protected override void Context()
{
base.Context();
_advancedParameter = A.Fake <AdvancedParameter>();
_advancedParameter.ParameterPath = "A NEW PARAMETER PATH";
sut.AddAdvancedParameter(_advancedParameter, generateRandomValues: false);
}
protected override void Context()
{
base.Context();
_parameterPath = "Liver|P1";
_originalSimulation = new PopulationSimulation();
_originalSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("Pop", PKSimBuildingBlockType.Population)
{
BuildingBlock = _population
});
_originalSimulation.Add(new AdvancedParameterCollection().WithName("AdvancedParameterCollection"));
_advancedParameter = A.Fake <AdvancedParameter>();
_advancedParameter.ParameterPath = _parameterPath;
A.CallTo(() => _advancedParameter.GenerateRandomValues(3)).Returns(new []
{
new RandomValue {
Percentile = 0.5, Value = 1
},
new RandomValue {
Percentile = 0.5, Value = 2
},
new RandomValue {
Percentile = 0.5, Value = 3
},
});
_originalSimulation.AddAdvancedParameter(_advancedParameter, generateRandomValues: true);
}
protected override void Context()
{
base.Context();
_anotherPopulation = A.Fake <RandomPopulation>();
_parameter = new AdvancedParameter();
sut.EditPopulation(_population);
}
protected override void Context()
{
base.Context();
_advancedParameter = A.Fake <AdvancedParameter>();
_advancedParameter.ParameterPath = "A NEW PARAMETER PATH";
sut.AddAdvancedParameter(_advancedParameter);
}
protected override void Context()
{
base.Context();
_individualPropertiesCache = A.Fake <IndividualValuesCache>();
_patchCache = new PathCacheForSpecs <IParameter>();
var individualParameter = A.Fake <IParameter>();
A.CallTo(() => individualParameter.IsChangedByCreateIndividual).Returns(true);
_patchCache.Add("Path1", individualParameter);
var advancedParameter = A.Fake <IParameter>();
A.CallTo(() => advancedParameter.IsChangedByCreateIndividual).Returns(false);
advancedParameter.CanBeVariedInPopulation = true;
_patchCache.Add("PathAdvanced", advancedParameter);
A.CallTo(() => _individualPropertiesCache.AllParameterPaths()).Returns(new[] { "Path1", "Path2", "PathAdvanced" });
A.CallTo(() => _individualPropertiesCache.ParameterValuesFor("Path1")).Returns(_value1);
A.CallTo(() => _individualPropertiesCache.ParameterValuesFor("Path2")).Returns(_value2);
A.CallTo(() => _individualPropertiesCache.ParameterValuesFor("PathAdvanced")).Returns(_value3);
_populationSimulation = A.Fake <PopulationSimulation>();
_parameterValueCache = A.Fake <ParameterValuesCache>();
A.CallTo(() => _populationSimulation.ParameterValuesCache).Returns(_parameterValueCache);
_mobiPopulation = A.Fake <MoBiPopulation>();
A.CallTo(_simulationFactory).WithReturnType <PopulationSimulation>().Returns(_populationSimulation);
A.CallTo(() => _objectBaseFactory.Create <MoBiPopulation>()).Returns(_mobiPopulation);
A.CallTo(() => _parameterRetriever.ParametersFrom(_populationSimulation)).Returns(_patchCache);
A.CallTo(() => _individualPropertiesCacheImporter.ImportFrom(_populationFile, _patchCache, A <IImportLogger> ._)).Returns(_individualPropertiesCache);
_advancedParameterContainer = new AdvancedParameter();
A.CallTo(() => _advancedParameterFactory.Create(advancedParameter, DistributionTypes.Unknown)).Returns(_advancedParameterContainer);
}
public void Edit(AdvancedParameter advancedParameter)
{
_advancedParameter = advancedParameter;
_advancedParameterDTO = _advancedParameterDTOMapper.MapFrom(_advancedParameter);
_distributionParameterPresenter.Edit(_advancedParameterDTO.Parameters);
_view.BindTo(_advancedParameterDTO);
}
public void RemoveSelectionFor(AdvancedParameter advancedParameter)
{
if (Equals(advancedParameter, _advancedParameter))
{
RemoveSelection();
}
}
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 <AdvancedParameter>().WithName("Molecule1RefConf");
_advancedParameterMolecule1RefConc.ParameterPath = "Path1";
_advancedParameterMolecule2HalfLifeIntestine = A.Fake <AdvancedParameter>().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();
_advancedParameter = new AdvancedParameter();
//in this scenario, _advancedPara1 is being deleted from the advanced parameters
_advancedParameter.ParameterPath = _pathAdvancedPara1;
sut.EditPopulation(_population);
}
protected override void Context()
{
base.Context();
_advancedParameter = A.Fake <AdvancedParameter>();
//in this scenario, para1 was selected to become and advanced parameter
_advancedParameter.ParameterPath = _pathPara1;
sut.EditPopulation(_population);
}
protected override void ClearReferences()
