor(IMoleculeStartValuesBuildingBlock moleculesStartValues)
{
var moleculeNames = (from moleculeStartValue in moleculesStartValues
where moleculeStartValue.IsPresent
select moleculeStartValue.MoleculeName).Distinct();
return(moleculeNames.Select(moleculeName => this[moleculeName]).Where(m => m != null));
}
protected override void Context()
{
base.Context();
_formula = new ExplicitFormula().WithName("F1").WithId("F11");
_templateFormula = new ExplicitFormula().WithName("F1").WithId("F12");
_moleculeStartValues = new MoleculeStartValuesBuildingBlock().WithName("MSV");
_moleculeStartValuesTemplate = new MoleculeStartValuesBuildingBlock().WithName("MSV");
_moleculeStartValuesTemplate.AddFormula(_templateFormula);
_allBuildingBlocks.Add(_moleculeStartValuesTemplate);
}
protected override void Context()
{
base.Context();
_msv = new MoleculeStartValue {
NegativeValuesAllowed = false
};
_moleculeStartValueBuildingBlock = new MoleculeStartValuesBuildingBlock {
_msv
};
}
private void addMoleculesFrom(IMoleculeStartValuesBuildingBlock moleculesStartValuesBuildingBlock, IEntity container, IEnumerable <IMoleculeBuilder> molecules)
{
foreach (var molecule in molecules)
{
var moleculeStartValue = CreateMoleculeStartValue(_objectPathFactory.CreateAbsoluteObjectPath(container), molecule.Name, molecule.Dimension, molecule.DisplayUnit);
setMoleculeStartValue(molecule, moleculeStartValue);
setMoleculeStartValueFormula(molecule.DefaultStartFormula, moleculeStartValue, moleculesStartValuesBuildingBlock);
moleculesStartValuesBuildingBlock.Add(moleculeStartValue);
}
}
public void TestComplexMoleculeStartValuesBuildingBlock()
{
MoleculeStartValuesBuildingBlock x1 = _buildConfiguration.MoleculeStartValues as MoleculeStartValuesBuildingBlock;
Assert.IsNotNull(x1);
IMoleculeStartValuesBuildingBlock x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualMoleculeStartValuesBuildingBlock(x2, x1);
}
protected override void Context()
{
base.Context();
_context = A.Fake <IMoBiContext>();
_buildingBlock = new MoleculeStartValuesBuildingBlock();
_moleculeStartValue = new MoleculeStartValue();
_path = new ObjectPath("A", "B");
_moleculeStartValue.ContainerPath = _path;
_moleculeStartValue.Name = "Name";
_buildingBlock.Add(_moleculeStartValue);
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <IMoBiSimulation>();
_templateBuildingBlock = new MoleculeStartValuesBuildingBlock();
_cloneSimulationStartValueBuildingBlock = new MoleculeStartValuesBuildingBlock();
IMoleculeStartValuesBuildingBlock simulationStartValueBuildingBlock = new MoleculeStartValuesBuildingBlock();
A.CallTo(() => _cloneManagerForBuildingBlock.Clone(simulationStartValueBuildingBlock)).Returns(_cloneSimulationStartValueBuildingBlock);
A.CallTo(() => _simulation.BuildConfiguration.MoleculeStartValues).Returns(simulationStartValueBuildingBlock);
}
protected override void Context()
{
_startValueBuildingBlock = new MoleculeStartValuesBuildingBlock();
_startValue = new MoleculeStartValue {
IsPresent = false
};
_startValueBuildingBlock.Add(_startValue);
_context = A.Fake <IMoBiContext>();
sut = new UpdateMoleculeStartValueIsPresentCommand(_startValueBuildingBlock, _startValue, true);
}
private void setMoleculeStartValues(IMoleculeStartValuesBuildingBlock moleculeStartValues)
{
var organsim_A = moleculeStartValues[_objectPathFactory.CreateObjectPathFrom(ConstantsForSpecs.Organism, "A")];
organsim_A.StartValue = 5;
var lung_B = moleculeStartValues[_objectPathFactory.CreateObjectPathFrom(ConstantsForSpecs.Organism, ConstantsForSpecs.Lung, "B")];
lung_B.Formula = null;
lung_B.StartValue = 100;
}
protected override void Context()
{
_moleculeStartValuesBuildingBlock = new MoleculeStartValuesBuildingBlock();
_changedMoleculeStartValue = A.Fake <IMoleculeStartValue>();
_newFormula = new ExplicitFormula {
Id = "newFormulaId"
};
_oldFormula = new ExplicitFormula {
Id = "oldFormulaId"
};
