private void updateMoleculeOntogeny(IndividualMolecule molecule, Ontogeny ontogeny, Population population, IReadOnlyList <double> allAges, IReadOnlyList <double> allGAs)
{
var ontogenyFactorPath = _entityPathResolver.PathFor(molecule.OntogenyFactorParameter);
var ontogenyFactorGIPath = _entityPathResolver.PathFor(molecule.OntogenyFactorGIParameter);
molecule.Ontogeny = ontogeny;
clearOntogenyFor(ontogenyFactorPath, ontogenyFactorGIPath, population);
if (ontogeny.IsUndefined())
{
return;
}
var ontogenyFactors = new ParameterValues(ontogenyFactorPath);
var ontogenyFactorsGI = new ParameterValues(ontogenyFactorGIPath);
for (int i = 0; i < population.NumberOfItems; i++)
{
var age = allAges[i];
var ga = allGAs[i];
ontogenyFactors.Add(_ontogenyRepository.OntogenyFactorFor(ontogeny, CoreConstants.Groups.ONTOGENY_LIVER, age, ga, population.RandomGenerator));
ontogenyFactorsGI.Add(_ontogenyRepository.OntogenyFactorFor(ontogeny, CoreConstants.Groups.ONTOGENY_DUODENUM, age, ga, population.RandomGenerator));
}
population.IndividualPropertiesCache.Add(ontogenyFactors);
population.IndividualPropertiesCache.Add(ontogenyFactorsGI);
}
private DistributedParameterValue distributedOntogenyFactorFor(Ontogeny ontogeny, string moleculeName, OriginData originData, string parameterName, string ontogenyLocation)
{
var parameterPath = new ObjectPath {
moleculeName, parameterName
};
var(mean, std, distributionType) = _ontogenyRepository.OntogenyParameterDistributionFor(ontogeny, originData, ontogenyLocation);
return(new DistributedParameterValue(parameterPath, mean, CoreConstants.DEFAULT_PERCENTILE, mean, std, distributionType));
}
private ParameterValue ontogenyFactorFor(Ontogeny ontogeny, string moleculeName, OriginData originData, string parameterName, string ontogenyLocation)
{
var path = new ObjectPath {
moleculeName, parameterName
};
double factor = _ontogenyRepository.OntogenyFactorFor(ontogeny, ontogenyLocation, originData);
return(new ParameterValue(path, factor, CoreConstants.DEFAULT_PERCENTILE));
}
protected override void Context()
{
base.Context();
_selectedOntogeny = new DatabaseOntogeny();
_individual = A.Fake <Individual>();
_protein = A.Fake <IndividualProtein>();
_command = A.Fake <IPKSimCommand>();
A.CallTo(() => _ontogenyTask.SetOntogenyForMolecule(_protein, _selectedOntogeny, _individual)).Returns(_command);
sut.Edit(_protein, _individual);
}
protected override void Context()
{
base.Context();
CYP3A4 = sut.All().FindByName("CYP3A4");
_originData = new OriginData {
Species = new Species {
Name = CoreConstants.Species.HUMAN
}
};
}
protected override void Context()
{
base.Context();
_cloneManager = A.Fake <ICloneManager>();
_sourceMolecule = new IndividualEnzyme {
Ontogeny = new UserDefinedOntogeny()
};
_clonedOntogeny = new UserDefinedOntogeny();
A.CallTo(() => _cloneManager.Clone(_sourceMolecule.Ontogeny)).Returns(_clonedOntogeny);
}
protected override void Context()
{
base.Context();
CYP3A4 = sut.All().FindByName("CYP3A4");
_randomGenerator = new RandomGenerator();
_originData = new OriginData {
Species = new Species {
Name = CoreConstants.Species.Human
}
};
}
protected override void Context()
{
base.Context();
_individual = A.Fake <Individual>();
_onto1 = new DatabaseOntogeny();
_onto2 = new DatabaseOntogeny();
_allOntogenies.AddRange(new[] { _onto1, _onto2 });
sut.Edit(new IndividualEnzyme {
Ontogeny = _onto1
}, _individual);
}
public void Show(Ontogeny ontogeny)
{
_speciesName = ontogeny.SpeciesName;
_ontogeny = ontogeny;
