public override void GlobalContext()
{
base.GlobalContext();
_allExpressionParameters[CoreConstants.Compartment.PLASMA].Value = 0;
_allExpressionParameters[CoreConstants.Compartment.BLOOD_CELLS].Value = 0;
_allExpressionParameters[CoreConstants.Compartment.VASCULAR_ENDOTHELIUM].Value = 0;
_allExpressionParameters[CoreConstants.Compartment.PERIPORTAL].Value = 1;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection
{
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
var objectPatFactory = new ObjectPathFactoryForSpecs();
var path = objectPatFactory.CreateObjectPathFrom(Constants.ORGANISM,
CoreConstants.Organ.LIVER,
CoreConstants.Compartment.PERICENTRAL,
CoreConstants.Compartment.INTRACELLULAR,
CoreConstants.Molecule.ProcessProductName(_compound.Name, _enzyme.Name, CoreConstants.Molecule.Metabolite),
CoreConstants.Observer.ObserverNameFrom(CoreConstants.Observer.FRACTION_OF_DOSE, _compound.Name));
var quantitySelection = new QuantitySelection(path.ToString(), QuantityType.Metabolite);
_simulation.OutputSelections.AddOutput(quantitySelection);
}
public override void GlobalContext()
{
base.GlobalContext();
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = 0;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = 0;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = 0;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Periportal).Value = 1;
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
var objectPatFactory = new ObjectPathFactoryForSpecs();
var path = objectPatFactory.CreateObjectPathFrom(Constants.ORGANISM,
CoreConstants.Organ.Liver,
CoreConstants.Compartment.Pericentral,
CoreConstants.Compartment.Intracellular,
CoreConstants.Molecule.ProcessProductName(_compound.Name, _enzyme.Name, CoreConstants.Molecule.Metabolite),
CoreConstants.Observer.ObserverNameFrom(CoreConstants.Observer.FRACTION_OF_DOSE, _compound.Name));
var quantitySelection = new QuantitySelection(path.ToString(), QuantityType.Metabolite);
_simulation.OutputSelections.AddOutput(quantitySelection);
}
private void addPKParametersForOutput(ISimulation simulation, int numberOfIndividuals, SimulationResults runResults, Action <int> performIndividualScalingAction,
QuantitySelection selectedQuantity, PopulationSimulationPKAnalyses popAnalyses, string moleculeName,
PKCalculationOptions pkCalculationOptions, IReadOnlyList <PKCalculationOptionsFactory.ApplicationParameters> allApplicationParameters)
{
var availablePKParameters = _pkParameterRepository.All().Where(p => PKParameterCanBeUsed(p, pkCalculationOptions)).ToList();
//create pk parameter for each quantities
foreach (var pkParameter in availablePKParameters)
{
var quantityPKParameter = new QuantityPKParameter {
Name = pkParameter.Name, QuantityPath = selectedQuantity.Path, Dimension = pkParameter.Dimension
};
quantityPKParameter.SetNumberOfIndividuals(numberOfIndividuals);
popAnalyses.AddPKAnalysis(quantityPKParameter);
}
//add the values for each individual
foreach (var individualResult in runResults.AllIndividualResults)
{
performIndividualScalingAction(individualResult.IndividualId);
_pkCalculationOptionsFactory.UpdateAppliedDose(simulation, moleculeName, pkCalculationOptions, allApplicationParameters);
var values = individualResult.ValuesFor(selectedQuantity.Path);
var pkValues = _pkValuesCalculator.CalculatePK(individualResult.Time.Values, values.Values, pkCalculationOptions);
foreach (var pkParameter in availablePKParameters)
{
var quantityPKParameter = popAnalyses.PKParameterFor(selectedQuantity.Path, pkParameter.Name);
quantityPKParameter.SetValue(individualResult.IndividualId, pkValues.ValueOrDefaultFor(pkParameter.Name));
}
}
}
protected override void Context()
{
sut = new ParameterIdentification();
_observedData = new WeightedObservedData(DomainHelperForSpecs.ObservedData());
_simulation = A.Fake <ISimulation>().WithName("Sim").WithId("Id");
_quantitySelection = new QuantitySelection("Organism|Liver|Cell|Asprin|Concentration", QuantityType.Drug);
_outputMapping = new OutputMapping {
