protected override void Context()
{
_distributedParameter = DomainHelperForSpecs.NormalDistributedParameter();
sut = new AdvancedParameter {
DistributedParameter = _distributedParameter
};
}
protected override void Context()
{
base.Context();
_molecule1RefConcDistribution = DomainHelperForSpecs.NormalDistributedParameter(defaultMean: 4, defaultDeviation: 2).WithId("Molecule1RefConf");
_molecule2HalfLifeIntestineDistribution = DomainHelperForSpecs.NormalDistributedParameter(defaultMean: 6, defaultDeviation: 3).WithId("Molecule2HalfLifeIntestine");
A.CallTo(() => _moleculeParameterFactory.ParameterFor(_molecule1.Name, _molecule1.ReferenceConcentration.Name)).Returns(_molecule1RefConcDistribution);
A.CallTo(() => _moleculeParameterFactory.ParameterFor(_molecule1.Name, _molecule1.HalfLifeLiver.Name)).Returns(null);
A.CallTo(() => _moleculeParameterFactory.ParameterFor(_molecule1.Name, _molecule1.HalfLifeIntestine.Name)).Returns(null);
A.CallTo(() => _moleculeParameterFactory.ParameterFor(_molecule2.Name, _molecule2.ReferenceConcentration.Name)).Returns(null);
A.CallTo(() => _moleculeParameterFactory.ParameterFor(_molecule2.Name, _molecule2.HalfLifeLiver.Name)).Returns(null);
A.CallTo(() => _moleculeParameterFactory.ParameterFor(_molecule2.Name, _molecule2.HalfLifeIntestine.Name)).Returns(_molecule2HalfLifeIntestineDistribution);
_advancedParameterMolecule1RefConc = A.Fake <IAdvancedParameter>().WithName("Molecule1RefConf");
_advancedParameterMolecule1RefConc.ParameterPath = "Path1";
_advancedParameterMolecule2HalfLifeIntestine = A.Fake <IAdvancedParameter>().WithName("Molecule2HalfLifeIntestine");
_advancedParameterMolecule2HalfLifeIntestine.ParameterPath = "Path2";
A.CallTo(() => _advancedParmeterFactory.Create(_molecule1.ReferenceConcentration, DistributionTypes.Normal)).Returns(_advancedParameterMolecule1RefConc);
A.CallTo(() => _advancedParmeterFactory.Create(_molecule2.HalfLifeIntestine, DistributionTypes.Normal)).Returns(_advancedParameterMolecule2HalfLifeIntestine);
}
protected override void Context()
{
base.Context();
_organism = new Organism();
_anotherTopContainer = new Container().WithName("Another container");
_spatialStructure = new PKSimSpatialStructure();
_spatialStructure.AddTopContainer(_organism);
_spatialStructure.AddTopContainer(_anotherTopContainer);
_ga = DomainHelperForSpecs.ConstantParameterWithValue().WithName(Constants.Parameters.GESTATIONAL_AGE);
_age = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.AGE);
_height = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.HEIGHT);
_distributedParameter = DomainHelperForSpecs.NormalDistributedParameter(isDefault: false, distributionParameterIsDefault: false).WithName("Distributed");
_p1 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P1");
_p2 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P2");
_organism.Add(_ga);
_organism.Add(_age);
_organism.Add(_height);
_organism.Add(_p1);
_anotherTopContainer.Add(_p2);
_organism.Add(_distributedParameter);
_mean = _distributedParameter.Parameter(Constants.Distribution.MEAN);
_deviation = _distributedParameter.Parameter(Constants.Distribution.DEVIATION);
}
protected override void Context()
{
base.Context();
_normalDistribution1 = new ParameterDistributionMetaData {
Age = 20, Mean = 5, Deviation = 10
};
_normalDistribution2 = new ParameterDistributionMetaData {
Age = 10, Mean = 15, Deviation = 30
};
_normalDistributions = new List <ParameterDistributionMetaData> {
_normalDistribution1, _normalDistribution2
};
_parameter = A.Fake <IDistributedParameter>();
IParameter meanParameter = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("Mean");
IParameter deviationParameter = DomainHelperForSpecs.ConstantParameterWithValue(2).WithName("Deviation");