_dto = new ShowOntogenyDataDTO {
SelectedOntogeny = ontogeny
};
updateAvailableContainerForOntogeny();
_view.BindTo(_dto);
updateChart();
_view.Display();
}
public void ShowOntogenyData(Ontogeny ontogeny)
{
if (ontogeny.IsUndefined())
{
return;
}
using (var presenter = _applicationController.Start <IShowOntogenyDataPresenter>())
{
presenter.Show(ontogeny);
}
}
protected override void Context()
{
_individual = new Individual();
_individual.OriginData = new OriginData();
_individual.OriginData.Species = new Species().WithName("Human");
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_executionContext = A.Fake <IExecutionContext>();
_proteinExpressionPresenter = A.Fake <IProteinExpressionsPresenter>();
_simpleMoleculePresenter = A.Fake <ISimpleMoleculePresenter>();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_applicationController = A.Fake <IApplicationController>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_containerTask = A.Fake <IContainerTask>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
_proteinExpressionDbPathManager = A.Fake <IProteinExpressionsDatabasePathManager>();
A.CallTo(() => _applicationController.Start <IProteinExpressionsPresenter>()).Returns(_proteinExpressionPresenter);
A.CallTo(() => _applicationController.Start <ISimpleMoleculePresenter>()).Returns(_simpleMoleculePresenter);
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp));
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp));
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
A.CallTo(() => proteinFactory.CreateFor(_individual)).Returns(_molecule);
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameter.REFERENCE_CONCENTRATION));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameter.HALF_LIFE_LIVER));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameter.HALF_LIFE_INTESTINE));
A.CallTo(() => _ontogenyRepository.AllFor(_individual.Species.Name)).Returns(new[] { _ontogeny, new DatabaseOntogeny {
Name = "tralala"
}, });
A.CallTo(() => _executionContext.Resolve <IOntogenyRepository>()).Returns(_ontogenyRepository);
_subjectExpressionTask = new IndividualExpressionTask(_executionContext);
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
sut = new MoleculeExpressionTask <Individual>(_applicationController, _executionContext,
_individualMoleculeFactoryResolver, _querySettingsMapper,
_containerTask, _proteinExpressionDbPathManager,
_ontogenyRepository, _transportContainerUpdater, _moleculeParameterRepository, _subjectExpressionTask, _ontogenyTask);
}
protected override void Context()
{
_molecule = new IndividualEnzyme
{
DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.ONTOGENY_FACTOR),
DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.ONTOGENY_FACTOR_GI)
};
_ontogeny = new DatabaseOntogeny();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_entityPathResolver = new EntityPathResolverForSpecs();
sut = new MoleculeOntogenyVariabilityUpdater(_ontogenyRepository, _entityPathResolver);
}
protected override void Context()
{
base.Context();
_ontogeny = new DatabaseOntogeny {
SpeciesName = "Dog", Name = "UD6"
};
_originData = new OriginData {
Species = new Species {
Name = "Dog"
}
};
A.CallTo(() => _ontogenyRepository.AllFor(_originData.Species.Name)).Returns(new[] { _ontogeny });
_moleculeNames.Add(new MoleculeOntogeny("CYP", "CYP3A4"));
}
protected override void Context()
{
_view = A.Fake <IShowOntogenyDataView>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_simpleChartPresenter = A.Fake <ISimpleChartPresenter>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_groupRepository = A.Fake <IGroupRepository>();
