protected override void Context()
{
base.Context();
var advancedParameterFactory = IoC.Resolve <IAdvancedParameterFactory>();
_advancedParameter = advancedParameterFactory.CreateDefaultFor(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("P"));
}
protected override void Context()
{
base.Context();
_parameters = new List <IParameter>();
var brain = new Organ().WithName(CoreConstants.Organ.BRAIN);
var brain_pls = new Compartment().WithName(CoreConstants.Compartment.PLASMA).WithParentContainer(brain);
var brain_pls_trans = new Container().WithName(_transporter.Name).WithParentContainer(brain_pls);
var relExp2Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(brain_pls_trans);
relExp2Param.Origin.SimulationId = "Sim";
var liver = new Organ().WithName(CoreConstants.Organ.LIVER);
var liver_cell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(liver);
var liver_enz = new Container().WithName(_enzyme.Name).WithParentContainer(liver_cell);
var relExp1Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(liver_enz);
relExp1Param.Origin.SimulationId = "Sim";
_referenceConcentrationParam = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION);
_halfLifeLiverParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_halfLifeLiverIntestineParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE);
_parameters.AddRange(new[]
{ _halfLifeLiverParameter, _halfLifeLiverIntestineParameter, _referenceConcentrationParam, relExp1Param, relExp2Param });
}
protected override void Context()
{
base.Context();
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName("toto");
_parameter.Formula = new ExplicitFormula("2*3").WithId("formula");
_parameter.IsFixedValue = false;
}
protected override void Context()
{
base.Context();
_amountDimension = A.Fake <IDimension>();
_targetContainer = new Container().WithName("TOTO");
A.CallTo(() => _amountDimension.Name).Returns(Constants.Dimension.MOLAR_AMOUNT);
_moleculeBuilder = new MoleculeBuilder().WithName("tralala").WithDimension(_amountDimension);
_parameterBuilder1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P1").WithMode(ParameterBuildMode.Local);
_parameterBuilder2 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P2").WithMode(ParameterBuildMode.Local);
_parameterBuilder3 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P3").WithMode(ParameterBuildMode.Local);
_parameterBuilder2.ContainerCriteria = Create.Criteria(x => x.With("TOTO"));
_parameterBuilder3.ContainerCriteria = Create.Criteria(x => x.With("TATA"));
_moleculeBuilder.AddParameter(_parameterBuilder1);
_moleculeBuilder.AddParameter(_parameterBuilder2);
_moleculeBuilder.AddParameter(_parameterBuilder3);
_mappedFormula = A.Fake <IFormula>();
_buildConfiguration = A.Fake <IBuildConfiguration>();
_para1 = new Parameter().WithName("P1");
_para2 = new Parameter().WithName("P2");
_para3 = new Parameter().WithName("P3");
A.CallTo(() => _objectBaseFactory.Create <IMoleculeAmount>()).Returns(new MoleculeAmount());
A.CallTo(() => _dimensionFactory.Dimension(Constants.Dimension.MOLAR_AMOUNT)).Returns(_amountDimension);
A.CallTo(() => _formulaMapper.MapFrom(_moleculeBuilder.DefaultStartFormula, _buildConfiguration)).Returns(_mappedFormula);
A.CallTo(() => _parameterMapper.MapFrom(_parameterBuilder1, _buildConfiguration)).Returns(_para1);
A.CallTo(() => _parameterMapper.MapFrom(_parameterBuilder2, _buildConfiguration)).Returns(_para2);
A.CallTo(() => _parameterMapper.MapFrom(_parameterBuilder3, _buildConfiguration)).Returns(_para3);
}
protected override void Context()
{
base.Context();
A.CallTo(() => _objectTypeResolver.TypeFor <IParameter>()).Returns("Parameter");
_data.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithId("ID1"));
_data.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithId("ID1"));
}
protected override void Context()
{
base.Context();
_updateTableFormulaCommand = A.Fake <ICommand>();
_editedTableFormula = new TableFormula();
_editSolubilityParameterPresenter = A.Fake <IEditTableSolubilityParameterPresenter>();
