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));
}
