protected override void Context() { _compoundProcessRepository = A.Fake <ICompoundProcessRepository>(); _executionContext = A.Fake <IExecutionContext>(); _applicationController = A.Fake <IApplicationController>(); sut = new CompoundProcessTask(_compoundProcessRepository, _executionContext, _applicationController); }
public CompoundProcessTask(ICompoundProcessRepository compoundProcessRepository, IExecutionContext executionContext, IApplicationController applicationController) { _compoundProcessRepository = compoundProcessRepository; _executionContext = executionContext; _applicationController = applicationController; }
public override void GlobalContext() { base.GlobalContext(); _compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>(); _cloneManager = IoC.Resolve <ICloneManager>(); _enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>(); _transporterFactory = IoC.Resolve <IIndividualTransporterFactory>(); _modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>(); _modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>(); _compound = DomainFactoryForSpecs.CreateStandardCompound(); _individual = DomainFactoryForSpecs.CreateStandardIndividual(); _protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol(); _enzyme = _enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP"); _enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls; _enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells; _enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo; _individual.AddMolecule(_enzyme); _hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value; _metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>()); _metabolizationProcess.Name = "My Partial Process"; _metabolizationProcess.Parameter(ConverterConstants.Parameter.CLspec).Value = 15; _compound.AddProcess(_metabolizationProcess); _simulationRunOptions = new SimulationRunOptions { RaiseEvents = false }; }
public CompoundProcessPresentationTask( IApplicationController applicationController, ICompoundProcessRepository compoundProcessRepository, IExecutionContext executionContext) { _applicationController = applicationController; _compoundProcessRepository = compoundProcessRepository; _executionContext = executionContext; }
public override void GlobalContext() { base.GlobalContext(); _compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>(); _cloneManager = IoC.Resolve <ICloneManager>(); _liverMicrosomeFirstOrder = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_LIVER_MICROSOME_FIRST_ORDER)); _liverMicrosomeFirstOrder.Name = "liverMicrosomeFirstOrder"; _liverMicrosomeRes = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.LIVER_MICROSOME_RES)); _liverMicrosomeRes.Name = "liverMicrosomeRes"; }
public override void GlobalContext() { base.GlobalContext(); _compound = DomainFactoryForSpecs.CreateStandardCompound(); _individual = DomainFactoryForSpecs.CreateStandardIndividual(); _protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol(); _compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>(); _parameterGroupTask = IoC.Resolve <IParameterGroupTask>(); _cloneManager = IoC.Resolve <ICloneManager>(); }
public override void GlobalContext() { base.GlobalContext(); _compoundProcessRepo = IoC.Resolve <ICompoundProcessRepository>(); _interactionTask = IoC.Resolve <IInteractionTask>(); var cloner = IoC.Resolve <ICloneManager>(); var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>(); var transporterFactory = IoC.Resolve <IIndividualTransporterFactory>(); var inhibitor = DomainFactoryForSpecs.CreateStandardCompound().WithName("Inhibitor"); var protocol2 = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("IV2"); var allPartialProcesses = PartialProcesses.ToList(); foreach (var metaTemplate in allPartialProcesses) { var moleculeName = "Molecule_" + metaTemplate.Name; if (metaTemplate as EnzymaticProcess != null) { var individualProtein = enzymeFactory.CreateFor(_individual).WithName(moleculeName); _individual.AddMolecule(individualProtein.DowncastTo <IndividualEnzyme>().WithName(moleculeName)); } else { var individualProtein = transporterFactory.CreateFor(_individual).WithName(moleculeName); _individual.AddMolecule(individualProtein.DowncastTo <IndividualTransporter>().WithName(moleculeName)); } var process = cloner.Clone(metaTemplate).DowncastTo <PartialProcess>(); process.Name = "Process " + moleculeName; process.MoleculeName = moleculeName; _compound.AddProcess(process); var inhibitionTemplate = _compoundProcessRepo.ProcessByName <InteractionProcess>(InhibitionProcessName); var inhibitionProcess = cloner.Clone(inhibitionTemplate); inhibitionProcess.Name = "InhibitionProcess " + moleculeName; inhibitionProcess.MoleculeName = moleculeName; inhibitor.AddProcess(inhibitionProcess); } _simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith( _individual, new[] { _compound, inhibitor }, new[] { _protocol, protocol2 }).DowncastTo <IndividualSimulation>(); foreach (var inhibitionProcess in inhibitor.AllProcesses <InteractionProcess>()) { var interactionSelection = new InteractionSelection { CompoundName = inhibitor.Name, MoleculeName = inhibitionProcess.MoleculeName, ProcessName = inhibitionProcess.Name }; _simulation.InteractionProperties.AddInteraction(interactionSelection); } DomainFactoryForSpecs.AddModelToSimulation(_simulation); }