_displayUnitRetriever = A.Fake <IDisplayUnitRetriever>();
_groupLiver = new Group {
Name = "Liver"
};
_groupDuodenum = new Group {
Name = "Duodenum"
};
_tableFormula = new TableFormula();
_ontogeny = new DatabaseOntogeny {
SpeciesName = "toto"
};
_anotherOntogeny = new DatabaseOntogeny {
SpeciesName = "toto"
};
_allOntongies = new List <Ontogeny> {
_ontogeny, _anotherOntogeny
};
_ontoData = new List <OntogenyMetaData>();
_ontoData.Add(new OntogenyMetaData {
GroupName = "Liver"
});
_ontoData.Add(new OntogenyMetaData {
GroupName = "Duodenum"
});
_allMetaData = new List <OntogenyMetaData>();
A.CallTo(() => _dimensionRepository.AgeInYears).Returns(A.Fake <IDimension>());
A.CallTo(() => _dimensionRepository.Fraction).Returns(DomainHelperForSpecs.FractionDimensionForSpecs());
A.CallTo(() => _simpleChartPresenter.Plot(A <TableFormula> ._)).Returns(new CurveChart().WithAxes());
A.CallTo(() => _simpleChartPresenter.Plot(A <DataRepository> ._, Scalings.Linear)).Returns(new CurveChart().WithAxes());
A.CallTo(() => _groupRepository.GroupByName("Liver")).Returns(_groupLiver);
A.CallTo(() => _groupRepository.GroupByName("Duodenum")).Returns(_groupDuodenum);
A.CallTo(() => _ontogenyRepository.AllValuesFor(_ontogeny)).Returns(_ontoData);
A.CallTo(() => _ontogenyRepository.AllFor(_ontogeny.SpeciesName)).Returns(_allOntongies);
A.CallTo(() => _ontogenyRepository.AllValuesFor(_ontogeny, _groupLiver.Name)).Returns(_allMetaData);
sut = new ShowOntogenyDataPresenter(_view, _ontogenyRepository, _simpleChartPresenter, _dimensionRepository, _groupRepository, _displayUnitRetriever);
A.CallTo(() => _view.BindTo(A <ShowOntogenyDataDTO> ._))
.Invokes(x => ShowOntogenyDataDTO = x.GetArgument <ShowOntogenyDataDTO>(0));
}
protected override void Context()
{
base.Context();
_ontogeny = new DatabaseOntogeny {
SpeciesName = "Dog", Name = "CYP3A4"
};
_originData = new OriginData {
Species = new Species {
Name = "Dog"
}
};
A.CallTo(() => _ontogenyRepository.AllFor(_originData.Species.Name)).Returns(new[] { _ontogeny });
A.CallTo(() => _ontogenyRepository.OntogenyFactorFor(_ontogeny, CoreConstants.Groups.ONTOGENY_LIVER, _originData, null)).Returns(0.5);
_moleculeNames.Add(new MoleculeOntogeny("CYP", "CYP3A4"));
}
protected SetOntogenyInMoleculeCommand(IndividualMolecule molecule, Ontogeny newOntogeny, TSimulationSubject simulationSubject, IExecutionContext context)
{
_molecule = molecule;
_oldOntogeny = molecule.Ontogeny ?? new NullOntogeny();
_newOntogeny = newOntogeny ?? new NullOntogeny();
_moleculeId = molecule.Id;
_simulationSubject = simulationSubject;
BuildingBlockId = simulationSubject.Id;
ObjectType = context.TypeFor(molecule);
CommandType = PKSimConstants.Command.CommandTypeEdit;
var subjectName = string.IsNullOrEmpty(_simulationSubject.Name) ? CoreConstants.ContainerName.NameTemplate : _simulationSubject.Name;
Description = PKSimConstants.Command.SetOntogenyInProteinDescription(subjectName, molecule.Name, _oldOntogeny.Name, _newOntogeny.Name);
context.UpdateBuildinBlockProperties(this, simulationSubject);
}
public void UpdateMoleculeOntogeny(IndividualMolecule molecule, Ontogeny ontogeny, ISimulationSubject simulationSubject)
{
switch (simulationSubject)
{
case Individual individual:
UpdateMoleculeOntogeny(molecule, ontogeny, individual);
break;
case Population population:
UpdateMoleculeOntogeny(molecule, ontogeny, population);
break;
default:
