public DistributedParameterToTableParameterConverter(
IFormulaFactory formulaFactory,
IEntityPathResolver entityPathResolver,
IParameterFactory parameterFactory,
ICloneManager cloneManager,
IParameterQuery parameterQuery,
IDimensionRepository dimensionRepository,
IOntogenyRepository ontogenyRepository,
IFullPathDisplayResolver fullPathDisplayResolver,
IInterpolation interpolation,
IParameterStartValuesCreator parameterStartValuesCreator,
IObjectPathFactory objectPathFactory,
IGenderRepository genderRepository)
{
_formulaFactory = formulaFactory;
_entityPathResolver = entityPathResolver;
_parameterFactory = parameterFactory;
_cloneManager = cloneManager;
_parameterQuery = parameterQuery;
_dimensionRepository = dimensionRepository;
_ontogenyRepository = ontogenyRepository;
_fullPathDisplayResolver = fullPathDisplayResolver;
_interpolation = interpolation;
_parameterStartValuesCreator = parameterStartValuesCreator;
_objectPathFactory = objectPathFactory;
_genderRepository = genderRepository;
_timeDimension = dimensionRepository.Time;
_yearUnit = _timeDimension.Unit(dimensionRepository.AgeInYears.BaseUnit.Name);
}
public MatlabPopulationFactory(IMatlabPopulationSettingsToPopulationSettingsMapper populationSettingsMapper, IRandomPopulationFactory randomPopulationFactory,
IOntogenyRepository ontogenyRepository, IMoleculeOntogenyVariabilityUpdater ontogenyVariabilityUpdater, IIndividualEnzymeFactory individualEnzymeFactory)
{
_populationSettingsMapper = populationSettingsMapper;
_randomPopulationFactory = randomPopulationFactory;
_ontogenyRepository = ontogenyRepository;
_ontogenyVariabilityUpdater = ontogenyVariabilityUpdater;
_individualEnzymeFactory = individualEnzymeFactory;
}
protected override void Context()
{
_context = A.Fake <IExecutionContext>();
_applicationController = A.Fake <IApplicationController>();
_dataImporter = A.Fake <IDataImporter>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_entityTask = A.Fake <IEntityTask>();
_formulaFactory = A.Fake <IFormulaFactory>();
sut = new IndividualOntogenyTask(_context, _applicationController, _dataImporter, _dimensionRepository, _ontogenyRepository, _entityTask, _formulaFactory);
}
public MoleculeParameterTask(
IMoleculeParameterRepository moleculeParameterRepository,
ITransportContainerUpdater transportContainerUpdater,
IOntogenyRepository ontogenyRepository,
IOntogenyTask ontogenyTask)
{
_moleculeParameterRepository = moleculeParameterRepository;
_transportContainerUpdater = transportContainerUpdater;
_ontogenyRepository = ontogenyRepository;
_ontogenyTask = ontogenyTask;
}
public ShowOntogenyDataPresenter(IShowOntogenyDataView view, IOntogenyRepository ontogenyRepository,
ISimpleChartPresenter simpleChartPresenter, IDimensionRepository dimensionRepository,
IGroupRepository groupRepository, IDisplayUnitRetriever displayUnitRetriever) : base(view)
{
_ontogenyRepository = ontogenyRepository;
_simpleChartPresenter = simpleChartPresenter;
_dimensionRepository = dimensionRepository;
_groupRepository = groupRepository;
_displayUnitRetriever = displayUnitRetriever;
_view.AddChart(_simpleChartPresenter.View);
}
protected override void Context()
{
_view = A.Fake <IOntogenySelectionView>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
_commandRegister = A.Fake <ICommandCollector>();
_allOntogenies = new List <Ontogeny>();
A.CallTo(() => _ontogenyRepository.AllFor(CoreConstants.Species.Human)).Returns(_allOntogenies);
sut = new OntogenySelectionPresenter <Individual>(_view, _ontogenyRepository, _ontogenyTask);
sut.InitializeWith(_commandRegister);
}
public OntogenyTask(IExecutionContext executionContext, IApplicationController applicationController, IDataImporter dataImporter,
IDimensionRepository dimensionRepository, IOntogenyRepository ontogenyRepository, IEntityTask entityTask, IFormulaFactory formulaFactory)
{
_executionContext = executionContext;
_applicationController = applicationController;
_dataImporter = dataImporter;
_dimensionRepository = dimensionRepository;
_ontogenyRepository = ontogenyRepository;
_entityTask = entityTask;
_formulaFactory = formulaFactory;
}
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()
{
_molecule = new IndividualEnzyme
{
DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.ONTOGENY_FACTOR),
DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.ONTOGENY_FACTOR_GI)
};
_ontogeny = new DatabaseOntogeny();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_entityPathResolver = new EntityPathResolverForSpecs();
sut = new MoleculeOntogenyVariabilityUpdater(_ontogenyRepository, _entityPathResolver);
}
protected override void Context()
{
_view = A.Fake <IShowOntogenyDataView>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_simpleChartPresenter = A.Fake <ISimpleChartPresenter>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_groupRepository = A.Fake <IGroupRepository>();
_displayUnitRetriever = A.Fake <IDisplayUnitRetriever>();
_groupLiver = new Group {
Name = "Liver"
};
_groupDuodenum = new Group {
Name = "Duodenum"
};
_tableFormula = new TableFormula();
_ontogeny = new DatabaseOntogeny {
SpeciesName = "toto"
};
_anotherOntogeny = new DatabaseOntogeny {
SpeciesName = "toto"
};
_allOntongies = new List <Ontogeny> {