_parameter = DomainHelperForSpecs.ConstantParameterWithValue().WithName("SOL");
A.CallTo(() => _applicationController.Start <IEditTableSolubilityParameterPresenter>()).Returns(_editSolubilityParameterPresenter);
A.CallTo(() => _editSolubilityParameterPresenter.Edit(_parameter)).Returns(true);
A.CallTo(() => _editSolubilityParameterPresenter.EditedFormula).Returns(_editedTableFormula);
A.CallTo(() => _parameterTask.UpdateTableFormula(_parameter, _editedTableFormula)).Returns(_updateTableFormulaCommand);
var solGroup = new ParameterAlternativeGroup().WithName(CoreConstants.Groups.COMPOUND_SOLUBILITY);
_alternative = new ParameterAlternative().WithName("ALT1");
_alternative.Add(_parameter);
solGroup.AddAlternative(_alternative);
var simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
A.CallTo(() => _buildingBlockRepository.All <Simulation>()).Returns(new[] { simulation });
var compoundProperties = new CompoundProperties();
simulation.Properties.AddCompoundProperties(compoundProperties);
compoundProperties.AddCompoundGroupSelection(new CompoundGroupSelection {
AlternativeName = _alternative.Name, GroupName = solGroup.Name
});
}
protected override void Context()
{
base.Context();
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("P1");
_parameter1.IsDefault = false;
var alternativeGroup = new ParameterAlternativeGroup().WithName("Gr");
_parameterAlternative = new ParameterAlternative {
_parameter1
};
_parameterAlternative.Name = "Alt";
alternativeGroup.AddAlternative(_parameterAlternative);
_newValueOrigin = new ValueOrigin
{
Method = ValueOriginDeterminationMethods.InVivo,
Source = ValueOriginSources.Database
};
var simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
A.CallTo(() => _buildingBlockRepository.All <Simulation>()).Returns(new[] { simulation });
}
protected override void Context()
{
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_geneExpressionsDatabasePathManager = A.Fake <IGeneExpressionsDatabasePathManager>();
_applicationController = A.Fake <IApplicationController>();
sut = new EditMoleculeTask <Individual>(_moleculeExpressionTask, _applicationController);
_expressionProfileSelectionPresenter = A.Fake <IExpressionProfileSelectionPresenter>();
A.CallTo(() => _applicationController.Start <IExpressionProfileSelectionPresenter>()).Returns(_expressionProfileSelectionPresenter);
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_individual = new Individual {
OriginData = new OriginData {
Species = new Species {
Name = "Human", DisplayName = "Human"
}
}
};
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
}
protected override void Context()
{
base.Context();
_solubilityGroup = new ParameterAlternativeGroup {
Name = CoreConstants.Groups.COMPOUND_SOLUBILITY
};
_refPhParameter = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameters.REFERENCE_PH);
_solubilityRefPh = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameters.SOLUBILITY_AT_REFERENCE_PH);
_solubilityTable = DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameters.SOLUBILITY_TABLE);
_solubilityGainParameter = DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameters.SOLUBILITY_GAIN_PER_CHARGE);
var compound = new Compound();
_solubilityAlternativeNameParameter = A.Fake <ISolubilityAlternativeNamePresenter>();
A.CallTo(() => _applicationController.Start <ISolubilityAlternativeNamePresenter>()).Returns(_solubilityAlternativeNameParameter);
A.CallTo(() => _solubilityAlternativeNameParameter.Edit(_solubilityGroup)).Returns(true);
A.CallTo(() => _solubilityAlternativeNameParameter.Name).Returns("new name");
_solubilityAlternativeNameParameter.CreateAsTable = true;
_newTableAlternative = new ParameterAlternative {
_solubilityRefPh, _solubilityTable, _refPhParameter, _solubilityGainParameter
};
A.CallTo(() => _parameterAlternativeFactory.CreateTableAlternativeFor(_solubilityGroup, CoreConstants.Parameters.SOLUBILITY_TABLE)).Returns(_newTableAlternative);
compound.Add(_solubilityGroup);
_solubilityTableFormula = new TableFormula();
_solubilityTable.Formula = _solubilityTableFormula;
}
protected override void Context()