throw new ArgumentOutOfRangeException(nameof(simulationSubject));
}
}
protected override void Context()
{
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
_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));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
A.CallTo(() => proteinFactory.AddMoleculeTo(_individual, A <string> ._)).Returns(_molecule);
A.CallTo(() => _ontogenyRepository.AllFor(_individual.Species.Name)).Returns(new[] { _ontogeny, new DatabaseOntogeny {
Name = "tralala"
}, });
A.CallTo(() => _executionContext.Resolve <IOntogenyRepository>()).Returns(_ontogenyRepository);
_subjectExpressionTask = new IndividualExpressionTask(_executionContext);
sut = new MoleculeExpressionTask <Individual>(
_executionContext,
_individualMoleculeFactoryResolver,
_subjectExpressionTask,
_expressionProfileUpdater
);
}
public void SelectedOntogenyIs(Ontogeny ontogeny)
{
AddCommand(_ontogenyTask.SetOntogenyForMolecule(_individualMolecule, ontogeny, _simulationSubject));
updateShowOntogenyButton();
}
public abstract ICommand SetOntogenyForMolecule(IndividualMolecule molecule, Ontogeny ontogeny, TSimulationSubject simulationSubject);
public override ICommand SetOntogenyForMolecule(IndividualMolecule molecule, Ontogeny ontogeny, Population population)
{
return(new SetOntogenyInMoleculeForPopulationCommand(molecule, ontogeny, population, _executionContext).Run(_executionContext));
}
public void UpdateMoleculeOntogeny(IndividualMolecule molecule, Ontogeny ontogeny, Population population)
{
updateMoleculeOntogeny(molecule, ontogeny, population, allAgesIn(population), allGAsIn(population));
}
public void UpdateMoleculeOntogeny(IndividualMolecule molecule, Ontogeny ontogeny, Individual individual)
{
molecule.Ontogeny = ontogeny;
molecule.OntogenyFactorGI = _ontogenyRepository.OntogenyFactorFor(ontogeny, CoreConstants.Groups.ONTOGENY_DUODENUM, individual.OriginData);
molecule.OntogenyFactor = _ontogenyRepository.OntogenyFactorFor(ontogeny, CoreConstants.Groups.ONTOGENY_LIVER, individual.OriginData);
}
public void ShowOntogenyData(Ontogeny ontogeny)
{
throw new NotSupportedException();
}
protected override void Because()
{
_ontogeny = new DatabaseOntogeny();
sut.ShowOntogenyData(_ontogeny);
}
protected override async Task Because()
{
_newOntogeny = await sut.MapToModel(_snapshot, _simulationSubject);
}
private TableFormula createOntogenyTableFormulaFrom(IParameter ontogenyFactor, Ontogeny ontogeny, OriginData originData, RandomGenerator randomize = null)
{
var containerName = containerNameForOntogenyFactor(ontogenyFactor);
var allOntogenies = _ontogenyRepository.AllOntogenyFactorForStrictBiggerThanPMA(ontogeny, originData, containerName, randomize).ToList();
return(createMoleculeOntogenyTableFormula(ontogenyFactor, originData, allOntogenies));
}
public ICommand SetOntogenyForMolecule(IndividualMolecule molecule, Ontogeny ontogeny, ISimulationSubject simulationSubject)
{
return(new SetOntogenyInMoleculeCommand(molecule, ontogeny, simulationSubject, _executionContext).Run(_executionContext));
}
public SetOntogenyInMoleculeForPopulationCommand(IndividualMolecule molecule, Ontogeny newOntogeny, Population population, IExecutionContext context)
: base(molecule, newOntogeny, population, context)
{
}
public override ICommand SetOntogenyForMolecule(IndividualMolecule molecule, Ontogeny ontogeny, Individual individual)
{
return(new SetOntogenyInMoleculeForIndividualCommand(molecule, ontogeny, individual, _executionContext).Run(_executionContext));
}