_ontogeny, _anotherOntogeny
};
_ontoData = new List <OntogenyMetaData>();
_ontoData.Add(new OntogenyMetaData {
GroupName = "Liver"
});
_ontoData.Add(new OntogenyMetaData {
GroupName = "Duodenum"
});
_allMetaData = new List <OntogenyMetaData>();
A.CallTo(() => _dimensionRepository.AgeInYears).Returns(A.Fake <IDimension>());
A.CallTo(() => _dimensionRepository.Fraction).Returns(DomainHelperForSpecs.FractionDimensionForSpecs());
A.CallTo(() => _simpleChartPresenter.Plot(A <TableFormula> ._)).Returns(new CurveChart().WithAxes());
A.CallTo(() => _simpleChartPresenter.Plot(A <DataRepository> ._, Scalings.Linear)).Returns(new CurveChart().WithAxes());
A.CallTo(() => _groupRepository.GroupByName("Liver")).Returns(_groupLiver);
A.CallTo(() => _groupRepository.GroupByName("Duodenum")).Returns(_groupDuodenum);
A.CallTo(() => _ontogenyRepository.AllValuesFor(_ontogeny)).Returns(_ontoData);
A.CallTo(() => _ontogenyRepository.AllFor(_ontogeny.SpeciesName)).Returns(_allOntongies);
A.CallTo(() => _ontogenyRepository.AllValuesFor(_ontogeny, _groupLiver.Name)).Returns(_allMetaData);
sut = new ShowOntogenyDataPresenter(_view, _ontogenyRepository, _simpleChartPresenter, _dimensionRepository, _groupRepository, _displayUnitRetriever);
A.CallTo(() => _view.BindTo(A <ShowOntogenyDataDTO> ._))
.Invokes(x => ShowOntogenyDataDTO = x.GetArgument <ShowOntogenyDataDTO>(0));
}
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"
} });
}
protected override void Context()
{
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_ontogenyTask = A.Fake <IOntogenyTask>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
sut = new MoleculeParameterTask(_moleculeParameterRepository, _transportContainerUpdater, _ontogenyRepository, _ontogenyTask);
_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));
}
protected override Task Context()
{
_distributedTableFormulaMapper = A.Fake <DistributedTableFormulaMapper>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
sut = new OntogenyMapper(_distributedTableFormulaMapper, _ontogenyRepository);
_distributedTableFormula = new DistributedTableFormula();
_snapshotTable = new Snapshots.DistributedTableFormula();
A.CallTo(() => _distributedTableFormulaMapper.MapToSnapshot(_distributedTableFormula)).Returns(_snapshotTable);
_simulationSubject = A.Fake <ISimulationSubject>();
return(Task.FromResult(true));
}
public override void GlobalContext()
{
base.GlobalContext();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_moleculeExpressionTask = IoC.Resolve <IMoleculeExpressionTask <Individual> >();
_ontogenyRepository = IoC.Resolve <IOntogenyRepository>();
_expressionProfileForEnzyme = DomainFactoryForSpecs.CreateExpressionProfile <IndividualEnzyme>();
_moleculeExpressionTask.AddExpressionProfile(_individual, _expressionProfileForEnzyme);
_individualEnzyme = _individual.MoleculeByName <IndividualEnzyme>(_expressionProfileForEnzyme.MoleculeName);
_expressionProfileEnzyme = _expressionProfileForEnzyme.Molecule.DowncastTo <IndividualEnzyme>();
_expressionProfileForTransporter = DomainFactoryForSpecs.CreateExpressionProfile <IndividualTransporter>(moleculeName: "TRANS");
_moleculeExpressionTask.AddExpressionProfile(_individual, _expressionProfileForTransporter);
_individualTransporter = _individual.MoleculeByName <IndividualTransporter>(_expressionProfileForTransporter.MoleculeName);
_expressionProfileTransporter = _expressionProfileForTransporter.Molecule.DowncastTo <IndividualTransporter>();
}
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;
}
public OntogenySelectionPresenter(IOntogenySelectionView view, IOntogenyRepository ontogenyRepository, IOntogenyTask <TSimulationSubject> ontogenyTask)
: base(view)
{
_ontogenyTask = ontogenyTask;
_allOntogenies = ontogenyRepository.AllFor(CoreConstants.Species.Human);
}
public OntogenySelectionPresenter(IOntogenySelectionView view, IOntogenyRepository ontogenyRepository, IOntogenyTask ontogenyTask)
: base(view)
{
_ontogenyTask = ontogenyTask;
_allOntogenies = ontogenyRepository.AllFor(CoreConstants.Species.HUMAN);
}
public MoleculeOntogenyVariabilityUpdater(IOntogenyRepository ontogenyRepository, IEntityPathResolver entityPathResolver)
{
_ontogenyRepository = ontogenyRepository;
_entityPathResolver = entityPathResolver;
}
public OntogenyFactorsRetriever(IOntogenyRepository ontogenyRepository)
{
_ontogenyRepository = ontogenyRepository;
}
public IndividualOntogenyTask(IExecutionContext executionContext, IApplicationController applicationController, IDataImporter dataImporter, IDimensionRepository dimensionRepository, IOntogenyRepository ontogenyRepository, IEntityTask entityTask, IFormulaFactory formulaFactory) : base(executionContext, applicationController, dataImporter, dimensionRepository, ontogenyRepository, entityTask, formulaFactory)
{
}
protected override void Context()
{
_ontogenyRepository = A.Fake <IOntogenyRepository>();
sut = new OntogenyFactorsRetriever(_ontogenyRepository);
_moleculeNames = new List <MoleculeOntogeny>();
}
public OntogenyMapper(DistributedTableFormulaMapper distributedTableFormulaMapper, IOntogenyRepository ontogenyRepository)
{
_distributedTableFormulaMapper = distributedTableFormulaMapper;
_ontogenyRepository = ontogenyRepository;
}