protected override void Context()
{
base.Context();
_eventGroupBuilder1 = new EventGroupBuilder().WithName("EG1");
_eventGroupBuilder2 = new EventGroupBuilder().WithName("EG2");
_eventBuildingBlockCreator = new EventGroupBuildingBlock {
_eventGroupBuilder1, _eventGroupBuilder2
};
_startTime1 = DomainHelperForSpecs.ConstantParameterWithValue().WithName(Constants.Parameters.START_TIME);
_startTime2 = DomainHelperForSpecs.ConstantParameterWithValue().WithName(Constants.Parameters.START_TIME);
_dose = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.DOSE);
_dosePerBodyWeight = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.DOSE_PER_BODY_WEIGHT);
_p1 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P1");
_p2 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P2");
_eventBuilder1 = new EventBuilder().WithName("E1");
_eventBuilder2 = new EventBuilder().WithName("E2");
_eventGroupBuilder1.Add(_eventBuilder1);
_eventGroupBuilder2.Add(_eventBuilder2);
_eventBuilder1.Add(_startTime1);
_eventBuilder1.Add(_p1);
_eventBuilder2.Add(_startTime2);
_eventBuilder1.Add(_dosePerBodyWeight);
_eventBuilder2.Add(_dose);
_eventBuilder2.Add(_p2);
}
protected override void Context()
{
base.Context();
_eventGroupBuildingBlock = new EventGroupBuildingBlock();
_eventGroup = new EventGroupBuilder().WithName("EG");
_eventGroupBuildingBlock.Add(_eventGroup);
var parameter = new Parameter().WithName("P1").WithParentContainer(_eventGroup);
}
public void Visit(IEventGroupBuildingBlock eventGroupBuildingBlock)
{
convert(eventGroupBuildingBlock);
var inversedVolume = _dimensionFactory.Dimension(AppConstants.DimensionNames.INVERSED_VOLUME);
eventGroupBuildingBlock.Each(eg => convertSpecialParameter(eg, "Number_Of_Particles_Factor", 1000, inversedVolume));
_converted = true;
}
protected override void Context()
{
base.Context();
_eventBuildingBlock = new EventGroupBuildingBlock();
var applicationBuilder = new ApplicationBuilder().WithName("App1");
_moleculeBuilder = new ApplicationMoleculeBuilder();
applicationBuilder.AddMolecule(_moleculeBuilder);
_eventBuildingBlock.Add(applicationBuilder);
}
protected override void Context()
{
sut = new Converter531To541();
_eventGroubBuildingBlock = new EventGroupBuildingBlock();
_eventGroup = new EventGroupBuilder().WithName("EG");
_rootApplication = new ApplicationBuilder().WithName("App").WithContainerType(ContainerType.Other);
_eventGroubBuildingBlock.Add(_eventGroup);
_eventGroubBuildingBlock.Add(_rootApplication);
_container = new Container().WithName("PSI").WithParentContainer(_eventGroup);
_application = new ApplicationBuilder().WithName("App").WithContainerType(ContainerType.Other).WithParentContainer(_eventGroup);
}
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);
}
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);
}
private void validateEventGroupBuildingBlock(IEventGroupBuildingBlock eventGroups, IMoleculeBuildingBlock moleculeBuildingBlock, ValidationResult validationResult)
{
var allMolecules = moleculeBuildingBlock.Select(mb => mb.Name);
foreach (var eventGroup in eventGroups)
{
var applicationBuilders = eventGroup.GetAllContainersAndSelf <IApplicationBuilder>();
foreach (var applicationBuilder in applicationBuilders.Where(applicationBuilder => !allMolecules.Contains(applicationBuilder.MoleculeName)))
{
