protected override void Context()
{
base.Context();
_quantityValue1 = new QuantityValues {
QuantityPath = "Path1"
};
_quantityValue2 = new QuantityValues {
QuantityPath = "Path1"
};
_anotherQuantityValue = new QuantityValues {
QuantityPath = "Path2"
};
var individualResults1 = new IndividualResults {
IndividualId = 3
};
individualResults1.Add(_quantityValue1);
individualResults1.Add(_anotherQuantityValue);
var individualResults2 = new IndividualResults {
IndividualId = 2
};
individualResults2.Add(_quantityValue2);
sut.Add(individualResults1);
sut.Add(individualResults2);
//reorder results before accessing them
sut.ReorderByIndividualId();
}
protected override void Context()
{
base.Context();
_newName = "TOTO";
_f1 = new ExplicitFormula("A+B");
_f2 = new ExplicitFormula("A+B");
_f3 = new ExplicitFormula("A+B");
_f1.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f1.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f2.AddObjectPath(new FormulaUsablePath("SU", "Liver", "Cell"));
_f2.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "LogP"));
var p1 = new PKSimParameter().WithName("P1").WithFormula(_f1);
var p2 = new PKSimParameter().WithName("P2").WithFormula(_f2);
var p3 = new PKSimParameter().WithName("P3").WithFormula(_f3);
var c1 = new Container().WithName("C1");
c1.Add(p3);
_root.Add(p1);
_root.Add(p2);
_root.Add(c1);
var results = new SimulationResults {
Time = new QuantityValues {
ColumnId = "0", QuantityPath = "baseGrid"
}
};
_individualResults = new IndividualResults {
IndividualId = 1
};
results.Add(_individualResults);
var quantityCache = new PathCacheForSpecs <IQuantity>
{
{ "Liver|Cell|Drug", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "Liver|Cell|Meta", new MoleculeAmount {
QuantityType = QuantityType.Metabolite
} },
};
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Drug" }.ToList()
});
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Meta" }.ToList()
});
_individualSimulation.Results = results;
_individualSimulation.DataRepository = new DataRepository();
_individualSimulation.Reactions = new ReactionBuildingBlock();
_individualSimulation.SimulationSettings = new SimulationSettings();
A.CallTo(_containerTask).WithReturnType <PathCache <IQuantity> >().Returns(quantityCache);
A.CallTo(() => _curveNamer.RenameCurvesWithOriginalNames(_individualSimulation, A <Action> ._, true)).Invokes(x => x.Arguments[1].DowncastTo <Action>()());
}
protected override void Context()
{
_dataFactory = A.Fake <IDataFactory>();
_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 }
});
}
protected override void Context()
{
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_pkValuesCalculator = A.Fake <IPKValuesCalculator>();
_pkParameterRepository = A.Fake <IPKParameterRepository>();
_pkCalculationOptionsFactory = A.Fake <IPKCalculationOptionsFactory>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_pkMapper = A.Fake <IPKValuesToPKAnalysisMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
sut = new PKAnalysesTask(_lazyLoadTask, _pkValuesCalculator, _pkParameterRepository, _pkCalculationOptionsFactory, _entityPathResolver, _pkMapper, _dimensionRepository);
_populationSimulation = A.Fake <PopulationSimulation>();
_outputSelections = new OutputSelections();
A.CallTo(() => _populationSimulation.OutputSelections).Returns(_outputSelections);
_allBodyWeights = new List <double>();
_bodyWeight = A.Fake <IParameter>();
var bodyWeightPath = "PATH";
A.CallTo(() => _populationSimulation.BodyWeight).Returns(_bodyWeight);
A.CallTo(() => _entityPathResolver.PathFor(_bodyWeight)).Returns(bodyWeightPath);
A.CallTo(() => _populationSimulation.AllValuesFor(bodyWeightPath)).Returns(_allBodyWeights);
A.CallTo(() => _populationSimulation.NumberOfItems).Returns(2);
_individualResult0 = new IndividualResults {
IndividualId = 0, Time = new QuantityValues {
Values = new[] { 1f, 2f }
}
};
_individualResult0.Add(new QuantityValues {
