protected override void Context()
{
_moleculeParameterFactory = A.Fake <IMoleculeParameterRepository>();
_advancedParmeterFactory = A.Fake <IAdvancedParameterFactory>();
_advancedParametersTask = A.Fake <IAdvancedParametersTask>();
_executionContext = A.Fake <IExecutionContext>();
sut = new MoleculeParameterVariabilityCreator(_advancedParmeterFactory, _moleculeParameterFactory, _advancedParametersTask, _executionContext);
_randomPopulation = new RandomPopulation {
Settings = new RandomPopulationSettings()
};
_randomPopulation.SetAdvancedParameters(new AdvancedParameterCollection());
var individual = A.Fake <Individual>();
_molecule1 = DomainHelperForSpecs.DefaultIndividualMolecule().WithName("CYP1");
_molecule2 = DomainHelperForSpecs.DefaultIndividualMolecule().WithName("CYP2");
A.CallTo(() => individual.AllMolecules()).Returns(new[] { _molecule1, _molecule2 });
_randomPopulation.Settings.BaseIndividual = individual;
A.CallTo(() => _advancedParametersTask.AddAdvancedParameter(A <IAdvancedParameter> ._, _randomPopulation))
.Invokes(x =>
{
var advancedParameter = x.GetArgument <IAdvancedParameter>(0);
_randomPopulation.AddAdvancedParameter(advancedParameter);
})
.Returns(new AddAdvancedParameterToContainerCommand(A.Fake <IAdvancedParameter>(), _randomPopulation, _executionContext));
}
public MoleculeParameterVariabilityCreator(IAdvancedParameterFactory advancedParameterFactory, IMoleculeParameterRepository moleculeParameterRepository,
IAdvancedParametersTask advancedParametersTask, IExecutionContext executionContext)
{
_advancedParameterFactory = advancedParameterFactory;
_moleculeParameterRepository = moleculeParameterRepository;
_advancedParametersTask = advancedParametersTask;
_executionContext = executionContext;
}
protected override void Context()
{
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
sut = new MoleculeParameterTask(_moleculeParameterRepository);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE));
}
public MoleculeParameterTask(
IMoleculeParameterRepository moleculeParameterRepository,
ITransportContainerUpdater transportContainerUpdater,
IOntogenyRepository ontogenyRepository,
IOntogenyTask ontogenyTask)
{
_moleculeParameterRepository = moleculeParameterRepository;
_transportContainerUpdater = transportContainerUpdater;
_ontogenyRepository = ontogenyRepository;
_ontogenyTask = ontogenyTask;
}
public UsedMoleculeRepository(
IPKSimProjectRetriever projectRetriever,
IOntogenyRepository ontogenyRepository,
IMoleculeParameterRepository moleculeParameterRepository,
ITransporterContainerTemplateRepository transporterContainerTemplateRepository)
{
_projectRetriever = projectRetriever;
_ontogenyRepository = ontogenyRepository;
_moleculeParameterRepository = moleculeParameterRepository;
_transporterContainerTemplateRepository = transporterContainerTemplateRepository;
}
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()
{
_project = new PKSimProject();
_projectRetriever = A.Fake <IPKSimProjectRetriever>();
_transporterContainerTemplateRepository = A.Fake <ITransporterContainerTemplateRepository>();
A.CallTo(() => _projectRetriever.Current).Returns(_project);
_compound1 = A.Fake <Compound>();
_compound1.IsLoaded = false;
_compound2 = new Compound {
IsLoaded = true
};
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjA", Name = "P1"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjC", Name = "P2"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjB", Name = "P3"
});
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
_expressionProfile = A.Fake <ExpressionProfile>();
_expressionProfile.IsLoaded = true;
A.CallTo(() => _expressionProfile.MoleculeName).Returns("ProjE");
_project.AddBuildingBlock(_compound1);
_project.AddBuildingBlock(_compound2);
_project.AddBuildingBlock(_expressionProfile);
sut = new UsedMoleculeRepository(_projectRetriever, _ontogenyRepository, _moleculeParameterRepository, _transporterContainerTemplateRepository);
var molParam1 = new MoleculeParameter {
MoleculeName = "DbB"
};
var molParam2 = new MoleculeParameter {
MoleculeName = "DbA"
};
A.CallTo(() => _moleculeParameterRepository.All()).Returns(new[] { molParam1, molParam2 });
A.CallTo(() => _transporterContainerTemplateRepository.AllTransporterNames).Returns(new[] { "ATRANS1", "TRANS2" });
A.CallTo(() => _ontogenyRepository.AllFor(CoreConstants.Species.HUMAN)).Returns(new[] { new DatabaseOntogeny {
Name = "OntoC"
} });
}
public MoleculeExpressionTask(IApplicationController applicationController, IExecutionContext executionContext,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IMoleculeToQueryExpressionSettingsMapper queryExpressionSettingsMapper,
IContainerTask containerTask,
IProteinExpressionsDatabasePathManager proteinExpressionsDatabasePathManager,
IOntogenyRepository ontogenyRepository,
ITransportContainerUpdater transportContainerUpdater,
IMoleculeParameterRepository moleculeParameterRepository,
ISimulationSubjectExpressionTask <TSimulationSubject> simulationSubjectExpressionTask,
IOntogenyTask <TSimulationSubject> ontogenyTask)
{
_applicationController = applicationController;
_executionContext = executionContext;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_queryExpressionSettingsMapper = queryExpressionSettingsMapper;
_containerTask = containerTask;
_proteinExpressionsDatabasePathManager = proteinExpressionsDatabasePathManager;
_ontogenyRepository = ontogenyRepository;
_transportContainerUpdater = transportContainerUpdater;
_moleculeParameterRepository = moleculeParameterRepository;
_simulationSubjectExpressionTask = simulationSubjectExpressionTask;
_ontogenyTask = ontogenyTask;
}
public MoleculeParameterTask(IMoleculeParameterRepository moleculeParameterRepository)
{
_moleculeParameterRepository = moleculeParameterRepository;
}