validationResult.AddMessage(NotificationType.Error, applicationBuilder, Validation.ApplicatedMoleculeNotPresent(applicationBuilder.MoleculeName, applicationBuilder.Name, moleculeBuildingBlock.Name), eventGroups);
}
}
validateBuildingBlockWithFormulaCache(eventGroups, validationResult);
}
public void TestComplexEventGroupBB()
{
EventGroupBuildingBlock x1 = _buildConfiguration.EventGroups as EventGroupBuildingBlock;
Assert.IsNotNull(x1);
ApplicationBuilder a1 = CreateObject <ApplicationBuilder>().WithName("App.Builder");
x1.Add(a1);
var applicationMoleculeBuilder = CreateObject <ApplicationMoleculeBuilder>().WithName("AppMolecule");
IFormula f2 = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(3.4);
applicationMoleculeBuilder.Formula = f2;
applicationMoleculeBuilder.RelativeContainerPath = new ObjectPath(new[] { "A", "B" });
a1.AddMolecule(applicationMoleculeBuilder);
IEventGroupBuildingBlock x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualBuildingBlock(x2, x1);
}
protected override void Context()
{
base.Context();
_eventBuildingBlock = new EventGroupBuildingBlock().WithName("Events");
_applicationBuilder = new ApplicationBuilder().WithName("Tada");
_applicationBuilder.MoleculeName = "B";
_eventBuildingBlock.Add(_applicationBuilder);
_molceuleBuidingBlock = new MoleculeBuildingBlock().WithName("Molecules");
_molceuleBuidingBlock.Add(new MoleculeBuilder().WithName("A"));
_buildConfiguration = new BuildConfiguration();
_buildConfiguration.Molecules = _molceuleBuidingBlock;
_buildConfiguration.MoleculeStartValues = new MoleculeStartValuesBuildingBlock();
_buildConfiguration.Observers = new ObserverBuildingBlock();
_buildConfiguration.ParameterStartValues = new ParameterStartValuesBuildingBlock();
_buildConfiguration.PassiveTransports = new PassiveTransportBuildingBlock();
_buildConfiguration.Reactions = new ReactionBuildingBlock();
_buildConfiguration.SpatialStructure = new SpatialStructure();
_buildConfiguration.EventGroups = _eventBuildingBlock;
}
public IEventGroupBuildingBlock CreateFor(Simulation simulation)
{
try
{
_simulation = simulation;
_eventGroupBuildingBlock = _objectBaseFactory.Create <IEventGroupBuildingBlock>().WithName(simulation.Name);
_cloneManagerForBuildingBlock.FormulaCache = _eventGroupBuildingBlock.FormulaCache;
createApplications(_simulation.CompoundPropertiesList);
createNonApplicationEvents();
return(_eventGroupBuildingBlock);
}
finally
{
_simulation = null;
_eventGroupBuildingBlock = null;
}
}
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
};
}
protected override void Context()
{
base.Context();
_eventGroupBuildingBlock = new EventGroupBuildingBlock();
var eventGroup = new EventGroupBuilder().WithName("EG");
_eventGroupBuildingBlock.Add(eventGroup);
var ehcStartEvent = new EventBuilder().WithName(Converter321To331.EHCStartEvent);
eventGroup.Add(ehcStartEvent);
var eabOldStart = new EventAssignmentBuilder().WithName("EAB1").WithFormula(new ExplicitFormula("ln(2) / EHC_Halftime * M * EHC_EjectionFraction"));
eabOldStart.UseAsValue = false;
eabOldStart.ObjectPath = new ObjectPath(new[] { "Organism", "Gallbladder", "Gallbladder emptying rate" });
ehcStartEvent.AddAssignment(eabOldStart);
var assignmentBuilder = new EventAssignmentBuilder().WithName("EAB2").WithFormula(new ExplicitFormula("DontChange"));
assignmentBuilder.ObjectPath = new ObjectPath(new[] { "PATH" });
ehcStartEvent.AddAssignment(assignmentBuilder);