QuantityPath = _quantityPath1, Values = new[] { 10f, 20f }
});
_individualResult0.Add(new QuantityValues {
QuantityPath = _quantityPath2, Values = new[] { 11f, 21f }
});
_individualResult1 = new IndividualResults {
IndividualId = 1, Time = new QuantityValues {
Values = new[] { 3f, 4f }
}
};
_individualResult1.Add(new QuantityValues {
QuantityPath = _quantityPath1, Values = new[] { 30f, 40f }
});
_individualResult1.Add(new QuantityValues {
QuantityPath = _quantityPath2, Values = new[] { 31f, 41f }
});
_simulationResults = new SimulationResults {
_individualResult0, _individualResult1
};
_populationSimulation.Results = _simulationResults;
_pkParameter1 = new PKParameter {
Mode = PKParameterMode.Always, Name = "Cmax"
};
_pkParameter2 = new PKParameter {
Mode = PKParameterMode.Always, Name = "tMax"
};
A.CallTo(() => _pkParameterRepository.All()).Returns(new[] { _pkParameter1, _pkParameter2 });
}
protected override void Context()
{
base.Context();
_newName = "TOTO";
_f1 = new ExplicitFormula("A+B");
_f2 = new ExplicitFormula("A+B");
_f3 = new ExplicitFormula("A+B");
_f1.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f1.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f2.AddObjectPath(new FormulaUsablePath("SU", "Liver", "Cell"));
_f2.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "LogP"));
var p1 = new PKSimParameter().WithName("P1").WithFormula(_f1);
var p2 = new PKSimParameter().WithName("P2").WithFormula(_f2);
var p3 = new PKSimParameter().WithName("P3").WithFormula(_f3);
var c1 = new Container().WithName("C1");
c1.Add(p3);
_root.Add(p1);
_root.Add(p2);
_root.Add(c1);
var results = new SimulationResults {
Time = new QuantityValues {
ColumnId = "0", QuantityPath = "baseGrid"
}
};
_individualResults = new IndividualResults {
IndividualId = 1
};
results.Add(_individualResults);
var quantityCache = new PathCacheForSpecs <IQuantity>
{
{ "Liver|Cell|Drug", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "Liver|Cell|Meta", new MoleculeAmount {
QuantityType = QuantityType.Metabolite
} },
};
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Drug" }.ToList()
});
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Meta" }.ToList()
});
_individualSimulation.Results = results;
A.CallTo(_containerTask).WithReturnType <PathCache <IQuantity> >().Returns(quantityCache);
}
public SimulationResults CreateResultsFrom(DataRepository dataRepository)
{
if (dataRepository.IsNull())
{
return(new NullSimulationResults());
}
var results = new SimulationResults();
var baseGrid = dataRepository.BaseGrid;
results.Time = valuesFrom(baseGrid);
foreach (var columnsForIndividual in dataRepository.AllButBaseGrid().GroupBy(selectIndividualIndex))
{
var individualResults = new IndividualResults {
IndividualId = columnsForIndividual.Key, Time = results.Time
};
foreach (var dataColumn in columnsForIndividual)
{
individualResults.Add(valuesFrom(dataColumn, pathWithoutIndividualIndex(dataColumn, columnsForIndividual.Key)));
}
individualResults.UpdateQuantityTimeReference();
results.Add(individualResults);
}
return(results);
}
protected override void Context()
{
base.Context();
var quantityValue1 = new QuantityValues {
QuantityPath = "Path1"
};
var quantityValue2 = new QuantityValues {
QuantityPath = "Path1"
};
var individualResults1 = new IndividualResults {
IndividualId = 1
};
individualResults1.Add(quantityValue1);
var individualResults2 = new IndividualResults {
IndividualId = 2
};
individualResults2.Add(quantityValue2);
sut.Time = new QuantityValues {
QuantityPath = "Time"
};
individualResults1.Time = sut.Time;
individualResults2.Time = sut.Time;
sut.AddRange(new[] { individualResults1, individualResults2 });
}
private SimulationResults createResultsFrom(DataRepository dataRepository, ISimModelBatch simModel, string[] parameters)
{
if (dataRepository.IsNull() || dataRepository.BaseGrid == null)
{
return(new NullSimulationResults());
}
var results = new SimulationResults {