public CompoundMapper(ICompoundFactory compoundFactory, ICompoundProcessRepository compoundProcessRepository, IBatchLogger batchLogger, ICloner cloner, ICompoundCalculationMethodCategoryRepository calculationMethodCategoryRepository, ICalculationMethodRepository calculationMethodRepository, ICompoundProcessTask compoundProcessTask, ISpeciesRepository speciesRepository) { _compoundFactory = compoundFactory; _compoundProcessRepository = compoundProcessRepository; _batchLogger = batchLogger; _cloner = cloner; _calculationMethodCategoryRepository = calculationMethodCategoryRepository; _calculationMethodRepository = calculationMethodRepository; _compoundProcessTask = compoundProcessTask; _speciesRepository = speciesRepository; }
public CompoundProcessMapper( ParameterMapper parameterMapper, IRepresentationInfoRepository representationInfoRepository, ICompoundProcessRepository compoundProcessRepository, ICloner cloner, ISpeciesRepository speciesRepository, ICompoundProcessTask compoundProcessTask, IOSPSuiteLogger logger ) : base(parameterMapper) { _representationInfoRepository = representationInfoRepository; _compoundProcessRepository = compoundProcessRepository; _cloner = cloner; _speciesRepository = speciesRepository; _compoundProcessTask = compoundProcessTask; _logger = logger; }
public Converter552To561(ICompoundCalculationMethodCategoryRepository compoundCalculationMethodCategoryRepository, IIndividualFactory individualFactory, ICloner cloner, INeighborhoodFinalizer neighborhoodFinalizer, IContainerTask containerTask, IPKSimXmlSerializerRepository serializerRepository, IReactionBuildingBlockCreator reactionBuildingBlockCreator, IDiagramModelFactory diagramModelFactory, ICompoundProcessRepository compoundProcessRepository, IParameterSetUpdater parameterSetUpdater, IDialogCreator dialogCreator, IRenalAgingCalculationMethodUpdater renalAgingCalculationMethodUpdater, IIndividualUpdater individualUpdater) { _compoundCalculationMethodCategoryRepository = compoundCalculationMethodCategoryRepository; _individualFactory = individualFactory; _cloner = cloner; _neighborhoodFinalizer = neighborhoodFinalizer; _containerTask = containerTask; _serializerRepository = serializerRepository; _reactionBuildingBlockCreator = reactionBuildingBlockCreator; _diagramModelFactory = diagramModelFactory; _compoundProcessRepository = compoundProcessRepository; _parameterSetUpdater = parameterSetUpdater; _dialogCreator = dialogCreator; _renalAgingCalculationMethodUpdater = renalAgingCalculationMethodUpdater; _individualUpdater = individualUpdater; }
public Converter721To730( ICompoundFactory compoundFactory, ICloner cloner, ICreationMetaDataFactory creationMetaDataFactory, IContainerTask containerTask, IFormulationRepository formulationRepository, IEventGroupRepository eventGroupRepository, Converter710To730 coreConverter, ICompoundProcessRepository compoundProcessRepository, ISchemaItemRepository schemaItemRepository ) { _compoundFactory = compoundFactory; _cloner = cloner; _creationMetaDataFactory = creationMetaDataFactory; _containerTask = containerTask; _formulationRepository = formulationRepository; _eventGroupRepository = eventGroupRepository; _coreConverter = coreConverter; _compoundProcessRepository = compoundProcessRepository; _schemaItemRepository = schemaItemRepository; }
protected override Task Context() { _parameterMapper = A.Fake <ParameterMapper>(); _representationInfoRepository = A.Fake <IRepresentationInfoRepository>(); _compoundProcessRepository = A.Fake <ICompoundProcessRepository>(); _cloner = A.Fake <ICloner>(); _speciesRepository = A.Fake <ISpeciesRepository>(); _compoundProcessTask = A.Fake <ICompoundProcessTask>(); _logger = A.Fake <IOSPSuiteLogger>(); sut = new CompoundProcessMapper(_parameterMapper, _representationInfoRepository, _compoundProcessRepository, _cloner, _speciesRepository, _compoundProcessTask, _logger); _enzymaticProcess = new EnzymaticProcess { Name = "Enzymatic Process", Description = "Process description", InternalName = "A", DataSource = "B", MetaboliteName = "Meta" }; //Same description as DB A.CallTo(() => _representationInfoRepository.DescriptionFor(RepresentationObjectType.PROCESS, _enzymaticProcess.InternalName)).Returns(_enzymaticProcess.Description); _enzymaticProcessWithSpecies = new EnzymaticProcessWithSpecies { Name = "Enzymatic process with species", Description = "toto", Species = new Species().WithName("Human"), InternalName = "C", DataSource = "D", }; A.CallTo(() => _representationInfoRepository.DescriptionFor(RepresentationObjectType.PROCESS, _enzymaticProcessWithSpecies.InternalName)).Returns("Process description"); return(Task.FromResult(true)); }