var ehcStopEvent = new EventBuilder().WithName(Converter321To331.EHCStopEvent);
var eabOldStop = new EventAssignmentBuilder().WithName("EAB1").WithFormula(new ConstantFormula(0));
eabOldStop.UseAsValue = false;
eabOldStop.ObjectPath = new ObjectPath(new[] { "Organism", "Gallbladder", "Gallbladder emptying rate" });
ehcStopEvent.AddAssignment(eabOldStop);
assignmentBuilder = new EventAssignmentBuilder().WithName("EAB2").WithFormula(new ExplicitFormula("DontChange"));
assignmentBuilder.ObjectPath = new ObjectPath(new[] { "PATH" });
ehcStopEvent.AddAssignment(assignmentBuilder);
eventGroup.Add(ehcStopEvent);
var protocolSchemaItem = new Container().WithName("ProtocolSchemaItem").WithParentContainer(eventGroup);
_drugMassParameter = new Parameter().WithName("DrugMass").WithParentContainer(protocolSchemaItem).WithValue(1);
applications = new EventGroupBuilder().WithName("Applications");
applications.Add(new Parameter().WithName("TotalDrugMass"));
_eventGroupBuildingBlock.Add(applications);
}
protected override void Context()
{
base.Context();
_project = A.Fake <IMoBiProject>();
_objectBaseRepository = A.Fake <IWithIdRepository>();
_spatialStructure = A.Fake <IMoBiSpatialStructure>();
_simulationSettings = A.Fake <ISimulationSettings>();
_moBiReactionBuildingBlock = A.Fake <IMoBiReactionBuildingBlock>();
_moleculeBuildingBlock = A.Fake <IMoleculeBuildingBlock>();
A.CallTo(() => _context.CurrentProject).Returns(_project);
A.CallTo(() => _context.Create <IMoleculeBuildingBlock>()).Returns(_moleculeBuildingBlock);
A.CallTo(() => _context.Create <IMoBiReactionBuildingBlock>()).Returns(_moBiReactionBuildingBlock);
A.CallTo(() => _spatialStructureFactory.CreateDefault(AppConstants.DefaultNames.SpatialStructure)).Returns(_spatialStructure);
A.CallTo(() => _simulationSettingsFactory.CreateDefault()).Returns(_simulationSettings);
_topContainer = A.Fake <IContainer>();
A.CallTo(() => _context.Create <IContainer>()).Returns(_topContainer);
_passiveTransportBuildingBlock = A.Fake <IPassiveTransportBuildingBlock>();
A.CallTo(() => _context.Create <IPassiveTransportBuildingBlock>()).Returns(_passiveTransportBuildingBlock);
_observerBuildingBlock = A.Fake <IObserverBuildingBlock>();
A.CallTo(() => _context.Create <IObserverBuildingBlock>()).Returns(_observerBuildingBlock);
_eventGroupBuildingBlock = A.Fake <IEventGroupBuildingBlock>();
A.CallTo(() => _context.Create <IEventGroupBuildingBlock>()).Returns(_eventGroupBuildingBlock);
A.CallTo(() => _context.ObjectRepository).Returns(_objectBaseRepository);
}
protected override void Context()
{
base.Context();
_eventGroupBuildingBlock = _simulationTransfer.Simulation.BuildConfiguration.EventGroups;
}
private void convertEventGroupBuildingBlock(IEventGroupBuildingBlock eventGroups)
{
var allApplications = eventGroups.SelectMany(eg => eg.GetAllContainersAndSelf <IApplicationBuilder>());
allApplications.Each(app => app.ContainerType = ContainerType.Application);
}
public void Visit(IEventGroupBuildingBlock eventGroupBuildingBlock)
{
convertEventGroupBuildingBlock(eventGroupBuildingBlock);
_converted = true;
}
protected override void Context()
{
base.Context();
_eventGroupBuilder = new EventGroupBuildingBlock();
A.CallTo(() => _context.Context.Create <IEventGroupBuilder>()).Returns(new EventGroupBuilder());
}
public void Visit(IEventGroupBuildingBlock eventGroupBuildingBlock)
{