Time = valuesFrom(dataRepository.BaseGrid, null, new string[] { })
};
foreach (var columnsForIndividual in dataRepository.AllButBaseGrid().GroupBy(selectIndividualIndex))
{
var individualResults = new IndividualResults {
IndividualId = columnsForIndividual.Key, Time = results.Time
};
foreach (var dataColumn in columnsForIndividual)
{
individualResults.Add(valuesFrom(dataColumn, pathWithoutIndividualIndex(dataColumn, columnsForIndividual.Key), simModel, parameters));
}
individualResults.UpdateQuantityTimeReference();
results.Add(individualResults);
}
return(results);
}
protected override void Context()
{
base.Context();
_quantityValue1 = new QuantityValues {
QuantityPath = "Path1"
};
_quantityValue2 = new QuantityValues {
QuantityPath = "Path2"
};
var individualResults1 = new IndividualResults {
IndividualId = 1
};
individualResults1.Add(_quantityValue1);
individualResults1.Add(_quantityValue2);
sut.Add(individualResults1);
}
private static IndividualResults newIndividualResults(int indIndex, int numberOfPaths, int numberOfPoints)
{
var ind = new IndividualResults {
IndividualId = indIndex
};
for (int i = 0; i < numberOfPaths; i++)
{
ind.Add(createValuesArray(i, numberOfPoints));
}
return(ind);
}
private QuantityValues quantityPathFor(IndividualResults individualResult, string path, Cache <QuantityValues, List <float> > cacheQuantitiesValues)
{
var quantity = individualResult.ValuesFor(path);
if (quantity == null)
{
quantity = new QuantityValues {
QuantityPath = path
};
cacheQuantitiesValues.Add(quantity, new List <float>());
individualResult.Add(quantity);
}
return(quantity);
}
protected override void Context()
{
base.Context();
var results = new SimulationResults {
Time = new QuantityValues {
ColumnId = "0", QuantityPath = "baseGrid"
}
};
_individualResults = new IndividualResults {
IndividualId = 1
};
results.Add(_individualResults);
_quantityCache = new PathCacheForSpecs <IQuantity>
{
{ "C|Liver|Cell|C2", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "C|Liver|Cell|Meta", new MoleculeAmount {
QuantityType = QuantityType.Metabolite
} }
};
_individualResults.Add(new QuantityValues {
ColumnId = "1", PathList = new[] { "C", "Liver", "Cell", "C" }.ToList()
});
_individualResults.Add(new QuantityValues {
ColumnId = "3", PathList = new[] { "C", "Liver", "Cell", "Meta" }.ToList()
});
_individualResults.Add(new QuantityValues {
ColumnId = "4", PathList = new[] { "S", "Liver", "Cell" }.ToList()
});
A.CallTo(_containerTask).WithReturnType <PathCache <IQuantity> >().Returns(_quantityCache);
_individualSimulation.Results = results;
}
protected override void Context()
{
base.Context();
_quantityValue1 = new QuantityValues {
QuantityPath = "Path1", Values = new [] { 1f, 2f, 3f }
};
_quantityValue2 = new QuantityValues {
QuantityPath = "Path1", Values = new[] { 4f, 5f, 6f }
};
_anotherQuantityValue = new QuantityValues {
QuantityPath = "Path2", Values = new[] { 7f, 8f, 9f }
};
_timeValues = new QuantityValues {
QuantityPath = "Time", Values = new[] { 10f, 20f, 30f }
};
var individualResults1 = new IndividualResults {
IndividualId = 3
};
individualResults1.Add(_quantityValue1);
individualResults1.Add(_anotherQuantityValue);
var individualResults2 = new IndividualResults {
IndividualId = 2
};
individualResults2.Add(_quantityValue2);
sut.Add(individualResults1);
sut.Add(individualResults2);
sut.Time = _timeValues;
//reorder results before accessing them
sut.ReorderByIndividualId();
}
/// <summary>
/// Get Results from SimModel
/// </summary>
/// <param name="simulation">SimModel simulation</param>
/// <param name="individualId">Individual id</param>
private IndividualResults individualResultsFrom(SimModelNET.ISimulation simulation, int individualId)
{
var results = new IndividualResults {
IndividualId = individualId
};
var simulationTimes = simulation.SimulationTimes;
var simulationTimesLength = simulationTimes.Length;