sut = new ChangeStartValueFormulaCommand <IMoleculeStartValue>(_moleculeStartValuesBuildingBlock, _changedMoleculeStartValue, _newFormula, _oldFormula);
}
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);
}
protected override void Context()
{
_fakeDimension = A.Fake <IDimension>();
_context = A.Fake <IMoBiContext>();
_buildingBlock = new MoleculeStartValuesBuildingBlock();
_moleculeStartValue = new MoleculeStartValue {
Path = new ObjectPath("path1"), Dimension = _fakeDimension, StartValue = -1, DisplayUnit = new Unit("Dimensionless", 1.0, 1)
};
sut = new AddMoleculeStartValueToBuildingBlockCommand(_buildingBlock, _moleculeStartValue);
A.CallTo(() => _context.Get <IStartValuesBuildingBlock <IMoleculeStartValue> >(A <string> ._)).Returns(_buildingBlock);
}
protected override void Context()
{
base.Context();
_buildingBlock = new MoleculeStartValuesBuildingBlock();
_project = A.Fake <IMoBiProject>();
_options = new SearchOptions()
{
CaseSensitive = false, Expression = "*", Scope = SearchScope.AllOfSameType, RegEx = true, WholeWord = true
};
A.CallTo(() => _context.CurrentProject).Returns(_project);
_otherBuildingBlock = new MoleculeStartValuesBuildingBlock();
A.CallTo(() => _project.MoleculeStartValueBlockCollection).Returns(new [] { _buildingBlock, _otherBuildingBlock });
}
protected override void Context()
{
_spatialStructureFactory = A.Fake <IPKSimSpatialStructureFactory>();
_modelObserverQuery = A.Fake <IModelObserverQuery>();
_modelPassiveTransportQuery = A.Fake <IModelPassiveTransportQuery>();
_parameterStartValueCreator = A.Fake <IPKSimParameterStartValuesCreator>();
_moleculesAndReactionsCreator = A.Fake <IMoleculesAndReactionsCreator>();
_eventBuildingBlockCreator = A.Fake <IEventBuildingBlockCreator>();
_moleculeStartValueCreator = A.Fake <IPKSimMoleculeStartValuesCreator>();
_moleculeCalculationRetriever = A.Fake <IMoleculeCalculationRetriever>();
_distributedTableConverter = A.Fake <IDistributedParameterToTableParameterConverter>();
_parameterDefaultStateUpdater = A.Fake <IParameterDefaultStateUpdater>();
_cm1 = new CoreCalculationMethod();
_cm2 = new CoreCalculationMethod();
_simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
_simulation.SimulationSettings = new SimulationSettings();
_simulation.ModelConfiguration = new ModelConfiguration();
_individual = new Individual().WithName("MyIndividuyal");
_compound = A.Fake <Compound>().WithName("MyCompound");
_protocol = new SimpleProtocol().WithName("MyProtocol");
_spatialStructure = A.Fake <ISpatialStructure>();
_passiveTransportBuilingBlock = A.Fake <IPassiveTransportBuildingBlock>();
_observerBuildingBlock = A.Fake <IObserverBuildingBlock>();
_eventBuildingBlock = A.Fake <IEventGroupBuildingBlock>();
_parameterValuesBuildingBlock = A.Fake <IParameterStartValuesBuildingBlock>();
_moleculeStartValueBuildingBlock = A.Fake <IMoleculeStartValuesBuildingBlock>();
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Individual", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Compound", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Protocol", PKSimBuildingBlockType.Protocol)
{
BuildingBlock = _protocol
});
A.CallTo(() => _moleculeCalculationRetriever.AllMoleculeCalculationMethodsUsedBy(_simulation)).Returns(new[] { _cm1, _cm2 });
A.CallTo(() => _spatialStructureFactory.CreateFor(_individual, _simulation)).Returns(_spatialStructure);
A.CallTo(() => _modelPassiveTransportQuery.AllPassiveTransportsFor(_simulation)).Returns(_passiveTransportBuilingBlock);
A.CallTo(() => _modelObserverQuery.AllObserversFor(A <IMoleculeBuildingBlock> .Ignored, _simulation)).Returns(_observerBuildingBlock);
A.CallTo(() => _eventBuildingBlockCreator.CreateFor(_simulation)).Returns(_eventBuildingBlock);
A.CallTo(() => _parameterStartValueCreator.CreateFor(A <IBuildConfiguration> .Ignored, A <Simulation> .Ignored)).Returns(_parameterValuesBuildingBlock);
A.CallTo(() => _moleculeStartValueCreator.CreateFor(A <IBuildConfiguration> .Ignored, A <Simulation> .Ignored)).Returns(_moleculeStartValueBuildingBlock);
