protected override void Context()
{
base.Context();
_project = new MoBiProject();
var molecule = new MoleculeBuilder().WithName(_moleculeName);
var moleculeParameter = new Parameter().WithName(_moleculeParameterName);
molecule.Add(moleculeParameter);
var molecules = new MoleculeBuildingBlock()
{
molecule
};
_project.AddBuildingBlock(molecules);
var parameter = new Parameter().WithName(_parameterName);
var root = new Container().WithName("Root");
root.Add(parameter);
var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root);
_project.AddBuildingBlock(spatialStructure);
var reactionBuilder = new ReactionBuilder().WithName(_reactionName);
var reactions = new MoBiReactionBuildingBlock()
{
reactionBuilder
};
_project.AddBuildingBlock(reactions);
A.CallTo(() => _context.CurrentProject).Returns(_project);
}
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();
var moleculeBuildingBlock1 = new MoleculeBuildingBlock().WithName("Tada");
var moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
var moleculeBuilderB = new MoleculeBuilder().WithName("MSVb");
moleculeBuildingBlock1.Add(moleculeBuilderA);
moleculeBuildingBlock1.Add(moleculeBuilderB);
var moleculeBuildingBlock2 = new MoleculeBuildingBlock().WithName("Toto");
moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
moleculeBuilderB = new MoleculeBuilder().WithName("MSVb");
moleculeBuildingBlock2.Add(moleculeBuilderA);
moleculeBuildingBlock2.Add(moleculeBuilderB);
_object1 = moleculeBuildingBlock1;
_object2 = moleculeBuildingBlock2;
_comparerSettings.OnlyComputingRelevant = false;
}
protected override void Context()
{
_quantity = A.Fake <IParameter>().WithName("P");
base.Context();
_parameter.Name = "P";
var moleculeBuilder1 = new MoleculeBuilder().WithName("Mol1");
var moleculeBuilder2 = new MoleculeBuilder().WithName("Mol2");
var transporterMolecule1 = new TransporterMoleculeContainer {
TransportName = "TRANSPORT", Name = "TRANSPORTER"
};
var molecule1 = new Container().WithName("Mol1");
molecule1.Add(transporterMolecule1);
var molecule2 = new Container().WithName("Mol2");
var transporterMolecule2 = new TransporterMoleculeContainer {
TransportName = "TRANSPORT", Name = "TRANSPORTER"
};
molecule2.Add(transporterMolecule2);
moleculeBuilder1.AddTransporterMoleculeContainer(transporterMolecule1);
moleculeBuilder2.AddTransporterMoleculeContainer(transporterMolecule2);
var moleculeBuildingBlock = new MoleculeBuildingBlock {
moleculeBuilder1, moleculeBuilder2
};
_buildingBlockInfo.UntypedBuildingBlock = moleculeBuildingBlock;
transporterMolecule1.AddParameter(_parameter);
_quantity.ParentContainer.Name = transporterMolecule1.TransportName;
_quantity.ParentContainer.ParentContainer.Name = moleculeBuilder1.Name;
}
protected override void Context()
{
base.Context();
_spatialStructure = new SpatialStructure();
var root = new Container {
Name = _rootContainerString, Mode = ContainerMode.Physical
};
root.Add(new Container {
Name = _childContainerString, Mode = ContainerMode.Physical
});
_spatialStructure.AddTopContainer(root);
_moleculeBuildingBlock = new MoleculeBuildingBlock {
Name = "MoleculeBB1"
};
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = M1, DefaultStartFormula = new ConstantFormula(5.0), Dimension = DimensionFactoryForSpecs.ConcentrationDimension
});
_defaultStartFormula = new ExplicitFormula("M/V");
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = M2, DefaultStartFormula = _defaultStartFormula, Dimension = DimensionFactoryForSpecs.ConcentrationDimension
});
A.CallTo(() => _cloneManagerForBuildingBlock.Clone(_defaultStartFormula, A <FormulaCache> ._)).Returns(new ExplicitFormula("M/V"));
}
protected override void Context()
{
base.Context();
_buildConfiguration = A.Fake <IMoBiBuildConfiguration>();
_psvInfo = new ParameterStartValuesBuildingBlockInfo {
UntypedBuildingBlock = new ParameterStartValuesBuildingBlock().WithId("psvbb1")
};
_templateMoleculeBuildingBlock = new MoleculeBuildingBlock {
Id = "templateMoleculeBuildingBlock"
};
_templateSpatialStructure = new MoBiSpatialStructure()
{
Id = "templateSpatialStructure"
};
_moleculesInfo = new MoleculesInfo {
UntypedBuildingBlock = _templateMoleculeBuildingBlock
};
_spatialStructureInfo = new SpatialStructureInfo {