{
_parameterTask = A.Fake <ISetParameterTask>();
_dialogCreator = A.Fake <IDialogCreator>();
_parameterIdentification = new ParameterIdentification();
_runResult = new ParameterIdentificationRunResult();
_runResult.BestResult.AddValue(new OptimizedParameterValue("P1", 10, 20));
_runResult.BestResult.AddValue(new OptimizedParameterValue("P2", 4, 5));
_identificationParameter1 = new IdentificationParameter {
Name = "P1"
};
_identificationParameter2 = new IdentificationParameter {
Name = "P2", UseAsFactor = true
};
_identificationParameter3 = new IdentificationParameter {
Name = "P3", IsFixed = true,
};
_identificationParameter3.Add(DomainHelperForSpecs.ConstantParameterWithValue(25).WithName(Constants.Parameters.START_VALUE));
_linkedParameter1 = A.Fake <ParameterSelection>();
A.CallTo(() => _linkedParameter1.Parameter).Returns(DomainHelperForSpecs.ConstantParameterWithValue(2));
_linkedParameter2 = A.Fake <ParameterSelection>();
A.CallTo(() => _linkedParameter2.Parameter).Returns(DomainHelperForSpecs.ConstantParameterWithValue(3));
A.CallTo(() => _linkedParameter2.Dimension).Returns(Constants.Dimension.NO_DIMENSION);
_linkedParameter3 = A.Fake <ParameterSelection>();
A.CallTo(() => _linkedParameter3.Parameter).Returns(DomainHelperForSpecs.ConstantParameterWithValue(4));
A.CallTo(() => _linkedParameter3.Dimension).Returns(Constants.Dimension.NO_DIMENSION);
_linkedParameter4 = A.Fake <ParameterSelection>();
A.CallTo(() => _linkedParameter4.Parameter).Returns(DomainHelperForSpecs.ConstantParameterWithValue(5));
A.CallTo(() => _linkedParameter4.Dimension).Returns(Constants.Dimension.NO_DIMENSION);
_identificationParameter1.AddLinkedParameter(_linkedParameter1);
_identificationParameter2.AddLinkedParameter(_linkedParameter2);
_identificationParameter2.AddLinkedParameter(_linkedParameter3);
_identificationParameter3.AddLinkedParameter(_linkedParameter4);
_parameterIdentification.AddIdentificationParameter(_identificationParameter1);
_parameterIdentification.AddIdentificationParameter(_identificationParameter2);
_parameterIdentification.AddIdentificationParameter(_identificationParameter3);
_context = A.Fake <IOSPSuiteExecutionContext>();
sut = new TestTransferOptimizedParametersToSimulationsTask(_parameterTask, _dialogCreator, _context);
_allValueOriginCommands = new List <ICommand>();
A.CallTo(() => _parameterTask.SetParameterValue(A <IParameter> ._, A <double> ._, A <ISimulation> ._)).ReturnsLazily(x => A.Fake <IOSPSuiteCommmand <IOSPSuiteExecutionContext> >());
A.CallTo(() => _parameterTask.UpdateParameterValueOrigin(A <IParameter> ._, A <ValueOrigin> ._, A <ISimulation> ._)).ReturnsLazily(x =>
{
var command = A.Fake <IOSPSuiteCommmand <IOSPSuiteExecutionContext> >();
_allValueOriginCommands.Add(command);
return(command);
});
}
protected override void Context()
{
_view = A.Fake <ISimulationExpressionsView>();
_simulationExpressionsDTOMapper = A.Fake <IExpressionParametersToSimulationExpressionsDTOMapper>();
_editParameterPresenterTask = A.Fake <IEditParameterPresenterTask>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_parameterTask = A.Fake <IParameterTask>();
_moleculeParametersPresenter = A.Fake <IMultiParameterEditPresenter>();
_commandCollector = A.Fake <ICommandCollector>();
sut = new SimulationExpressionsPresenter(_view, _simulationExpressionsDTOMapper, _editParameterPresenterTask, _moleculeExpressionTask, _entityPathResolver, _parameterTask, _moleculeParametersPresenter);
sut.InitializeWith(_commandCollector);
_simulationExpressionDTO = new SimulationExpressionsDTO(new ParameterDTO(_propertyParameter), new ParameterDTO(_propertyParameter), new ParameterDTO(_propertyParameter),
new List <ExpressionContainerDTO>());
_propertyParameter = DomainHelperForSpecs.ConstantParameterWithValue().WithName("PROP");
_relativeExpressionParameter = DomainHelperForSpecs.ConstantParameterWithValue().WithName("REL_EXP");
_allParameters = new List <IParameter> {
_propertyParameter, _relativeExpressionParameter
};
_pathCache = new PathCacheForSpecs <IParameter>();