A.CallTo(() => _parameter.MeanParameter).Returns(meanParameter);
A.CallTo(() => _parameter.DeviationParameter).Returns(deviationParameter);
A.CallTo(() => _distrFormulaFactory.CreateNormalDistributionFormulaFor(_parameter, meanParameter, deviationParameter)).Returns(new NormalDistributionFormula());
_originData = new OriginData {
Age = 12
};
}
protected override void Context()
{
base.Context();
_executionContext = A.Fake <IExecutionContext>();
var container = new Container();
var objectPathFactory = new ObjectPathFactoryForSpecs();
_paraWithValueUnchanged1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("para1").WithDimension(A.Fake <IDimension>());
_paraWithValueUnchanged1.IsFixedValue = false;
_paraWithValueChanged2 = DomainHelperForSpecs.ConstantParameterWithValue(2).WithName("para2").WithDimension(A.Fake <IDimension>());
_paraWithValueChanged2.Id = "tralala";
_paraWithValueChanged2.Formula = new ExplicitFormula("15");
_paraWithValueChanged2.Formula.AddObjectPath(objectPathFactory.CreateRelativeFormulaUsablePath(_paraWithValueChanged2, _paraWithValueUnchanged1));
_paraWithValueChanged2.Value = 20;
_paraWithValueUnchanged3 = DomainHelperForSpecs.ConstantParameterWithValue(3).WithName("para3");
_distributedParameter = DomainHelperForSpecs.NormalDistributedParameter().WithName("para4");
_distributedParameter.Value = 1.2;
_distributedParameter.IsFixedValue = false;
_paraWithValueUnchanged3.IsFixedValue = false;
container.Add(_paraWithValueChanged2);
container.Add(_paraWithValueUnchanged1);
container.Add(_paraWithValueUnchanged3);
container.Add(_distributedParameter);
_parameterToReset.Add(_paraWithValueUnchanged1);
_parameterToReset.Add(_paraWithValueChanged2);
_parameterToReset.Add(_paraWithValueUnchanged3);
_parameterToReset.Add(_distributedParameter);
A.CallTo(() => _executionContext.BuildingBlockContaining(_paraWithValueChanged2)).Returns(A.Fake <IPKSimBuildingBlock>());
}
protected override void Context()
{
base.Context();
_valueOrigin1 = new ValueOrigin {
Method = ValueOriginDeterminationMethods.Assumption
};
_valueOrigin2 = new ValueOrigin {
Method = ValueOriginDeterminationMethods.Other
};
_distributionFormula = A.Fake <IDistributionFormula>();
_parameter = A.Fake <IDistributedParameter>();
_subParameter = A.Fake <IParameter>();
_originData = new OriginData {
Age = new OriginDataParameter(40)
};
_distributions.Add(new ParameterDistributionMetaData {
DistributionType = CoreConstants.Distribution.Normal, Age = 20, ValueOrigin = _valueOrigin1
});
_distributions.Add(new ParameterDistributionMetaData {
DistributionType = CoreConstants.Distribution.Normal, Age = 50, ValueOrigin = _valueOrigin2
});
A.CallTo(() => _formulaFactory.DistributionFor(A <IEnumerable <ParameterDistributionMetaData> > ._, _parameter, _originData)).Returns(_distributionFormula);
A.CallTo(() => _objectBaseFactory.CreateDistributedParameter()).Returns(_parameter);
A.CallTo(() => _objectBaseFactory.CreateParameter()).Returns(_subParameter);
A.CallTo(() => _objectBaseFactory.Create <ExplicitFormula>()).Returns(new ExplicitFormula());
A.CallTo(() => _dimensionRepository.DimensionByName(A <string> .Ignored)).Returns(_dimension);
}
protected override void Context()
{
base.Context();
_percentileToSet = 0.8;
_distributedParameter = DomainHelperForSpecs.NormalDistributedParameter();
A.CallTo(() => _executionContext.BuildingBlockContaining(_distributedParameter)).Returns(A.Fake <IPKSimBuildingBlock>());
}
public ICommand UpdateDistributedTableFormula(IParameter tableParameter, IDistributedParameter distributedParameter)
{
var distributedTableFormula = tableParameter.Formula as DistributedTableFormula;
if (distributedTableFormula == null)
{
return(new PKSimEmptyCommand());
}