UntypedBuildingBlock = _templateSpatialStructure
};
_buildConfiguration.ParameterStartValuesInfo = _psvInfo;
_buildConfiguration.SpatialStructureInfo = _spatialStructureInfo;
_buildConfiguration.MoleculesInfo = _moleculesInfo;
A.CallTo(() => _buildConfiguration.AllBuildingBlockInfos()).Returns(new IBuildingBlockInfo[] { _psvInfo, _moleculesInfo, _spatialStructureInfo });
_cloneBuildingBlock = new ParameterStartValuesBuildingBlock().WithId("psvbb2");
A.CallTo(() => _cloneManager.CloneBuidingBlock(_psvInfo.BuildingBlock)).Returns(_cloneBuildingBlock);
A.CallTo(() => _simulation.MoBiBuildConfiguration).Returns(_buildConfiguration);
A.CallTo(_nameCorrector).WithReturnType <bool>().Returns(true);
}
public void TestComplexMoleculeBB()
{
MoleculeBuildingBlock x1 = _buildConfiguration.Molecules as MoleculeBuildingBlock;
Assert.IsNotNull(x1);
IMoleculeBuildingBlock x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualBuildingBlock(x2, x1);
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock {
Id = "1"
};
sut.AddBuildingBlock(new MoleculeStartValuesBuildingBlock {
MoleculeBuildingBlockId = "1", SpatialStructureId = "2"
});
sut.AddBuildingBlock(new ParameterStartValuesBuildingBlock {
MoleculeBuildingBlockId = "2", SpatialStructureId = "2"
});
}
protected override void Context()
{
_quantity = _parameter;
base.Context();
var moleculeBuilder = new MoleculeBuilder();
moleculeBuilder.AddParameter(_parameter);
var moleculeBuildingBlock = new MoleculeBuildingBlock {
moleculeBuilder
};
_buildingBlockInfo.UntypedBuildingBlock = moleculeBuildingBlock;
}
protected override void Context()
{
base.Context();
var moleculeBuindingBlock = new MoleculeBuildingBlock();
var molecule = new MoleculeBuilder {
Name = "Mol", Dimension = Constants.Dimension.NO_DIMENSION
};
moleculeBuindingBlock.Add(molecule);
_nullStartValue = new MoleculeStartValue {
Name = molecule.Name, StartValue = 1, Dimension = Constants.Dimension.NO_DIMENSION
};
_moleculeStartValueBuildingBlock.Add(_nullStartValue);
A.CallTo(_context.Context).WithReturnType <IMoleculeBuildingBlock>().Returns(moleculeBuindingBlock);
}
protected override void Context()
{
base.Context();
_project = new MoBiProject();
var molecule = new MoleculeBuilder().WithName(_moleculeName);
var moleculeParameter = new Parameter().WithName(_moleculeParameterName);
molecule.Add(moleculeParameter);
var molecules = new MoleculeBuildingBlock()
{
molecule
};
_project.AddBuildingBlock(molecules);
var parameter = new Parameter().WithName(_parameterName);
var root = new Container().WithName(_topContainerName);
root.Add(parameter);
var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root);
spatialStructure.GlobalMoleculeDependentProperties = new Container().WithName(Constants.MOLECULE_PROPERTIES);
spatialStructure.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_project.AddBuildingBlock(spatialStructure);
var reactionBuilder = new ReactionBuilder().WithName(_reactionName);
var reactions = new MoBiReactionBuildingBlock()
{
reactionBuilder
};
_project.AddBuildingBlock(reactions);
_project.AddSimulation(new MoBiSimulation().WithName(_simulationName));
var eventGroupBuilder = new EventGroupBuilder().WithName(_eventGroupName);
var eventGroupBuildingBlock = new EventGroupBuildingBlock();
eventGroupBuildingBlock.Add(eventGroupBuilder);
_project.AddBuildingBlock(eventGroupBuildingBlock);
A.CallTo(() => _context.CurrentProject).Returns(_project);
}
protected override void Context()
{
base.Context();
_passiveTransports2 = new PassiveTransportBuildingBlock();
_project.AddBuildingBlock(_passiveTransports);
_project.AddBuildingBlock(_passiveTransports2);
_project.AddBuildingBlock(_molecules);
var anotherMoleculeWithPassiveTransport = new MoleculeBuilder().WithName("MOLECULE");
var molecules2 = new MoleculeBuildingBlock {
anotherMoleculeWithPassiveTransport
}.WithName("MBB2");
var samePassiveTransport = new TransportBuilder().WithName("PASSIVE TRANSPORT").WithFormula(A.Fake <IFormula>());
anotherMoleculeWithPassiveTransport.Add(samePassiveTransport);
A.CallTo(() => _formulaTask.FormulasAreTheSame(_passiveTransportKinetic, samePassiveTransport.Formula)).Returns(true);
A.CallTo(() => _cloneManagerForModel.Clone <ITransportBuilder>(_passiveTransport)).ReturnsLazily(x => new TransportBuilder().WithFormula(_passiveTransportKinetic));