A.CallTo(() => _parameterTask.PathCacheFor(A <IEnumerable <IParameter> > .That.Matches(x => x.ContainsAll(_allParameters)))).Returns(_pathCache);
A.CallTo(() => _simulationExpressionsDTOMapper.MapFrom(A <IEnumerable <IParameter> > .That.Matches(x => x.ContainsAll(_allParameters)))).Returns(_simulationExpressionDTO);
}
protected override void Context()
{
_view = A.Fake <IMultiParameterEditView>();
_scaleParametersPresenter = A.Fake <IScaleParametersPresenter>();
_editParameterPresenterTask = A.Fake <IEditParameterPresenterTask>();
_parameterTask = A.Fake <IParameterTask>();
_parameterDTOMapper = A.Fake <IParameterToParameterDTOMapper>();
_contextMenuFactory = A.Fake <IParameterContextMenuFactory>();
_withIdRepository = A.Fake <IWithIdRepository>();
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P1");
_parameter2 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P1");
_parameter3 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P2");
_parameterDTO1 = new ParameterDTO(_parameter1);
_parameterDTO2 = new ParameterDTO(_parameter2);
_parameterDTO3 = new ParameterDTO(_parameter3);
_parameters = new List <IParameter> {
_parameter1, _parameter2, _parameter3
};
A.CallTo(() => _parameterDTOMapper.MapFrom(_parameter1)).Returns(_parameterDTO1);
A.CallTo(() => _parameterDTOMapper.MapFrom(_parameter2)).Returns(_parameterDTO2);
A.CallTo(() => _parameterDTOMapper.MapFrom(_parameter3)).Returns(_parameterDTO3);
sut = new SimulationCompoundParametersPresenter(_view, _scaleParametersPresenter, _editParameterPresenterTask, _parameterTask, _parameterDTOMapper, _contextMenuFactory, _withIdRepository);
}
protected override void Context()
{
_sensitivityAnalysisTask = A.Fake <ISensitivityAnalysisTask>();
_simulationAnalyzer = A.Fake <ISimulationAnalyzer>();
_parameterSelector = A.Fake <IParameterAnalysableParameterSelector>();
_containerTask = A.Fake <IContainerTask>();
_simulation = A.Fake <ISimulation>();
_sensitivityAnalysis = new SensitivityAnalysis(_simulation);
_coreSensitivityAnalysis = new Core.Domain.SensitivityAnalyses.SensitivityAnalysis();
sut = new SensitivityAnalysisToCoreSensitivityAnalysisMapper(_sensitivityAnalysisTask, _simulationAnalyzer, _parameterSelector, _containerTask);
_constantParameterCache = new PathCacheForSpecs <IParameter>
{
{ _parameterPath1, DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("P1") },
{ _parameterPath2, DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("P2") },
{ _parameterPath3, DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("P3") }
};
A.CallTo(() => _sensitivityAnalysisTask.CreateSensitivityAnalysisFor(_simulation)).Returns(_coreSensitivityAnalysis);
A.CallTo(_containerTask).WithReturnType <PathCache <IParameter> >().Returns(_constantParameterCache);
_allSensitivityParametersCreated = new List <ParameterSelection>();
A.CallTo(() => _sensitivityAnalysisTask.AddParametersTo(_coreSensitivityAnalysis, A <IReadOnlyList <ParameterSelection> > ._))
.Invokes(x => _allSensitivityParametersCreated.AddRange(x.GetArgument <IReadOnlyList <ParameterSelection> >(1)));
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <ISimulation>();
var rootContainer = new Container();
_simulation.Model.Root = rootContainer;
_constantParameter = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("ConstantParameter");
_formulaParameter = new Parameter().WithFormula(new ExplicitFormula("1+2")).WithName("FormulaParameter");
_formulaFixedParameter = new Parameter().WithFormula(new ExplicitFormula("1+2")).WithName("FormulaFixedParameter");
_formulaFixedParameter.Value = 10;
rootContainer.Add(_constantParameter);
rootContainer.Add(_formulaParameter);
rootContainer.Add(_formulaFixedParameter);
_constantParameterSelection = new ParameterSelection(_simulation, _constantParameter.Name);
_formulaParameterSelection = new ParameterSelection(_simulation, _formulaParameter.Name);
_formulaFixedParameterSelection = new ParameterSelection(_simulation, _formulaFixedParameter.Name);