if (distributedParameter.Formula.DistributionType() == DistributionTypes.Discrete)
{
if (ValueComparer.AreValuesEqual(distributedParameter.Value, tableParameter.Value, CoreConstants.DOUBLE_RELATIVE_EPSILON))
{
return(new PKSimEmptyCommand());
}
return(executeAndUpdatedDefaultStateAndValue(new UpdateDistributedTableFormulaRatioCommand(tableParameter, distributedParameter.Value / tableParameter.Value), tableParameter));
}
if (ValueComparer.ArePercentilesEqual(distributedTableFormula.Percentile, distributedParameter.Percentile))
{
return(new PKSimEmptyCommand());
}
return(executeAndUpdatedDefaultStateAndValue(new UpdateDistributedTableFormulaPercentileCommand(tableParameter, distributedParameter.Percentile), tableParameter));
}
private void createSpatialStructureTableParameter(
IParameter structureParameter,
IDistributedParameter baseIndividualParameter,
IReadOnlyList <ParameterDistributionMetaData> distributionsForMale,
IReadOnlyList <ParameterDistributionMetaData> distributionsForFemale,
IBuildConfiguration buildConfiguration)
{
var allDistributionsForParameter = allDistributionsWithAgeStrictBiggerThanOriginData(distributionsForMale, distributionsForFemale, _baseIndividual.OriginData);
if (!allDistributionsForParameter.Any())
{
return;
}
//remove the parameter from the parent container and add a new one that will contain the table formula
//retrieve the table formula corresponding to the individual values
var newParameter = _parameterFactory.CreateFor(structureParameter.Name, structureParameter.BuildingBlockType);
newParameter.UpdatePropertiesFrom(structureParameter, _cloneManager);
var parentContainer = structureParameter.ParentContainer;
parentContainer.RemoveChild(structureParameter);
parentContainer.Add(newParameter);
newParameter.Editable = false;
var formula = createTableFormulaFrom(baseIndividualParameter, allDistributionsForParameter);
updateConstantParameterToFormula(newParameter, formula, buildConfiguration);
}
public void UpdateDistributedParameterTo3_1_3(IDistributedParameter distributedParameter)
{
var geoSDParameter = distributedParameter.GetSingleChildByName <IParameter>(Constants.Distribution.GEOMETRIC_DEVIATION);
var constantFormula = ((ConstantFormula)geoSDParameter.Formula);
constantFormula.Value = Math.Exp(constantFormula.Value);
}
protected override void ClearReferences()
{
_advancedParameter = null;
_advancedParameterContainer = null;
_parameter = null;
_oldDistributedParameter = null;
_newDistributedParameter = null;
}
public DiscreteDistributionFormula CreateDiscreteDistributionFormulaFor(IDistributedParameter distributedParameter, IParameter meanParameter)
{
var distribution = createDistribution <DiscreteDistributionFormula>();
distribution.Dimension = meanParameter.Dimension;
addObjectPathToDistributionFormula(distribution, distributedParameter, meanParameter, Constants.Distribution.MEAN);
return(distribution);
}
public IMoBiCommand UpdateDistributedFormula(IDistributedParameter distributedParameter, IDistributionFormula newDistributedFormula, string formulaType, IBuildingBlock buildingBlock)
{
_context.Register(newDistributedFormula);
_context.Register(distributedParameter.Formula);
var command = new UpdateDistributedFormulaCommand(distributedParameter, newDistributedFormula, formulaType, buildingBlock).Run(_context);
return(withUpdatedDefaultStateAndValueOrigin(command, newDistributedFormula, buildingBlock));
}
protected override void Context()
{
base.Context();
_parent = new Container().WithName("bla");
_distributedParameter = new DistributedParameter().WithName("Dis").WithParentContainer(_parent);
_spatialStructure = new MoBiSpatialStructure().WithTopContainer(_parent);
sut.Edit(_spatialStructure);
}