A.CallTo(() => _containerTask.CreateUniqueName(_passiveTransports, A <string> ._, true)).ReturnsLazily(x => x.Arguments[1].ConvertedTo <string>());
_project.AddBuildingBlock(molecules2);
}
protected override void Context()
{
base.Context();
sut.SelectionPredicate = p => true;
var id = "mp";
var physical = new Container().WithName("PHYS").WithMode(ContainerMode.Physical);
var moleculeProperties = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(physical);
var p1 = new Parameter().WithName("P1");
moleculeProperties.Add(p1);
var moleculeName = "Drug";
_moleculePropertiesDTO =
new DummyMoleculeContainerDTO()
{
MoleculePropertiesContainer = new ObjectBaseDTO().WithId(id)
}.WithId("ANY")
.WithName(moleculeName);
A.CallTo(() => _context.Get <IContainer>(id)).Returns(moleculeProperties);
var objectBaseRepository = A.Fake <IWithIdRepository>();
A.CallTo(() => _context.ObjectRepository).Returns(objectBaseRepository);
A.CallTo(() => objectBaseRepository.ContainsObjectWithId(id)).Returns(true);
A.CallTo(() => _parameterMapper.MapFrom(p1, A <IContainer> ._, A <IObjectBaseDTO> ._)).Returns(_dtoP1);
var project = A.Fake <IMoBiProject>();
var moleculeBuildingBlock = new MoleculeBuildingBlock();
var molecule = new MoleculeBuilder().WithName(moleculeName);
var localP = new Parameter().WithName("local").WithMode(ParameterBuildMode.Local).WithParentContainer(molecule);
var globalP =
new Parameter().WithName("global").WithMode(ParameterBuildMode.Global).WithParentContainer(molecule);
moleculeBuildingBlock.Add(molecule);
A.CallTo(() => project.MoleculeBlockCollection).Returns(new[] { moleculeBuildingBlock });
A.CallTo(() => _parameterMapper.MapFrom(localP, A <IContainer> ._, A <IObjectBaseDTO> ._)).Returns(_dtoPlocal);
A.CallTo(() => _parameterMapper.MapFrom(globalP, A <IContainer> ._, A <IObjectBaseDTO> ._)).Returns(_dtoPglobal);
A.CallTo(() => _context.CurrentProject).Returns(project);
}
protected override void Context()
{
base.Context();
var moleculeBuildingBlock1 = new MoleculeBuildingBlock().WithName("Tada");
var moleculeBuilderA = new MoleculeBuilder().WithName("DrugA");
var moleculeBuilderB = new MoleculeBuilder().WithName("DrugB");
moleculeBuildingBlock1.Add(moleculeBuilderA);
moleculeBuildingBlock1.Add(moleculeBuilderB);
var moleculeBuildingBlock2 = new MoleculeBuildingBlock().WithName("Tada");
moleculeBuilderA = new MoleculeBuilder().WithName("DrugA");
moleculeBuilderB = new MoleculeBuilder().WithName("DrugC");
moleculeBuildingBlock2.Add(moleculeBuilderA);
moleculeBuildingBlock2.Add(moleculeBuilderB);
_object1 = moleculeBuildingBlock1;
_object2 = moleculeBuildingBlock2;
}
protected override void Context()
{
base.Context();
_originalFormula1 = new ExplicitFormula().WithName("F1").WithId("X1");
_originalFormula2 = new ExplicitFormula().WithName("F2").WithId("X2");
_buildingBlockToClone = new MoleculeBuildingBlock();
var clonedBuildinBlock = new MoleculeBuildingBlock();
_buildingBlockToClone.AddFormula(_originalFormula1);
_buildingBlockToClone.AddFormula(_originalFormula2);
_cloneFormula1 = new ExplicitFormula().WithName("F1").WithId("X11");
_cloneFormula2 = new ExplicitFormula().WithName("F2").WithId("X22");
A.CallTo(() => _cloneManagerForBuildingBlock.Clone(_originalFormula2)).Returns(_cloneFormula2);
A.CallTo(() => _cloneManagerForBuildingBlock.Clone(_buildingBlockToClone, A <IFormulaCache> ._))
.Invokes(x =>
{
var formulaCache = x.GetArgument <IFormulaCache>(1);
formulaCache.Add(_cloneFormula1);
})
.Returns(clonedBuildinBlock);
}
protected override void Context()
{
base.Context();
var moleculeBuildingBlock1 = new MoleculeBuildingBlock().WithName("X");
moleculeBuildingBlock1.Version = 1;
var moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
moleculeBuilderA.AddParameter(new Parameter().WithMode(ParameterBuildMode.Local));
moleculeBuildingBlock1.Add(moleculeBuilderA);
var moleculeBuildingBlock2 = new MoleculeBuildingBlock().WithName("X");
moleculeBuildingBlock2.Version = 1;
moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
moleculeBuildingBlock2.Add(moleculeBuilderA);
_object1 = moleculeBuildingBlock1;
_object2 = moleculeBuildingBlock2;
}
protected override void Context()
{
sut = new MoleculeBuildingBlock();
}