A.CallTo(() => _simulationParametersPresenter.AllParameters).Returns(new [] { _constantParameterSelection, _formulaParameterSelection, _formulaFixedParameterSelection });
A.CallTo(() => _sensitivityAnalysisParametersPresenter.AddParameters(A <IReadOnlyList <ParameterSelection> > ._))
.Invokes(x => _addedParameters = x.GetArgument <IReadOnlyList <ParameterSelection> >(0));
}
protected override void Context()
{
base.Context();
_simulation.RemoveAllBuildingBlockOfType(PKSimBuildingBlockType.Individual);
_parameters = new List <IParameter>();
var kidney = new Organ().WithName(CoreConstants.Organ.KIDNEY);
var kidney_cell = new Compartment().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(kidney);
var kid_cell_trans = new Container().WithName(_transporter.Name).WithParentContainer(kidney_cell);
var relExp2Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(kid_cell_trans);
relExp2Param.Origin.SimulationId = "Sim";
var liver = new Organ().WithName(CoreConstants.Organ.LIVER);
var liver_cell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(liver);
var liver_enz = new Container().WithName(_enzyme.Name).WithParentContainer(liver_cell);
var relExp1Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(liver_enz);
relExp1Param.Origin.SimulationId = "Sim";
_referenceConcentrationParam = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION);
_halfLifeLiverParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_halfLifeLiverIntestineParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE);
_parameters.AddRange(new[]
{ _halfLifeLiverParameter, _halfLifeLiverIntestineParameter, _referenceConcentrationParam, relExp1Param, relExp2Param });
}
public void should_exclude_parameters_that_are_constant_with_a_value_of_zero()
{
var parameter = DomainHelperForSpecs.ConstantParameterWithValue(0);
A.CallTo(() => _parameterSelector.CanUseParameter(parameter)).Returns(true);
sut.ParameterCanBeUsedForSensitivity(parameter).ShouldBeFalse();
}
private ExpressionParameterDTO createParameter(string parameterName)
{
return(new ExpressionParameterDTO
{
Parameter = new ParameterDTO(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(parameterName))
});
}
protected override void Context()
{
base.Context();
_compound = new Compound();
var solDim = new Dimension(new BaseDimensionRepresentation(), "Solubility", "m");
solDim.AddUnit(new Unit("cm", 0.01, 0));
_refPhValue = 7;
_solValue = 100;
_gainPerChargeValue = 1000;
A.CallTo(() => _formulaFactory.CreateTableFormula()).Returns(new TableFormula());
var refPh = DomainHelperForSpecs.ConstantParameterWithValue(_refPhValue).WithName(CoreConstants.Parameter.RefpH).WithDimension(DomainHelperForSpecs.NoDimension());
var solubilty = DomainHelperForSpecs.ConstantParameterWithValue(_solValue).WithName(CoreConstants.Parameter.SolubilityAtRefpH).WithDimension(solDim);
var gainPerCharge = DomainHelperForSpecs.ConstantParameterWithValue(_gainPerChargeValue).WithName(CoreConstants.Parameter.SolubilityGainPerCharge).WithDimension(DomainHelperForSpecs.NoDimension());
_solubility_pKa_pH_Factor = new PKSimParameter().WithName(CoreConstants.Parameter.SOLUBILITY_P_KA__P_H_FACTOR);
_solubility_pKa_pH_Factor.Formula = new ExplicitFormula("10 * (pH +1)");
_solubility_pKa_pH_Factor.Formula.AddObjectPath(new FormulaUsablePath(new[] { ObjectPath.PARENT_CONTAINER, CoreConstants.Parameter.RefpH }).WithAlias("pH"));
_compound.Add(refPh);
_compound.Add(solubilty);
_compound.Add(gainPerCharge);
_compound.Add(_solubility_pKa_pH_Factor);
_solubilityAlternative = new ParameterAlternative();
_solubilityAlternative.Add(refPh);
_solubilityAlternative.Add(solubilty);
_solubilityAlternative.Add(gainPerCharge);
var solubilityAlternativeGroup = new ParameterAlternativeGroup();
solubilityAlternativeGroup.AddAlternative(_solubilityAlternative);
_compound.AddParameterAlternativeGroup(solubilityAlternativeGroup);
}
protected override void Context()
{
base.Context();
_relativeVMaxValue = 25;
_relExp = DomainHelperForSpecs.ConstantParameterWithValue(10);
A.CallTo(() => _executionContext.BuildingBlockContaining(_relExp)).Returns(_individual);
}
