protected override void Context()
{
_buildingBlock = A.Fake <IReactionBuildingBlock>();
sut = new PresenterSubject {
Subject = _buildingBlock
};
}
protected override void Context()
{
base.Context();
_reactionBuildingBlock = A.Fake <IReactionBuildingBlock>();
_simulation.Reactions = null;
A.CallTo(() => _reactionBuildingBlockCreator.CreateFor(_simulation)).Returns(_reactionBuildingBlock);
}
protected override void Context()
{
_reactionBuildingBlock = A.Fake <IReactionBuildingBlock>();
sut = new SimulationReactionDiagramDTO {
ReactionBuildingBlock = _reactionBuildingBlock
};
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <Simulation>();
A.CallTo(() => _simulation.IsImported).Returns(true);
_reactionBuildingBlock = A.Fake <IReactionBuildingBlock>();
A.CallTo(() => _objectBaseFactory.Create <IReactionBuildingBlock>()).Returns(_reactionBuildingBlock);
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <Simulation>();
_reactionBuildingBlock = A.Fake <IReactionBuildingBlock>();
A.CallTo(() => _moleculeAndReactionCreator.CreateFor(A <IBuildConfiguration> ._, _simulation))
.Invokes(x => x.GetArgument <IBuildConfiguration>(0).Reactions = _reactionBuildingBlock);
}
public void TestComplexReactionBB()
{
ReactionBuildingBlock x1 = _buildConfiguration.Reactions as ReactionBuildingBlock;
Assert.IsNotNull(x1);
IReactionBuildingBlock x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualBuildingBlock(x2, x1);
}
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 clearFormulaCacheInReactionBuildingBlock(IReactionBuildingBlock reactions)
{
if (reactions == null)
{
return;
}
reactions.FormulaCache.Clear();
foreach (var reaction in reactions.Where(x => x.Formula != null))
{
reactions.FormulaCache.Add(reaction.Formula);
}
}
protected override void Context()
{
base.Context();
_reaction1 = new ReactionBuilder().WithName("Reaction");
_parameter = new Parameter().WithName("ReferencFrom").WithParentContainer(_reaction1);
_otherParameter = new Parameter().WithName("ToReference").WithParentContainer(_reaction1);
_reaction2 = new ReactionBuilder().WithName("Reaction2");
_reaction3 = new ReactionBuilder().WithName("A Reaction");
_otherParameter2 = new Parameter().WithName("ToReference").WithParentContainer(_reaction2);
_reactionBuilidingBlock = new ReactionBuildingBlock();
_reactionBuilidingBlock.Add(_reaction1);
_reactionBuilidingBlock.Add(_reaction2);
_reactionBuilidingBlock.Add(_reaction3);
}
protected override void Context()
{
base.Context();
_reactionBuildingBlock = new ReactionBuildingBlock();
_firstNode = A.Fake <IBaseNode>();
A.CallTo(() => _firstNode.Id).Returns("Id1");
A.CallTo(() => _firstNode.Name).Returns("Name");
_secondBuilder = new ReactionBuilder {
Name = "Name", Id = "Id2"
};
_simulation.Reactions = _reactionBuildingBlock;
_reactionBuildingBlock.Add(_secondBuilder);
_diagramModel = A.Fake <IDiagramModel>();
A.CallTo(() => _simulation.ReactionDiagramModel).Returns(_diagramModel);
A.CallTo(() => _diagramModel.FindByName(_secondBuilder.Name)).Returns(_firstNode);
}
protected override void Context()
{
base.Context();
_metaboliteName = "metabolite";
_compoundName = "compound";
_secondMetaboliteName = "secondMetabolite";
_reactionBuildingBlock = new ReactionBuildingBlock();
A.CallTo(() => _simulation1.Reactions).Returns(_reactionBuildingBlock);
var reaction = CreateReactionForCompoundAndMetabolite(new[] { _metaboliteName }, _compoundName);
_simulation1.Reactions.Add(reaction);
reaction = CreateReactionForCompoundAndMetabolite(new[] { _secondMetaboliteName }, _metaboliteName);
_simulation1.Reactions.Add(reaction);
CreateMultipleAdministrationForMolecule(_compoundName);
A.CallTo(() => _simulation1.EndTime).Returns(1000);
}
public void CreateFor(IBuildConfiguration buildConfiguration, Simulation simulation)
{
try
{
_simulation = simulation;
_individual = simulation.Individual;
_buildConfiguration = buildConfiguration;
_passiveTransports = _buildConfiguration.PassiveTransports;
_moleculeBuildingBlock = _objectBaseFactory.Create <IMoleculeBuildingBlock>()
.WithName(simulation.Name);
_reactionBuildingBlock = _objectBaseFactory.Create <IReactionBuildingBlock>()
.WithName(simulation.Name);
addIndividualMolecules(simulation.CompoundPropertiesList);
addCompoundMolecules(simulation.CompoundPropertiesList, simulation.InteractionProperties);
addTwoPoreModelsReactionAndMolecules(simulation.CompoundPropertiesList, simulation.ModelConfiguration);
addPartialProcesses(simulation.CompoundPropertiesList);
addInteractions(simulation);
_buildConfiguration.Molecules = _moleculeBuildingBlock;
_buildConfiguration.Reactions = _reactionBuildingBlock;
}
finally
{
_moleculeBuildingBlock = null;
_reactionBuildingBlock = null;
_individual = null;
_buildConfiguration = null;
_passiveTransports = null;
_simulation = null;
_allMoleculeNames.Clear();
_moleculeWithTurnoverReactions.Clear();
}
}
public void Visit(IReactionBuildingBlock reactionBuildingBlock)
{
convert(reactionBuildingBlock);
_converted = true;
}
public void Visit(IReactionBuildingBlock reactionBuildingBlock)
{
Convert(reactionBuildingBlock);
}
public void Convert(IReactionBuildingBlock reactionBuildingBlock)
{
reactionBuildingBlock.Each(r => Convert(r, reactionBuildingBlock.FormulaCache));
}
public void Visit(IReactionBuildingBlock reactionBuildingBlock)
{
updateAllParameters(reactionBuildingBlock.SelectMany(c => c.GetAllChildren <IParameter>()));
_converted = true;
}
protected override void Context()
{
base.Context();
_presenterToMatch = A.Fake <ISubjectPresenter>();
_anotherBuildingBlock = A.Fake <IReactionBuildingBlock>();
}
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(IReactionBuildingBlock objToVisit)
{
retrieveTask <IMoBiReactionBuildingBlock>();
}
public void Visit(IReactionBuildingBlock reactionBuildingBlock)
{
ConvertAllParametersIn(reactionBuildingBlock);
}