foreach (var result in simulation.AllValues)
{
//Add quantity name and remove simulation name
var quantityPath = _objectPathFactory.CreateObjectPathFrom(result.Path.ToPathArray());
quantityPath.Remove(_simulationName);
results.Add(quantityValuesFor(quantityPath.ToString(), result, simulationTimesLength));
}
results.Time = quantityValuesFor(Constants.TIME, simulation.SimulationTimes);
return(results);
}
protected override void Context()
{
base.Context();
_pkParameter1 = new QuantityPKParameter {
QuantityPath = "Output1", Name = "AUC"
};
_pkParameter1.SetValue(0, 10);
_pkParameter1.SetValue(1, 11);
_pkParameter1.SetValue(2, 12);
_pkParameter1.SetValue(4, _defaultPK1Value);
_pkParameter2 = new QuantityPKParameter {
QuantityPath = "Output2", Name = "Cmax"
};
_pkParameter2.SetValue(0, 20);
_pkParameter2.SetValue(1, 21);
_pkParameter2.SetValue(2, 22);
_pkParameter2.SetValue(3, 23);
_pkParameter2.SetValue(4, _defaultPK2Value);
_pkAnalyses.AddPKAnalysis(_pkParameter1);
_pkAnalyses.AddPKAnalysis(_pkParameter2);
_sensitivityParameter1 = A.Fake <SensitivityParameter>().WithName("SP1");
A.CallTo(() => _sensitivityParameter1.DefaultValue).Returns(10);
A.CallTo(() => _sensitivityParameter1.ParameterSelection.Path).Returns("SP1-PATH");
_sensitivityParameter2 = A.Fake <SensitivityParameter>().WithName("SP2");
A.CallTo(() => _sensitivityParameter2.DefaultValue).Returns(20);
A.CallTo(() => _sensitivityParameter2.ParameterSelection.Path).Returns("SP2-PATH");
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter1);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter2);
var pv11 = new ParameterVariation(parameterName: _sensitivityParameter1.Name, parameterIndex: 0, variationId: 0, variation: new[] { 15d, 200d, 300d });
var pv12 = new ParameterVariation(parameterName: _sensitivityParameter1.Name, parameterIndex: 0, variationId: 1, variation: new[] { 20d, 200d, 300d });
var pv21 = new ParameterVariation(parameterName: _sensitivityParameter2.Name, parameterIndex: 1, variationId: 2, variation: new[] { 100d, 21d, 300d });
var pv22 = new ParameterVariation(parameterName: _sensitivityParameter2.Name, parameterIndex: 1, variationId: 3, variation: new[] { 100d, 31d, 300d });
_variationData.DefaultValues = new[] { 100d, 200d, 300d };
_variationData.AddVariation(pv11);
_variationData.AddVariation(pv12);
_variationData.AddVariation(pv21);
_variationData.AddVariation(pv22);
_timeValues = new QuantityValues {
QuantityPath = "Time", Values = new[] { 1, 2, 3, 4, 5f }
};
_resV11 = new IndividualResults {
IndividualId = 0, Time = _timeValues
};
_resV11.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 111.1f, 211.1f, 311.1f, 411.1f, 511.1f }
});
_resV11.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 111.2f, 211.2f, 311.2f, 411.2f, 511.2f }
});
_resV11.UpdateQuantityTimeReference();
_resV12 = new IndividualResults {
IndividualId = 1, Time = _timeValues
};
_resV12.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 112.1f, 212.1f, 312.1f, 412.1f, 512.1f }
});
_resV12.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 112.2f, 212.2f, 312.2f, 412.2f, 512.2f }
});
_resV12.UpdateQuantityTimeReference();
_resV21 = new IndividualResults {
IndividualId = 2, Time = _timeValues
};
_resV21.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 121.1f, 221.1f, 321.1f, 421.1f, 521.1f }
});
_resV21.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 121.2f, 221.2f, 321.2f, 421.2f, 521.2f }
});
_resV21.UpdateQuantityTimeReference();
_resV22 = new IndividualResults {
IndividualId = 3, Time = _timeValues
};
_resV22.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 122.1f, 222.1f, 322.1f, 422.1f, 522.1f }
});
_resV22.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 122.2f, 222.2f, 322.2f, 422.2f, 522.2f }
});
_resV22.UpdateQuantityTimeReference();
_simulationResults.Add(_resV11);
_simulationResults.Add(_resV12);
_simulationResults.Add(_resV21);
_simulationResults.Add(_resV22);
}