protected override void Context()
{
_normParameter = new ParameterDTO(DomainHelperForSpecs.ConstantParameterWithValue(0.10).WithDimension(DomainHelperForSpecs.FractionDimensionForSpecs()));
sut = new ExpressionContainerDTO {
RelativeExpressionNormParameter = _normParameter
};
}
protected override void Context()
{
base.Context();
_formulaParameter = DomainHelperForSpecs.ConstantParameterWithValue(10);
_formulaParameter.Formula = new ExplicitFormula("10");
_constantParameter = DomainHelperForSpecs.ConstantParameterWithValue(10);
_distributedParameter = DomainHelperForSpecs.NormalDistributedParameter();
}
private IParameter parameterNamed(double parmaeterValue, string parameterName)
{
var parameter = DomainHelperForSpecs.ConstantParameterWithValue(parmaeterValue).WithName(parameterName);
//change display unit to ensure that we test conversion to display unit
parameter.DisplayUnit = parameter.Dimension.Units.ElementAt(1);
return(parameter);
}
protected override void Context()
{
base.Context();
_identificationParameter = new IdentificationParameter {
DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.START_VALUE)
};
}
protected override void Context()
{
base.Context();
sut.AddInterval(new OutputInterval {
DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.END_TIME)
}.WithName("Int1"));
sut.AddTimePoint(5);
}
protected override void Context()
{
base.Context();
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName("toto");
_parameter.IsDefault = true;
_parameter.ValueOrigin.Description = "Hello";
_parameter.ValueOrigin.Method = ValueOriginDeterminationMethods.InVitro;
_parameter.ValueOrigin.Source = ValueOriginSources.ParameterIdentification;
}
protected override void Context()
{
base.Context();
_container = new Container().WithName("Container");
_container.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName("Valid"));
_invalidParameter = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("Invalid");
_invalidParameter.Info.MaxIsAllowed = false;
_invalidParameter.Info.MaxValue = 10;
_container.Add(_invalidParameter);
}
protected override void Context()
{
_parameterMapper = A.Fake <IParameterToParameterDTOMapper>();
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(5);
_parameterDTO = new ParameterDTO(_parameter);
_parameterContainer = new ParameterContainerForSpecs();
A.CallTo(() => _parameterMapper.MapFrom(_parameter)).Returns(_parameterDTO);
sut = new ParameterToParameterDTOInContainerMapper <ParameterContainerForSpecs>(_parameterMapper);
_result = sut.MapFrom(_parameter, _parameterContainer, x => x.ParameterValue, x => x.ParmaeterDTO);
}
public Compound Create()
{
var compound = new Compound();
compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(2).WithName(CoreConstants.Parameters.EFFECTIVE_MOLECULAR_WEIGHT));
compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(4).WithName(CoreConstants.Parameters.LIPOPHILICITY));
compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(8).WithName(CoreConstants.Parameters.PERMEABILITY));
compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.IS_SMALL_MOLECULE));
return(compound);
}
protected override void Context()
{
base.Context();
_rootContainer = new Container().WithName("ROOT");
_moleculeContainer = new Container().WithName("CYP").WithContainerType(ContainerType.Molecule);
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(4).WithName("P").WithParentContainer(_moleculeContainer);
_parameter.Formula = new ExplicitFormula();
_objectPath = new FormulaUsablePath("SIM", ObjectPathKeywords.MOLECULE, "test");
_parameter.Formula.AddObjectPath(_objectPath);
}
protected override void Context()
{
base.Context();
_targetProtocol = new SimpleProtocol();
_targetProtocol.Add(WithExtensions.WithName <IParameter>(DomainHelperForSpecs.ConstantParameterWithValue(1), "SimpleParameter"));
_sourceProtocol = new AdvancedProtocol {
Id = "Id", Name = "Advanced Protocol", Description = "tralala"
};
_sourceProtocol.Add(WithExtensions.WithName <IParameter>(DomainHelperForSpecs.ConstantParameterWithValue(1), "AdvancedParameter"));
}