WeightedObservedData = _observedData, OutputSelection = new SimulationQuantitySelection(_simulation, _quantitySelection)
};
}
protected override void Context()
{
base.Context();
_cloner = A.Fake <ICloneManager>();
_output1 = new QuantitySelection("A", QuantityType.Drug);
_output2 = new QuantitySelection("B", QuantityType.Complex);
sut.AddOutput(_output1);
_newOutputSelection = new OutputSelections();
_newOutputSelection.AddOutput(_output2);
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <Simulation>();
A.CallTo(() => _simulation.OutputSelections).Returns(new OutputSelections());
var q1Selection = new QuantitySelection(_q1.Name, _q1.QuantityType);
var q2Selection = new QuantitySelection(_q2.Name, _q2.QuantityType);
_simulation.OutputSelections.AddOutput(q1Selection);
_simulation.OutputSelections.AddOutput(q2Selection);
A.CallTo(() => _containerTask.CacheAllChildrenSatisfying(_simulation.Model.Root, A <Func <IQuantity, bool> > ._)).Returns(new PathCacheForSpecs <IQuantity> {
_q1, _q2, _q3
});
}
protected override void Context()
{
base.Context();
_simulationOutput1 = new QuantitySelection("OUTPUT1", QuantityType.Drug);
_simulationOutput2 = new QuantitySelection("OUTPUT2", QuantityType.Drug);
_simulationOutput3 = new QuantitySelection("OUTPUT3", QuantityType.Drug);
_selectedOutput3 = new QuantitySelection("OUTPUT3", QuantityType.Drug);
_selectedOutput4 = new QuantitySelection("OUTPUT4", QuantityType.Drug);
_outputSelection.AddOutput(_simulationOutput1);
_outputSelection.AddOutput(_simulationOutput2);
_outputSelection.AddOutput(_simulationOutput3);
_mappedOutputs.Add(_simulationOutput1);
_mappedOutputs.Add(_selectedOutput3);
_mappedOutputs.Add(_selectedOutput4);
}
private void addPKParametersForOutput(
IModelCoreSimulation simulation,
SimulationResults simulationResults,
Action <int> performIndividualScalingAction,
QuantitySelection selectedQuantity,
PopulationSimulationPKAnalyses popAnalyses,
string moleculeName,
PKCalculationOptions pkCalculationOptions,
IReadOnlyList <ApplicationParameters> allApplicationParameters)
{
var allPKParameters = _pkParameterRepository.All().Where(p => PKParameterCanBeUsed(p, pkCalculationOptions)).ToList();
var allUserDefinedPKParameters = allPKParameters.OfType <UserDefinedPKParameter>().ToList();
//create pk parameter for each pk parameters (predefined and dynamic)
foreach (var pkParameter in allPKParameters)
{
var quantityPKParameter = new QuantityPKParameter {
Name = pkParameter.Name, QuantityPath = selectedQuantity.Path, Dimension = pkParameter.Dimension
};
popAnalyses.AddPKAnalysis(quantityPKParameter);
}
//add the values for each individual
foreach (var individualResult in simulationResults.AllIndividualResults)
{
performIndividualScalingAction(individualResult.IndividualId);
_pkCalculationOptionsFactory.UpdateTotalDrugMassPerBodyWeight(simulation, moleculeName, pkCalculationOptions, allApplicationParameters);
var values = individualResult.QuantityValuesFor(selectedQuantity.Path);
//This can happen is the results do not match the simulation
if (values == null)
{
continue;
}
var pkValues = _pkValuesCalculator.CalculatePK(individualResult.Time.Values, values.Values, pkCalculationOptions, allUserDefinedPKParameters);
foreach (var quantityPKParameter in popAnalyses.AllPKParametersFor(selectedQuantity.Path))
{
quantityPKParameter.SetValue(individualResult.IndividualId, pkValues.ValueOrDefaultFor(quantityPKParameter.Name));
}
}
}
protected override Task Context()
{
_entitiesInContainerRetriever = A.Fake <IEntitiesInContainerRetriever>();
_logger = A.Fake <ILogger>();
sut = new OutputSelectionsMapper(_entitiesInContainerRetriever, _logger);
_quantitySelection1 = new QuantitySelection("PATH1", QuantityType.Drug);
_quantitySelection2 = new QuantitySelection("PATH2", QuantityType.Observer);
_outputSelections = new OutputSelections();
_outputSelections.AddOutput(_quantitySelection1);
_outputSelections.AddOutput(_quantitySelection2);
_simulation = new IndividualSimulation();
_allQuantities = new PathCacheForSpecs <IQuantity>();