{
_advancedParameter = null;
_advancedParameterContainer = null;
_parameter = null;
_oldDistributedParameter = null;
_newDistributedParameter = null;
}
protected override void Context()
{
base.Context();
_command = A.Fake <IPKSimCommand>();
_advancedParameter = new AdvancedParameter();
_advancedParameter.ParameterPath = _pathAdvancedPara1;
A.CallTo(() => _advancedParametersTask.SwitchDistributionTypeFor(_advancedPara1, _population, DistributionTypes.Normal)).Returns(_command);
sut.EditPopulation(_population);
}
protected override void Context()
{
base.Context();
_parameter = A.Fake <IParameter>();
_node = A.Fake <ITreeNode>();
_advancedParameter = new AdvancedParameter();
sut.EditPopulation(_population);
A.CallTo(() => _population.AdvancedParameterFor(_entityPathResolver, _parameter)).Returns(_advancedParameter);
}
protected override void Context()
{
base.Context();
sut.EditPopulation(_population);
_advancedParameter = new AdvancedParameter();
_parameter = new PKSimParameter().WithName("tralala");
_treeNode = new ObjectWithIdAndNameNode <IParameter>(_parameter);
A.CallTo(() => _population.AdvancedParameterFor(_entityPathResolver, _parameter)).Returns(_advancedParameter);
}
public AdvancedParameterDTO MapFrom(AdvancedParameter advancedParameter)
{
return(new AdvancedParameterDTO
{
DistributionType = advancedParameter.DistributionType,
ParameterFullDisplayName = advancedParameter.FullDisplayName,
Parameters = advancedParameter.AllParameters
});
}
protected override void Context()
{
base.Context();
_p1 = A.Fake <IParameter>();
_allParameters.AddRange(new[] { _p1 });
sut.EditPopulation(_population);
_advancedParameterThatDoesNotExist = new AdvancedParameter {
ParameterPath = "DOES NOT EXIT"
};
}
public void RemoveAdvancedParameter(AdvancedParameter advancedParameter)
{
var parameter = parameterFor(advancedParameter);
if (parameter == null)
{
return;
}
_parametersPresenter.RemoveParameter(parameter);
refresh();
}
public void AddAdvancedParameter(AdvancedParameter advancedParameter)
{
var parameter = parameterFor(advancedParameter);
if (parameter == null)
{
return;
}
_parametersPresenter.AddParameter(parameter);
_parametersPresenter.SelectParameter(parameter);
}
protected override async Task Context()
{
await base.Context();
_allImportedParameters.AddRange(new[] { "P1", "P2" });
_allParameters.Add("P1", new PKSimParameter().WithName("P1"));
_allParameters.Add("P2", new PKSimParameter().WithName("P2"));
_allCreateIndividualParameters.Add("P1", _allParameters.FindByName("P1"));
_advancedParameter = new AdvancedParameter();
A.CallTo(() => _advancedParameterFactory.Create(_allParameters.FindByName("P2"), DistributionTypes.Unknown)).Returns(_advancedParameter);
A.CallTo(() => _createdPopulation.IndividualPropertiesCache.AllParameterPaths()).Returns(_allImportedParameters);
}
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;
}
protected override void Context()
{
base.Context();
_allImportedParameters.AddRange(new[] { "P1", "P2" });
_allParameters.Add("P1", new PKSimParameter().WithName("P1"));
_allParameters.Add("P2", new PKSimParameter().WithName("P2"));
_allCreateIndividualParameters.Add("P1", _allParameters.FindByName("P1"));
_advancedParameter = new AdvancedParameter();
A.CallTo(() => _containerTask.CacheAllChildren <IParameter>(_cloneIndividual)).Returns(_allParameters);
A.CallTo(() => _containerTask.CacheAllChildrenSatisfying(_cloneIndividual, A <Func <IParameter, bool> > ._)).Returns(_allCreateIndividualParameters);
A.CallTo(() => _advancedParameterFactory.Create(_allParameters.FindByName("P2"), DistributionTypes.Unknown)).Returns(_advancedParameter);
A.CallTo(() => _createdPopulation.IndividualPropertiesCache.AllParameterPaths()).Returns(_allImportedParameters);
}
protected override void Context()
{
base.Context();
_parameter = A.Fake <IParameter>();
_advancedParameter = A.Fake <AdvancedParameter>().WithId("Id");
_advancedParameter.ParameterPath = "A NEW PARAMETER PATH";
A.CallTo(() => _entityPathResolver.PathFor(_parameter)).Returns(_advancedParameter.ParameterPath);
_randomValues = new List <RandomValue>
{
new RandomValue {
Value = 1, Percentile = 0.5
},
};
A.CallTo(() => _advancedParameter.GenerateRandomValues(sut.NumberOfItems)).Returns(_randomValues);
}
protected override void Context()
{
base.Context();
_parameter = A.Fake <IDistributedParameter>();
_distributedParameters = new PathCacheForSpecs <IParameter> {
{ "P1", _parameter }
};
_populationSimulation = A.Fake <PopulationSimulation>();