public UniformDistributionFormula CreateUniformDistributionFormulaFor(IDistributedParameter distributedParameter, IParameter minParameter, IParameter maxParameter)
{
var distribution = createDistribution <UniformDistributionFormula>();
distribution.Dimension = minParameter.Dimension;
addObjectPathToDistributionFormula(distribution, distributedParameter, minParameter, Constants.Distribution.MINIMUM);
addObjectPathToDistributionFormula(distribution, distributedParameter, maxParameter, Constants.Distribution.MAXIMUM);
return(distribution);
}
protected override void Context()
{
base.Context();
A.CallTo(() => _formulaTypeMapper.MapFrom(_targetParameter)).Returns(FormulaType.Distribution);
_targetDistributedParameter = DomainHelperForSpecs.NormalDistributedParameter();
_targetParameter = _targetDistributedParameter;
_sourceParameter.Value = 1.2;
_targetParameter.Value = 1.2;
}
protected override void Context()
{
base.Context();
_distributedParameter = new DistributedParameter().WithName("DP").WithFormula(new LogNormalDistributionFormula());
_distributedParameter.Add(
new Parameter().WithName(Constants.Distribution.MEAN).WithFormula(new ConstantFormula().WithValue(2)));
_geoSDParameter = new Parameter().WithName(Constants.Distribution.GEOMETRIC_DEVIATION).WithFormula(new ConstantFormula().WithValue(_geometricDeviation));
_distributedParameter.Add(_geoSDParameter);
}
protected override void Context()
{
base.Context();
_unit = A.Fake <Unit>();
_distributedParameter = A.Fake <IDistributedParameter>();
_meanParameter = A.Fake <IParameter>();
_distributedParmaeterDTO = new DistributionParameterDTO(_meanParameter);
sut.Edit(_distributedParameter);
}
public LogNormalDistributionFormula CreateLogNormalDistributionFormulaFor(IDistributedParameter distributedParameter, IParameter meanParameter, IParameter deviationParameter)
{
var distribution = createDistribution <LogNormalDistributionFormula>();
distribution.Dimension = meanParameter.Dimension;
addObjectPathToDistributionFormula(distribution, distributedParameter, meanParameter, Constants.Distribution.MEAN);
addObjectPathToDistributionFormula(distribution, distributedParameter, deviationParameter, Constants.Distribution.GEOMETRIC_DEVIATION);
return(distribution);
}
public UpdateDistributedFormulaCommand(IDistributedParameter parameter, IDistributionFormula newFormula, string formulaType, IBuildingBlock buildingBlock) : base(buildingBlock)
{
_parameter = parameter;
_parameterId = parameter.Id;
_newFormula = newFormula;
_oldFormula = _parameter.Formula;
Description = AppConstants.Commands.UpdateDistributedFormulaCommandDescription(parameter.EntityPath(), formulaType);
ObjectType = ObjectTypes.DistributedParameter;
CommandType = Command.CommandTypeEdit;
}
protected override void Context()
{
_buildingBlock = A.Fake <IBuildingBlock>();
_parameter = new DistributedParameter();
_parameter.Formula = new DiscreteDistributionFormula();
_newFormula = new LogNormalDistributionFormula();
_formulaType = "XX";
sut = new UpdateDistributedFormulaCommand(_parameter, _newFormula, _formulaType, _buildingBlock);
_context = A.Fake <IMoBiContext>();
}
protected override void Context()
{
_entityPathResolver = A.Fake <IEntityPathResolver>();
_parameterFactory = A.Fake <IParameterFactory>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_distributedParameter = A.Fake <IDistributedParameter>();
A.CallTo(() => _parameterFactory.CreateFor(A <ParameterDistributionMetaData> ._))
.Invokes(x => _distributionMetaData = x.GetArgument <ParameterDistributionMetaData>(0)).Returns(_distributedParameter);
sut = new AdvancedParameterFactory(_entityPathResolver, _parameterFactory, _objectBaseFactory);
}
protected override void Context()
{
base.Context();
A.CallTo(() => _formulaTypeMapper.MapFrom(_targetParameter)).Returns(FormulaType.Distribution);