A.CallTo(() => _entitiesInContainerRetriever.QuantitiesFrom(_simulation)).Returns(_allQuantities);
return(Task.FromResult(true));
}
protected override void Context()
{
base.Context();
_defaultSettings = new OutputSelections();
_allQuantities = new List <IQuantity>();
var moleculeSelection1 = new QuantitySelection("PATH1", QuantityType.Drug);
_defaultSettings.AddOutput(moleculeSelection1);
_allQuantities.Add(q1);
q1.QuantityType = QuantityType.Drug;
A.CallTo(() => _keyPathMapper.MapFrom(q1)).Returns("KEY1");
A.CallTo(() => _keyPathMapper.MapFrom(moleculeSelection1)).Returns("KEY2");
_project.OutputSelections = _defaultSettings;
A.CallTo(() => _populationSimulationSettingsPresenter.CreateSettings(_populationSimulation)).Returns(_originalSettings);
A.CallTo(() => _populationSimulation.All <IQuantity>()).Returns(_allQuantities);
}
protected override void Context()
{
base.Context();
_defaultSettings = new OutputSelections();
_allQuantities = new List <IQuantity>();
var moleculeSelection1 = new QuantitySelection("PATH1", QuantityType.Drug);
_defaultSettings.AddOutput(moleculeSelection1);
var moleculeSelection2 = new QuantitySelection("PATH2", QuantityType.Drug);
_defaultSettings.AddOutput(moleculeSelection2);
var moleculeSelection3 = new QuantitySelection("PATH3", QuantityType.Drug);
_defaultSettings.AddOutput(moleculeSelection3);
_allQuantities.AddRange(new[] { q1, q2, q3, q4 });
q1.QuantityType = QuantityType.Drug;
q2.QuantityType = QuantityType.Drug;
q3.QuantityType = QuantityType.Drug;
q4.QuantityType = QuantityType.Drug;
A.CallTo(() => _keyPathMapper.MapFrom(q1)).Returns("KEY1");
A.CallTo(() => _keyPathMapper.MapFrom(q2)).Returns("KEY2");
A.CallTo(() => _keyPathMapper.MapFrom(q3)).Returns("KEY3");
A.CallTo(() => _keyPathMapper.MapFrom(q4)).Returns("KEY2");
A.CallTo(() => _keyPathMapper.MapFrom(moleculeSelection1)).Returns("KEY1");
A.CallTo(() => _keyPathMapper.MapFrom(moleculeSelection2)).Returns("KEY2");
A.CallTo(() => _keyPathMapper.MapFrom(moleculeSelection3)).Returns("DOES NOT EXIST");
A.CallTo(() => _entityPathResolver.PathFor(q1)).Returns("Q1");
A.CallTo(() => _entityPathResolver.PathFor(q2)).Returns("Q2");
A.CallTo(() => _entityPathResolver.PathFor(q3)).Returns("Q3");
A.CallTo(() => _entityPathResolver.PathFor(q4)).Returns("Q4");
_project.OutputSelections = _defaultSettings;
_userSettings.OutputSelections = null;
A.CallTo(() => _populationSimulationSettingsPresenter.CreateSettings(_populationSimulation)).Returns(_originalSettings);
A.CallTo(() => _populationSimulation.All <IQuantity>()).Returns(_allQuantities);
}
protected override void Context()
{
base.Context();
_defaultSettings = new OutputSelections();
_allQuantities = new List <IQuantity>();
var moleculeSelection1 = new QuantitySelection("PATH1", QuantityType.Drug);
_defaultSettings.AddOutput(moleculeSelection1);
_allQuantities.AddRange(new[] { _q1, _q2 });
_q1.QuantityType = QuantityType.Drug;
_q2.QuantityType = QuantityType.Transporter;
A.CallTo(() => _keyPathMapper.MapFrom(_q1)).Returns("KEY1");
A.CallTo(() => _keyPathMapper.MapFrom(_q2)).Returns("KEY1");
A.CallTo(() => _keyPathMapper.MapFrom(moleculeSelection1)).Returns("KEY1");
A.CallTo(() => _entityPathResolver.PathFor(_q1)).Returns("Q1");
_userSettings.OutputSelections = _defaultSettings;
A.CallTo(() => _populationSimulationSettingsPresenter.CreateSettings(_populationSimulation)).Returns(_originalSettings);
A.CallTo(() => _populationSimulation.All <IQuantity>()).Returns(_allQuantities);
}
protected override void Context()
{
_quantitySelection = new QuantitySelection("A|B", QuantityType.Drug);
_simulation = A.Fake <ISimulation>().WithName("S");
sut = new SimulationQuantitySelection(_simulation, _quantitySelection);
}
private static string moleculeNameFrom(QuantitySelection selectedQuantity)
{
return(selectedQuantity.Path.ToPathArray().MoleculeName());
}
protected override void Because()
{
_result = sut.SelectionFrom(_quantity);
}
public string MapFrom(QuantitySelection quantitySelection)
{
return(MapFrom(quantitySelection.Path, quantitySelection.QuantityType, removeFirstEntry: true).Path);
}