sut = new BuildConfigurationTask(_spatialStructureFactory, _modelObserverQuery, _modelPassiveTransportQuery, _parameterStartValueCreator,
_moleculesAndReactionsCreator, _eventBuildingBlockCreator, _moleculeStartValueCreator, _moleculeCalculationRetriever,
_distributedTableConverter, _parameterDefaultStateUpdater);
}
protected override void Context()
{
_oldScaleDivisor = 0;
_startValue = new MoleculeStartValue {
Id = "startValueId"
};
_buildingBlock = new MoleculeStartValuesBuildingBlock {
Id = "id"
};
_context = A.Fake <IMoBiContext>();
sut = new UpdateMoleculeStartValueScaleDivisorCommand(_buildingBlock, _startValue, _newScaleDivisor, _oldScaleDivisor);
A.CallTo(() => _context.Get <IMoleculeStartValuesBuildingBlock>(_buildingBlock.Id)).Returns(_buildingBlock);
}
protected override void Context()
{
_fakeDimension = A.Fake <IDimension>();
_context = A.Fake <IMoBiContext>();
_buildingBlock = new MoleculeStartValuesBuildingBlock();
_msv = new MoleculeStartValue {
Path = new ObjectPath("path1"), Dimension = _fakeDimension, StartValue = -1, DisplayUnit = new Unit("Dimensionless", 1.0, 1)
};
_buildingBlock.Add(_msv);
sut = new RemoveMoleculeStartValueFromBuildingBlockCommand(_buildingBlock, _msv.Path);
A.CallTo(() => _context.Get <IStartValuesBuildingBlock <IMoleculeStartValue> >(_buildingBlock.Id)).Returns(_buildingBlock);
}
protected override void Context()
{
base.Context();
_moleculeStartValuesBuildingBlock = new MoleculeStartValuesBuildingBlock {
Name = _changedName
};
_moleculeStartValue = new MoleculeStartValue();
_path = new ObjectPath(new[] { "A", "B", _changedName });
_moleculeStartValue.Path = _path;
_moleculeStartValuesBuildingBlock.Add(_moleculeStartValue);
_project.AddBuildingBlock(_moleculeStartValuesBuildingBlock);
_moleculeStartValue2 = new MoleculeStartValue();
_path = new ObjectPath(new[] { "A", _changedName, "B" });
_moleculeStartValue2.Path = _path;
_moleculeStartValuesBuildingBlock.Add(_moleculeStartValue2);
}
protected override void Context()
{
_fakeDimension = A.Fake <IDimension>();
_context = A.Fake <IMoBiContext>();
_buildingBlock = new MoleculeStartValuesBuildingBlock();
var msv = new MoleculeStartValue {
Path = new ObjectPath("path1"), Dimension = _fakeDimension, StartValue = -1, DisplayUnit = new Unit("Dimensionless", 1.0, 1), IsPresent = false
};
_buildingBlock.Add(msv);
_path = msv.Path;
sut = new UpdateMoleculeStartValueInBuildingBlockCommand(_buildingBlock, _path, 1.0, true, 22.0, true);
A.CallTo(() => _context.Get <IMoleculeStartValuesBuildingBlock>(_buildingBlock.Id)).Returns(_buildingBlock);
}
protected override void Context()
{
_context = A.Fake <IMoBiContext>();
_liver = new Container().WithName("LIVER");
_simulation = A.Fake <IMoBiSimulation>();
_simulation.Model.Root = new Container().WithContainerType(ContainerType.Simulation);
_simulation.Model.Root.Add(_liver);
_moleculeStartValues = new MoleculeStartValuesBuildingBlock();
_simulation.BuildConfiguration.MoleculeStartValues = _moleculeStartValues;
sut = new ResetMoleculeValuesToDefaultFromStartValuesInSimulationCommand(_simulation);
_formulaTask = A.Fake <IMoBiFormulaTask>();
_entityPathResolver = new EntityPathResolver(new ObjectPathFactory(new AliasCreator()));
_cloneManagerForModel = A.Fake <ICloneManagerForModel>();
A.CallTo(_formulaTask).WithReturnType <ConstantFormula>().Returns(new ConstantFormula());
A.CallTo(() => _context.Resolve <IMoBiFormulaTask>()).Returns(_formulaTask);
A.CallTo(() => _context.Resolve <IEntityPathResolver>()).Returns(_entityPathResolver);
A.CallTo(() => _context.Resolve <ICloneManagerForModel>()).Returns(_cloneManagerForModel);
}
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);
}
protected override void Context()
{
_buildConfiguration = new MoBiBuildConfiguration();
_moleculeBuidingBlock = new MoleculeBuildingBlock().WithName("M");
_buildConfiguration.Molecules = _moleculeBuidingBlock;