A.CallTo(() => _formulaTypeMapper.MapFrom(_sourceParameter)).Returns(FormulaType.Table);
_targetDistributedParameter = DomainHelperForSpecs.NormalDistributedParameter();
_targetParameter = _targetDistributedParameter;
_sourceParameter.Formula = new DistributedTableFormula {
Percentile = 0.2
};
}
public IDistributionFormula CreateFor(IDistributionMetaData distribution, IDistributedParameter parameter)
{
foreach (var factory in _allDistributionFactory)
{
if (factory.IsSatisfiedBy(distribution))
{
return(factory.CreateFor(distribution, parameter));
}
}
throw new DistributionNotFoundException(distribution);
}
public override void UpdateInternalFrom(IBuildingBlockChangeCommand originalCommand)
{
base.UpdateInternalFrom(originalCommand);
var switchDistributionTypeCommand = originalCommand as SwitchAdvancedParameterDistributionTypeCommand;
if (switchDistributionTypeCommand == null)
{
return;
}
_newDistributedParameter = switchDistributionTypeCommand._oldDistributedParameter;
_oldDistributedParameter = switchDistributionTypeCommand._newDistributedParameter;
}
protected override void Context()
{
_topContainer = new Container().WithName("top");
_organ = new Container().WithName("organ").WithParentContainer(_topContainer);
_comp = new Container().WithName("comp").WithParentContainer(_organ);
_parameter = new DistributedParameter().WithName("P1").WithParentContainer(_comp);
new Parameter().WithName("LALA").WithParentContainer(_parameter);
_reak = A.Fake <IUsingFormula>();
A.CallTo(() => _reak.ParentContainer).Returns(_topContainer);
A.CallTo(() => _reak.RootContainer).Returns(_topContainer);
sut = new ObjectPathFactory(new AliasCreator());
}
public override void RestoreExecutionData(IExecutionContext context)
{
base.RestoreExecutionData(context);
_advancedParameterContainer = context.Get <RandomPopulation>(BuildingBlockId);
_parameter = context.Get <IParameter>(ParameterId);
var entityPathResolver = context.Resolve <IEntityPathResolver>();
_advancedParameter = _advancedParameterContainer.AdvancedParameterFor(entityPathResolver, _parameter);
_oldDistributedParameter = context.Deserialize <IDistributedParameter>(_serializationStream);
_newDistributedParameter = _advancedParameter.DistributedParameter;
_newDistributionType = _advancedParameter.DistributionType;
}
private void addObjectPathToDistributionFormula(IDistributionFormula distribution,
IDistributedParameter distributedParameter,
IParameter usedParameter,
string alias)
{
var usedParameterPath = _objectPathFactory.CreateRelativeFormulaUsablePath(distributedParameter, usedParameter);
usedParameterPath.Alias = alias;
usedParameterPath.Dimension = usedParameter.Dimension;
distribution.AddObjectPath(usedParameterPath);
}
protected override void Context()
{
base.Context();
_buildingBlock = A.Fake <IBuildingBlock>();
_parentContainer = A.Fake <IContainer>();
var modalPresenter = A.Fake <IModalPresenter>();
_distributedParameter = A.Fake <IDistributedParameter>();
A.CallTo(_context.ApplicationController).WithReturnType <IModalPresenter>().Returns(modalPresenter);
A.CallTo(() => modalPresenter.Show()).Returns(true);
A.CallTo(() => _context.Context.Create <IDistributedParameter>()).Returns(_distributedParameter);
}
private TableFormula createTableFormulaFrom(IDistributedParameter individualParameter, IReadOnlyList <ParameterDistributionMetaData> allDistributionsWithAgeStrictBiggerThanOriginData)
{
var parameter = new TableFormulaParameter <IDistributedParameter>
{
OriginData = _baseOriginData,
Parameter = individualParameter,
Value = individualParameter.Value,
Percentile = individualParameter.Percentile
};
return(createTableFormulaFrom(parameter, allDistributionsWithAgeStrictBiggerThanOriginData));
}