private void addDefaultOutputsFor(Simulation simulation, Compound compound, OutputSelections outputSelections)
{
var individual = simulation.Individual;
if (individual == null)
{
return;
}
//Default is peripheral venous blood plasma
var observer = peripheralVenousBloodObserverFor(simulation, compound);
if (speciesUsesVenousBlood(individual.Species))
{
observer = venousBloodObservedFor(simulation, compound);
}
if (observer == null)
{
return;
}
var observedPath = _entityPathResolver.PathFor(observer);
outputSelections.AddOutput(new QuantitySelection(observedPath, observer.QuantityType));
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <ISimulation>();
_runResults = A.Fake <SimulationResults>();
var outputSelections = new OutputSelections();
outputSelections.AddOutput(new QuantitySelection("Liver|Cell|Drug|Concentration", QuantityType.Drug));
A.CallTo(() => _simulation.OutputSelections).Returns(outputSelections);
var pKCalculationOptions = new PKCalculationOptions();
A.CallTo(_pkCalculationOptionsFactory).WithReturnType <PKCalculationOptions>().Returns(pKCalculationOptions);
_p1 = new PKParameter().WithName("AUC");
_p1.Mode = PKParameterMode.Single;
_p2 = new PKParameter().WithName("AUC" + Constants.PKParameters.NormSuffix);
_p2.Mode = PKParameterMode.Single;
A.CallTo(() => _pkParameterRepository.All()).Returns(new[] { _p1, _p2 });
var individualResults = A.Fake <IndividualResults>();
A.CallTo(() => _runResults.AllIndividualResults).Returns(new HashSet <IndividualResults>(new [] { individualResults }));
var pKValues = new PKValues();
pKValues.AddValue(_p1.Name, 10f);
pKValues.AddValue(_p2.Name, 20f);
A.CallTo(_pkValuesCalculator).WithReturnType <PKValues>().Returns(pKValues);
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <ISimulation>();
_runResults = A.Fake <SimulationResults>();
var outputSelections = new OutputSelections();
outputSelections.AddOutput(new QuantitySelection("Liver|Cell|Drug|Concentration", QuantityType.Drug));
A.CallTo(() => _simulation.OutputSelections).Returns(outputSelections);
var pKCalculationOptions = new PKCalculationOptions();
A.CallTo(_pkCalculationOptionsFactory).WithReturnType <PKCalculationOptions>().Returns(pKCalculationOptions);
_p1 = new PKParameter {
Name = "AUC", Mode = PKParameterMode.Single
};
_userDefinedParameter1 = new UserDefinedPKParameter {
Name = "Dynamic1", Mode = PKParameterMode.Single
};
A.CallTo(() => _pkParameterRepository.All()).Returns(new[] { _p1, _userDefinedParameter1 });
var individualResults = A.Fake <IndividualResults>();
A.CallTo(() => _runResults.AllIndividualResults).Returns(new HashSet <IndividualResults>(new[] { individualResults }));
var pKValues = new PKValues();
pKValues.AddValue(_p1.Name, 10f);
pKValues.AddValue(_userDefinedParameter1.Name, 30f);
A.CallTo(_pkValuesCalculator).WithReturnType <PKValues>().Returns(pKValues);
}
private void updateSettingsFromSelection()
{
_editedOutputSelections.Clear();
foreach (var quantitySelection in _quantitySelectionPresenter.SelectedQuantities())
{
_editedOutputSelections.AddOutput(quantitySelection);
}
}
private OutputSelections createOutputSelectionWithAllMoleculeAmountSelected()
{
var outputSelection = new OutputSelections();
foreach (var keyValue in _allMoleculeAmounts.KeyValues)
{
outputSelection.AddOutput(new QuantitySelection(keyValue.Key, keyValue.Value.QuantityType));
}
return(outputSelection);
}
protected override Task Context()
{
_entitiesInContainerRetriever = A.Fake <IEntitiesInContainerRetriever>();
_logger = A.Fake <IOSPSuiteLogger>();
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();
_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);
}
public void TestSerialization()
{
var schema = new OutputSchema();
var interval = new OutputInterval();
var quantitySelection = new OutputSelections();
var solverSettingsFactory = IoC.Resolve <ISolverSettingsFactory>();
var x1 = new SimulationSettings {
Solver = solverSettingsFactory.CreateCVODE(), OutputSchema = schema, OutputSelections = quantitySelection
};
interval.Add(CreateObject <Parameter>().WithName(Constants.Parameters.START_TIME).WithFormula(new ConstantFormula(0)));
interval.Add(CreateObject <Parameter>().WithName(Constants.Parameters.END_TIME).WithFormula(new ConstantFormula(1440)));
interval.Add(CreateObject <Parameter>().WithName(Constants.Parameters.RESOLUTION).WithFormula(new ConstantFormula(240)));
quantitySelection.AddOutput(new QuantitySelection("A|B|C", QuantityType.Protein));
quantitySelection.AddOutput(new QuantitySelection("A|B", QuantityType.Enzyme));
var x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualSimulationSettings(x2, x1);
}
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();
_outputSelections = new OutputSelections();
_outputSelections.AddOutput(new QuantitySelection("A", QuantityType.Drug));