_reactionBuildingBlock = new MoBiReactionBuildingBlock().WithName("R");
_reactionBuildingBlock.Add(new ReactionBuilder().WithName("R1"));
_buildConfiguration.Reactions = _reactionBuildingBlock;
_passiveTransportBuildingBlock = new PassiveTransportBuildingBlock().WithName("PT");
_passiveTransportBuildingBlock.Add(new TransportBuilder().WithName("PT2"));
_passiveTransportBuildingBlock.Add(new TransportBuilder().WithName("PT1"));
_buildConfiguration.PassiveTransports = _passiveTransportBuildingBlock;
_eventGroupBuildingBlock = new EventGroupBuildingBlock().WithName("EG");
_buildConfiguration.EventGroups = _eventGroupBuildingBlock;
_msvBuildingBlock = new MoleculeStartValuesBuildingBlock().WithName("MSV");
_buildConfiguration.MoleculeStartValues = _msvBuildingBlock;
_psvBuildingBlock = new ParameterStartValuesBuildingBlock().WithName("PSV");
_buildConfiguration.ParameterStartValues = _psvBuildingBlock;
_spatialStructure = new MoBiSpatialStructure().WithName("SPST");
_buildConfiguration.SpatialStructure = _spatialStructure;
_observerBuildingBlock = new ObserverBuildingBlock().WithName("O");
_buildConfiguration.Observers = _observerBuildingBlock;
_objectPathFactory = new ObjectPathFactory(new AliasCreator());
_entityPathResolver = new EntityPathResolver(_objectPathFactory);
sut = new AffectedBuildingBlockRetriever(_entityPathResolver);
//common setup
_simulation = new MoBiSimulation {
BuildConfiguration = _buildConfiguration
};
}
private void setStartFormulasForStaticMolecules(IMoleculeStartValuesBuildingBlock defaultStartValues, Simulation simulation, IEnumerable <Compound> compounds)
{
var modelName = simulation.ModelConfiguration.ModelName;
//get the names of molecules that are static (e.g. not enzymes, metabolites, etc.)
// (e.g. FcRn in 2pores-model)
var staticMoleculeNames = _modelContainerMoleculeRepository.MoleculeNamesIncludingDrug(modelName);
var compoundNames = compounds.AllNames().ToList();
foreach (var moleculeStartValue in defaultStartValues)
{
var dbMoleculeName = getDbMoleculeName(moleculeStartValue.MoleculeName, compoundNames);
if (staticMoleculeNames.Contains(dbMoleculeName))
{
moleculeStartValue.IsPresent = _modelContainerMoleculeRepository.IsPresent(modelName, moleculeStartValue.ContainerPath, dbMoleculeName);
moleculeStartValue.NegativeValuesAllowed = _modelContainerMoleculeRepository.NegativeValuesAllowed(modelName, moleculeStartValue.ContainerPath, dbMoleculeName);
}
else
{
moleculeStartValue.IsPresent = false;
moleculeStartValue.NegativeValuesAllowed = false;
}
var moleculeDbPath = moleculeStartValue.ContainerPath.Clone <IObjectPath>();
moleculeDbPath.Add(dbMoleculeName);
var rateKey = _moleculeStartFormulaRepository.RateKeyFor(moleculeDbPath, simulation.ModelProperties);
if (rateKey == null)
{
continue; //no start formula available
}
//set molecule start formula
moleculeStartValue.Formula = _formulaFactory.RateFor(rateKey, defaultStartValues.FormulaCache);
}
}
protected override void Context()
{
base.Context();
_moleculeStartValues = new MoleculeStartValuesBuildingBlock();
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "drug", IsPresent = true
});
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "molecule", IsPresent = true
});
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "moleculeThatDoesNotExist", IsPresent = true
});
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "moleculeThatDoesExistButNotPresent", IsPresent = false
});
_drug = new MoleculeBuilder().WithName("drug");
sut.Add(_drug);
_molecule = new MoleculeBuilder().WithName("molecule");
sut.Add(_molecule);
sut.Add(new MoleculeBuilder().WithName("moleculeThatDoesExistButNotPresent"));
}
public void Visit(IMoleculeStartValuesBuildingBlock moleculeStartValuesBuildingBlock)
{
moleculeStartValuesBuildingBlock.Each(msv => msv.Dimension = _dimensionFactory.Dimension(Constants.Dimension.AMOUNT));
convert(moleculeStartValuesBuildingBlock);
_converted = true;
}
