public IndividualMapper(IIndividualFactory individualFactory, IOriginDataMapper originDataMapper,
IIndividualMoleculeFactoryResolver moleculeFactoryResolver, IBatchLogger batchLogger)
{
_individualFactory = individualFactory;
_originDataMapper = originDataMapper;
_moleculeFactoryResolver = moleculeFactoryResolver;
_batchLogger = batchLogger;
}
public MoleculeExpressionTask(IExecutionContext executionContext,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
ISimulationSubjectExpressionTask <TSimulationSubject> simulationSubjectExpressionTask,
IExpressionProfileUpdater expressionProfileUpdater)
{
_executionContext = executionContext;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_simulationSubjectExpressionTask = simulationSubjectExpressionTask;
_expressionProfileUpdater = expressionProfileUpdater;
}
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);
}
public Converter9To10(
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IDefaultIndividualRetriever defaultIndividualRetriever,
IMoleculeExpressionTask <Individual> moleculeExpressionTask,
ICloner cloner,
Converter90To100 coreConverter90To100
)
{
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_defaultIndividualRetriever = defaultIndividualRetriever;
_moleculeExpressionTask = moleculeExpressionTask;
_cloner = cloner;
_coreConverter90To100 = coreConverter90To100;
}
public ExpressionProfileFactory(
ISpeciesRepository speciesRepository,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IPKSimObjectBaseFactory objectBaseFactory,
IIndividualFactory individualFactory,
IUsedExpressionProfileCategoryRepository usedExpressionProfileCategoryRepository
)
{
_speciesRepository = speciesRepository;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_objectBaseFactory = objectBaseFactory;
_individualFactory = individualFactory;
_usedExpressionProfileCategoryRepository = usedExpressionProfileCategoryRepository;
}
public MoleculeMapper(
ParameterMapper parameterMapper,
ExpressionContainerMapper expressionContainerMapper,
OntogenyMapper ontogenyMapper,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IExecutionContext executionContext,
IOntogenyTask <ModelIndividual> ontogenyTask,
IMoleculeParameterTask moleculeExpressionTask
) : base(parameterMapper)
{
_expressionContainerMapper = expressionContainerMapper;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_executionContext = executionContext;
_ontogenyTask = ontogenyTask;
_moleculeExpressionTask = moleculeExpressionTask;
_ontogenyMapper = ontogenyMapper;
}
protected override void Context()
{
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
A.CallTo(() => proteinFactory.AddMoleculeTo(_individual, A <string> ._)).Returns(_molecule);
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);
sut = new MoleculeExpressionTask <Individual>(
_executionContext,
_individualMoleculeFactoryResolver,
_subjectExpressionTask,
_expressionProfileUpdater
);
}
public MoleculeExpressionTask(IApplicationController applicationController, IExecutionContext executionContext,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IMoleculeToQueryExpressionSettingsMapper queryExpressionSettingsMapper,
IContainerTask containerTask,
IProteinExpressionsDatabasePathManager proteinExpressionsDatabasePathManager,
IOntogenyRepository ontogenyRepository,
ITransportContainerUpdater transportContainerUpdater,
ISimulationSubjectExpressionTask <TSimulationSubject> simulationSubjectExpressionTask,
IOntogenyTask <TSimulationSubject> ontogenyTask,
IMoleculeParameterTask moleculeParameterTask)
{
_applicationController = applicationController;
_executionContext = executionContext;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_queryExpressionSettingsMapper = queryExpressionSettingsMapper;
_containerTask = containerTask;
_proteinExpressionsDatabasePathManager = proteinExpressionsDatabasePathManager;
_ontogenyRepository = ontogenyRepository;
_transportContainerUpdater = transportContainerUpdater;
_simulationSubjectExpressionTask = simulationSubjectExpressionTask;
_ontogenyTask = ontogenyTask;
_moleculeParameterTask = moleculeParameterTask;
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionContainerMapper = A.Fake <ExpressionContainerMapper>();
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyMapper = A.Fake <OntogenyMapper>();
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
_individualMoleculeParametersTask = A.Fake <IMoleculeParameterTask>();
sut = new MoleculeMapper(_parameterMapper, _expressionContainerMapper,
_ontogenyMapper, _individualMoleculeFactoryResolver, _executionContext, _ontogenyTask, _individualMoleculeParametersTask);
_ontogeny = new DatabaseOntogeny
{
Name = "Ontogeny"
};
_enzyme = new IndividualEnzyme
{
Name = "Enzyme",
Description = "Help",
Ontogeny = _ontogeny,
};
_transporter = new IndividualTransporter
{
Name = "Transporter",
Description = "Help"
};
_otherProtein = new IndividualOtherProtein
{
Name = "OtherProtein",
Description = "Help"
};
_enzymeGlobalParameter = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: true).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_enzymeGlobalParameterSnapshot = new Parameter();
A.CallTo(() => _parameterMapper.MapToSnapshot(_enzymeGlobalParameter)).Returns(_enzymeGlobalParameterSnapshot);
_expressionContainer1 = new MoleculeExpressionContainer {
Name = "Exp Container1"
};
_expressionContainer2 = new MoleculeExpressionContainer {
Name = "Exp Container2"
};
_enzyme.AddChildren(_expressionContainer1, _expressionContainer2, _enzymeGlobalParameter);
_relativeExpressionParameter1 = DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameters.REL_EXP);
_relativeExpressionParameterNorm1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.REL_EXP_NORM);
_expressionContainer1.Add(_relativeExpressionParameter1);
_expressionContainer1.Add(_relativeExpressionParameterNorm1);
_relativeExpressionParameterNotSet = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP);
_relativeExpressionParameterNotSetNorm = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP_NORM);
_expressionContainer2.Add(_relativeExpressionParameterNotSet);
_expressionContainer2.Add(_relativeExpressionParameterNotSetNorm);
_relativeExpressionContainerSnapshot1 = new ExpressionContainer();
_relativeExpressionContainerSnapshot2 = new ExpressionContainer();
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer1)).Returns(_relativeExpressionContainerSnapshot1);
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer2)).Returns(_relativeExpressionContainerSnapshot2);
_snapshotOntogeny = new Snapshots.Ontogeny();
A.CallTo(() => _ontogenyMapper.MapToSnapshot(_ontogeny)).Returns(_snapshotOntogeny);
_individual = new Individual();
return(_completed);
}