_newOutputSelection = new OutputSelections();
_newOutputSelection.AddOutput(new QuantitySelection("B", QuantityType.Drug));
_simulation = A.Fake <IMoBiSimulation>();
A.CallTo(() => _simulation.OutputSelections).Returns(_outputSelections);
A.CallTo(() => _outputSelectionsRetriever.OutputSelectionsFor(_simulation)).Returns(_newOutputSelection);
}
protected override void Context()
{
_dataFactory = A.Fake <IDataRepositoryTask>();
_dimensionRepository = A.Fake <IDimensionRepository>();
sut = new DataRepositoryFromResultsCreator(
_dimensionRepository, new ObjectPathFactoryForSpecs(), _dataFactory);
_simulation = new IndividualSimulation().WithName("S");
_simulation.Model = new OSPSuite.Core.Domain.Model();
var root = new Container().WithContainerType(ContainerType.Simulation).WithName(_simulation.Name);
_simulation.Model.Root = root;
var liver = new Container().WithName("LIVER");
liver.Add(new Observer().WithName("C"));
var kidney = new Container().WithName("KIDNEY");
kidney.Add(new Observer().WithName("C"));
root.Add(liver);
root.Add(kidney);
_simulationResults = new SimulationResults();
_simulation.Results = _simulationResults;
_timeValues = new QuantityValues {
QuantityPath = "Time", Values = new[] { 1f, 2f, 3f }
};
_simulationResults.Time = _timeValues;
_individualResults = new IndividualResults();
_individualResults.Add(new QuantityValues {
QuantityPath = "LIVER|C", Time = _timeValues, Values = new[] { 10f, 20f, 30f }
});
_individualResults.Add(new QuantityValues {
QuantityPath = "KIDNEY|C", Time = _timeValues, Values = new[] { 11f, 22f, 33f }
});
_outputSelection = new OutputSelections();
_outputSelection.AddOutput(new QuantitySelection(new[] { "LIVER", "C" }.ToPathString(), QuantityType.Molecule));
_simulation.SimulationSettings = new SimulationSettings();
_simulation.SimulationSettings.OutputSelections = _outputSelection;
}
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();
var dimension = A.Fake <IDimension>();
_outputSelection = new OutputSelections();
_simulation = new IndividualSimulation {
SimulationSettings = new SimulationSettings {
OutputSelections = _outputSelection
}
};
_compound = A.Fake <Compound>();
A.CallTo(() => _compound.Name).Returns("Drug");
A.CallTo(() => _compound.MolWeight).Returns(20);
_dataRepository = new DataRepository();
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("toto", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_newBaseGrid = new BaseGrid("baseGrid1", "baseGrid1", dimension);
_newColumn = new DataColumn("col1", "col1", dimension, _newBaseGrid)
{
QuantityInfo = new QuantityInfo("Obs", new List <string> {
"Sim", "Liver", "Cell", "Drug", "Obs"
}, QuantityType.Observer | QuantityType.Drug)
};
_otherColumn = new DataColumn("col2", "col2", dimension, _newBaseGrid)
{
QuantityInfo = new QuantityInfo("Obs", new List <string> {
"Sim", "Liver", "Cell", "Sp1", "Obs"
}, QuantityType.Observer | QuantityType.Metabolite)
};
_dataRepository.Add(_newBaseGrid);
_dataRepository.Add(_newColumn);
_dataRepository.Add(_otherColumn);
_simulationResults = A.Fake <SimulationResults>();
A.CallTo(() => _simulationResultsCreator.CreateResultsFrom(_dataRepository)).Returns(_simulationResults);
_outputSelection.AddOutput(new QuantitySelection(new[] { "Liver", "Cell", "Drug", "Obs" }.ToPathString(), _newColumn.QuantityInfo.Type));
}
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()
{
base.Context();
_simulation = new MoBiSimulation();
_simModelManager = A.Fake <ISimModelManager>();
_outputSelections = new OutputSelections();
_drug = new MoleculeBuilder().WithName("DRUG");
_drug.AddParameter(new Parameter().WithName(AppConstants.Parameters.MOLECULAR_WEIGHT).WithFormula(new ConstantFormula(400)));
_outputSelections.AddOutput(new QuantitySelection("A", QuantityType.Drug));
_simulation.BuildConfiguration = new MoBiBuildConfiguration
{
SimulationSettings = new SimulationSettings
{
OutputSelections = _outputSelections
},
Molecules = new MoleculeBuildingBlock
{
_drug
}
};
A.CallTo(() => _simModelManagerFactory.Create()).Returns(_simModelManager);
_oldResults = new DataRepository("OLD");
_simulation.Results = _oldResults;
_newResults = new DataRepository("NEW");
_simulationResults = new SimulationRunResults(success: true, warnings: Enumerable.Empty <SolverWarning>(), results: _newResults);
A.CallTo(() => _simModelManager.RunSimulation(_simulation)).Returns(_simulationResults);
var baseGrid = new BaseGrid("Time", DomainHelperForSpecs.TimeDimension);
_concentrationColumn = new DataColumn("Drug", DomainHelperForSpecs.ConcentrationDimension, baseGrid);
_fractionColumn = new DataColumn("Fraction", DomainHelperForSpecs.FractionDimension, baseGrid);
_newResults.Add(_concentrationColumn);
_newResults.Add(_fractionColumn);
A.CallTo(() => _keyPathMapper.MoleculeNameFrom(_concentrationColumn)).Returns(_drug.Name);
}