Visit(eventGroupBuildingBlock.DowncastTo <IBuildingBlock>());
eventGroupBuildingBlock.OfType <IApplicationBuilder>().Each(Visit);
_converted = false;
}
public void UpdateDefaultFor(IEventGroupBuildingBlock eventGroupBuildingBlock)
{
eventGroupBuildingBlock.Each(updateDefaultStateForEventParameters);
}
public void Visit(IEventGroupBuildingBlock eventGroupBuildingBlock)
{
ConvertAllParametersIn(eventGroupBuildingBlock);
}
protected override void Context()
{
base.Context();
_buildingBlock = A.Fake <IEventGroupBuildingBlock>().WithId("BB");
_eventGroupBuilder = A.Fake <IEventGroupBuilder>().WithId("EGB");
}
protected override void Context()
{
base.Context();
_returnedBuildingBlocks = new List <IBuildingBlock>();
_childReactionBuilder = new ReactionBuilder().WithName("Test").WithId("FindME");
_reactionBuildingBlock = new MoBiReactionBuildingBlock()
{
_childReactionBuilder
};
_allBuildingBlocks.Add(_reactionBuildingBlock);
_moleculeBuilder = new MoleculeBuilder();
_moleculeBuildingBlock = new MoleculeBuildingBlock()
{
_moleculeBuilder
};
_allBuildingBlocks.Add(_moleculeBuildingBlock);
_obseverBuilder = new ObserverBuilder();
_observerBuildingBlock = new ObserverBuildingBlock()
{
_obseverBuilder
};
_allBuildingBlocks.Add(_observerBuildingBlock);
_passiveTranportBuilder = new TransportBuilder();
_passiveTranportBuildingBlock = new PassiveTransportBuildingBlock()
{
_passiveTranportBuilder
};
_allBuildingBlocks.Add(_passiveTranportBuildingBlock);
_applicationBuilder = new ApplicationBuilder();
_eventGroupBuildingBlock = new EventGroupBuildingBlock()
{
_applicationBuilder
};
_allBuildingBlocks.Add(_eventGroupBuildingBlock);
_parameter = new Parameter().WithName("Para");
var container = new Container().WithName("Cont");
container.Add(_parameter);
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_parmaeterFactory = A.Fake <IParameterFactory>();
A.CallTo(() => _objectBaseFactory.Create <IContainer>()).Returns(A.Fake <IContainer>());
A.CallTo(() => _objectBaseFactory.Create <IMoBiSpatialStructure>()).Returns(new MoBiSpatialStructure());
var diagramManagerFactory = A.Fake <IDiagramManagerFactory>();
_spatialStructure = new MoBiSpatialStructureFactory(_objectBaseFactory, _parmaeterFactory, A.Fake <IconRepository>(), diagramManagerFactory).Create().DowncastTo <IMoBiSpatialStructure>();
_spatialStructure.AddTopContainer(container);
_allBuildingBlocks.Add(_spatialStructure);
_formula = new ExplicitFormula();
_moleculeBuildingBlock.AddFormula(_formula);
_parameterStartValue = new ParameterStartValue {
Path = new ObjectPath {
"test"
}, StartValue = 1, Dimension = A.Fake <IDimension>()
};
_parameterStartValueBuildingBlock = new ParameterStartValuesBuildingBlock()
{
_parameterStartValue
};
_allBuildingBlocks.Add(_parameterStartValueBuildingBlock);
_moleculeStartValue = new MoleculeStartValue {
ContainerPath = new ObjectPath {
"test"
}, Name = "drug"
};
_moleculeStartValuesBuildingBlock = new MoleculeStartValuesBuildingBlock()
{
_moleculeStartValue
};
_allBuildingBlocks.Add(_moleculeStartValuesBuildingBlock);
}
public void Visit(IEventGroupBuildingBlock objToVisit)
{
retrieveTask(objToVisit);
}
public void Visit(IEventGroupBuildingBlock eventGroupBuildingBlock)
{
_found = eventGroupBuildingBlock.Contains(_entity);
}
public override void GlobalContext()
{
base.GlobalContext();
_eventGroupBuildingBlock = LoadPKML <IEventGroupBuildingBlock>("Events");
}