_mobiPopulation = A.Fake <MoBiPopulation>();
_advancedParameter = new AdvancedParameter();
_parameterValueCache = A.Fake <ParameterValuesCache>();
A.CallTo(() => _populationSimulation.ParameterValuesCache).Returns(_parameterValueCache);
A.CallTo(_simulationFactory).WithReturnType <PopulationSimulation>().Returns(_populationSimulation);
A.CallTo(() => _objectBaseFactory.Create <MoBiPopulation>()).Returns(_mobiPopulation);
A.CallTo(() => _objectBaseFactory.Create <AdvancedParameter>()).Returns(_advancedParameter);
A.CallTo(_parameterRetriever).WithReturnType <PathCache <IParameter> >().Returns(_distributedParameters);
}
protected override void Context()
{
base.Context();
_populationSimulation = new PopulationSimulation();
_populationSimulation.Model = new OSPSuite.Core.Domain.Model();
_populationSimulation.Model.Root = new Container();
var randomPopulation = new RandomPopulation();
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("id", PKSimBuildingBlockType.Population)
{
BuildingBlock = randomPopulation
});
_populationSimulation.SetAdvancedParameters(new AdvancedParameterCollection());
_populationSimulation.Add(new Parameter().WithName("Param1"));
_advancedParameter = new AdvancedParameter {
ParameterPath = "OLD|Param1"
};
_populationSimulation.AddAdvancedParameter(_advancedParameter);
_populationSimulation.Name = "NEW";
}
public SwitchAdvancedParameterDistributionTypeCommand(IParameter parameter, IAdvancedParameterContainer advancedParameterContainer, DistributionType newDistributionType, IExecutionContext context)
{
_advancedParameterContainer = advancedParameterContainer;
_newDistributionType = newDistributionType;
_parameter = parameter;
ParameterId = parameter.Id;
BuildingBlockId = _advancedParameterContainer.Id;
var entityPathResolver = context.Resolve <IEntityPathResolver>();
var advancedParameterFactory = context.Resolve <IAdvancedParameterFactory>();
_advancedParameter = _advancedParameterContainer.AdvancedParameterFor(entityPathResolver, _parameter);
_oldDistributedParameter = _advancedParameter.DistributedParameter;
_oldDistributionType = _advancedParameter.DistributionType;
var newParameter = advancedParameterFactory.Create(_parameter, _newDistributionType);
_newDistributedParameter = newParameter.DistributedParameter;
ObjectType = context.TypeFor(_advancedParameter);
Description = PKSimConstants.Command.SwitchAdvancedParameterDistributionTypeDescription(_advancedParameter.ParameterPath, _oldDistributionType.ToString(), _newDistributionType.ToString());
context.UpdateBuildingBlockPropertiesInCommand(this, _advancedParameterContainer);
}
protected override void Context()
{
base.Context();
_moleculeParameterAsAdvanced = A.Fake <IParameter>();
_molecule = new IndividualEnzyme();
_population = new RandomPopulation {
Settings = new RandomPopulationSettings {
BaseIndividual = new Individual()
}
};
_population.Add(new AdvancedParameterCollection());
_population.AddMolecule(_molecule);
A.CallTo(() => _entityPathResolver.PathFor(_moleculeParameterAsAdvanced)).Returns("A|B");
_molecule.Add(_moleculeParameterAsAdvanced);
_advancedParameter = new AdvancedParameter {
ParameterPath = "A|B", Name = "A|B"
};
_population.AddAdvancedParameter(_advancedParameter);
_population.AddAdvancedParameter(new AdvancedParameter {
ParameterPath = "ANOTHER PARAMETER", Name = "ANOTHER PARAMETER"
});
}
private void addSurfaceAreaVariabilityTo(Population population)
{
var individual = population.FirstIndividual;
if (individual == null)
{
return;
}
var factor = effectiveSurfaceAreaVariabilityParameterIn(individual) as IDistributedParameter;
if (factor == null)
{
return;
}
var parameterPath = _entityPathResolver.PathFor(factor);
//use a clone as this parameter will be used to create the advanced parameter
var clone = _cloner.Clone(factor);
var advancedParameter = new AdvancedParameter {
DistributedParameter = clone, Seed = population.Seed
};
var randomValues = advancedParameter.GenerateRandomValues(population.NumberOfItems);
population.IndividualPropertiesCache.Add(randomValues.Select(rv => new ParameterValue(parameterPath, rv.Value, rv.Percentile)).ToList());
}
private IParameter parameterFor(AdvancedParameter advancedParameter)
{
return(_allParametersCache[advancedParameter.ParameterPath]);
}
public void Select(AdvancedParameter advancedParameter)
{
_parametersPresenter.SelectParameter(_allParametersCache[advancedParameter.ParameterPath]);
}
protected override void Because()
{
_advancedParameter = sut.Create(_parameter, DistributionTypes.Uniform);
}