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()
{
base.Context();
_simulation = A.Fake <ISimulation>().WithName("S");
_parameter1 = A.Fake <IParameter>();
_parameter2 = A.Fake <IParameter>();
_parameter1.Origin.SimulationId = "S";
_parameter2.Origin.SimulationId = "S";
A.CallTo(() => _withIdRepository.Get <ISimulation>(_parameter1.Origin.SimulationId)).Returns(_simulation);
A.CallTo(() => _withIdRepository.Get <ISimulation>(_parameter2.Origin.SimulationId)).Returns(_simulation);
A.CallTo(() => _parameterIdentificationFactory.Create()).Returns(new ParameterIdentification());
A.CallTo(() => _executionContext.Project).Returns(A.Fake <IProject>());
var parameterCache = new PathCacheForSpecs <IParameter> {
{ _parameterPath1, _parameter1 }, { _parameterPath2, _parameter2 }
};
A.CallTo(() => _entitiesInSimulationRetriever.ParametersFrom(_simulation)).Returns(parameterCache);
A.CallTo(() => _favoriteRepository.All()).Returns(new[] { _parameterPath1, _parameterPath2, });
A.CallTo(() => _entityPathResolver.PathFor(_parameter1)).Returns(_parameterPath1);
A.CallTo(() => _entityPathResolver.PathFor(_parameter2)).Returns(_parameterPath2);
A.CallTo(() => _parameterAnalysableParameterSelector.CanUseParameter(_parameter1)).Returns(true);
A.CallTo(() => _parameterAnalysableParameterSelector.CanUseParameter(_parameter2)).Returns(false);
_parameter1IdentificationParameter = new IdentificationParameter();
A.CallTo(() => _identificationParameterFactory.CreateFor(A <ParameterSelection> .That.Matches(x => x.Path == _parameterPath1), A <ParameterIdentification> ._)).Returns(_parameter1IdentificationParameter);
}
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);
}
protected override void Context()
{
base.Context();
_outputPath = "Liver|Cell|Drug";
_simulation = A.Fake <ISimulation>().WithId("Sim");
_parameterIdentification = new ParameterIdentification();
_output1 = A.Fake <IQuantity>();
var allOutputs = new PathCacheForSpecs <IQuantity> {
{ _outputPath, _output1 }
};
A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation)).Returns(allOutputs);
_observedData1 = DomainHelperForSpecs.ObservedData("OBS1");
_observedData2 = DomainHelperForSpecs.ObservedData("OBS2");
_observedData3 = DomainHelperForSpecs.ObservedData("OBS3");
A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation)).Returns(new[] { _observedData1, _observedData2 });
var simulationQuantitySelection = A.Fake <SimulationQuantitySelection>();
A.CallTo(() => simulationQuantitySelection.Path).Returns(_outputPath);
_parameterIdentification.AddOutputMapping(new OutputMapping {
WeightedObservedData = new WeightedObservedData(_observedData2), OutputSelection = simulationQuantitySelection
});
_observedData1.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.MOLECULE, Value = "Drug"
});
_observedData1.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.ORGAN, Value = "Liver"
});
_observedData1.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.COMPARTMENT, Value = "Cell"
});
_observedData3.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.ORGAN, Value = "Kidney"
});
}
