public override void GlobalContext()
{
base.GlobalContext();
_induction = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.INDUCTION).DowncastTo <InductionProcess>());
_induction.Name = "Induction";
_induction.Parameter(CoreConstantsForSpecs.Parameter.EC50).Value = 10;
_compound.AddProcess(_induction);
_irreversibleInhibiton = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.IRREVERSIBLE_INHIBITION).DowncastTo <InhibitionProcess>());
_irreversibleInhibiton.Name = "IrreversibleProcess";
_irreversibleInhibiton.Parameter(CoreConstantsForSpecs.Parameter.KINACT).Value = 10;
_compound.AddProcess(_irreversibleInhibiton);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, new[] { _compound }, new[] { _protocol })
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesFor(_compound.Name)
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
_simulation.InteractionProperties.AddInteraction(new InteractionSelection {
CompoundName = _compound.Name, MoleculeName = _enzyme.Name, ProcessName = _induction.Name
});
_simulation.InteractionProperties.AddInteraction(new InteractionSelection {
CompoundName = _compound.Name, MoleculeName = _enzyme.Name, ProcessName = _irreversibleInhibiton.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
protected override Task Context()
{
sut = new ProcessMappingMapper();
_compound = new Compound
{
Name = "COMP",
};
_enzymaticProcess = new EnzymaticProcess().WithName("MetaProcess");
_enzymaticProcessSelection = new EnzymaticProcessSelection
{
CompoundName = _compound.Name,
MetaboliteName = "META",
MoleculeName = "CYP",
ProcessName = _enzymaticProcess.Name
};
_specificBindingProcess = new SpecificBindingPartialProcess().WithName("BindingProcess");
_specificBindingPartialProcessSelection = new ProcessSelection
{
CompoundName = _compound.Name,
MoleculeName = "BINDER",
ProcessName = _specificBindingProcess.Name
};
_transportSystemicProcess = new SystemicProcess
{
Name = "SystemicTransport",
SystemicProcessType = SystemicProcessTypes.GFR
};
_transportSystemicProcessSelection = new SystemicProcessSelection
{
CompoundName = _compound.Name,
ProcessName = _transportSystemicProcess.Name,
ProcessType = _transportSystemicProcess.SystemicProcessType
};
_interactionProcess = new InductionProcess().WithName("InteractionProcess");
_interactionSelection = new InteractionSelection
{
CompoundName = _compound.Name,
ProcessName = _interactionProcess.Name,
MoleculeName = "INHIBITOR"
};
_compound.AddProcess(_enzymaticProcess);
_compound.AddProcess(_transportSystemicProcess);
_compound.AddProcess(_interactionProcess);
_compound.AddProcess(_specificBindingProcess);
return(_completed);
}
protected override void Context()
{
base.Context();
_moleculeMappable = new IndividualEnzyme().WithName("MoleculeMapped");
_moleculeAlreadySelected = new IndividualEnzyme().WithName("MoleculeAlreadySelected");
_moleculeNotMapped = new IndividualEnzyme().WithName("MoleculeNotMapped");
_inhibitionProcess1 = new InhibitionProcess().WithName("InhibitionProcess1");
_inhibitionProcess2 = new InhibitionProcess().WithName("InhibitionProcess2");
_inductionProcess1 = new InductionProcess().WithName("InductionProcess1");
_inhibitionProcess3 = new InhibitionProcess().WithName("InhibitionProcess3");
_individual.AddMolecule(_moleculeNotMapped);
_individual.AddMolecule(_moleculeMappable);
_individual.AddMolecule(_moleculeAlreadySelected);
_compound.AddProcess(_inhibitionProcess1);
_compound2 = new Compound().WithName("Comp2");
_compound2.AddProcess(_inhibitionProcess2);
_inhibitionProcess2.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inhibitionProcess3);
_inhibitionProcess3.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inductionProcess1);
_inductionProcess1.MoleculeName = _moleculeMappable.Name;
var interactionProperties = new InteractionProperties();
interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeAlreadySelected.Name, ProcessName = _inhibitionProcess1.Name, CompoundName = _compound.Name
});
A.CallTo(() => _simulation.InteractionProperties).Returns(interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound, _compound2 });
}
protected override Task Context()
{
_solverSettingsMapper = A.Fake <SolverSettingsMapper>();
_outputSchemaMapper = A.Fake <OutputSchemaMapper>();
_outputSelectionMapper = A.Fake <OutputSelectionsMapper>();
_parameterMapper = A.Fake <ParameterMapper>();
_compoundPropertiesMapper = A.Fake <CompoundPropertiesMapper>();
_advancedParameterMapper = A.Fake <AdvancedParameterMapper>();
_eventMappingMapper = A.Fake <EventMappingMapper>();
_observerSetMappingMapper = A.Fake <ObserverSetMappingMapper>();
_curveChartMapper = A.Fake <SimulationTimeProfileChartMapper>();
_processMappingMapper = A.Fake <ProcessMappingMapper>();
_simulationFactory = A.Fake <ISimulationFactory>();
_executionContext = A.Fake <IExecutionContext>();
_simulationModelCreator = A.Fake <ISimulationModelCreator>();
_simulationBuildingBlockUpdater = A.Fake <ISimulationBuildingBlockUpdater>();
_modelPropertiesTask = A.Fake <IModelPropertiesTask>();
_simulationRunner = A.Fake <ISimulationRunner>();
_populationAnalysisChartMapper = A.Fake <PopulationAnalysisChartMapper>();
_simulationParameterOriginIdUpdater = A.Fake <ISimulationParameterOriginIdUpdater>();
_logger = A.Fake <ILogger>();
_containerTask = A.Fake <IContainerTask>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
sut = new SimulationMapper(_solverSettingsMapper, _outputSchemaMapper,
_outputSelectionMapper, _compoundPropertiesMapper, _parameterMapper,
_advancedParameterMapper, _eventMappingMapper, _observerSetMappingMapper, _curveChartMapper,
_populationAnalysisChartMapper, _processMappingMapper,
_simulationFactory, _executionContext, _simulationModelCreator,
_simulationBuildingBlockUpdater, _modelPropertiesTask,
_simulationRunner, _simulationParameterOriginIdUpdater,
_logger, _containerTask, _entityPathResolver
);
_project = new PKSimProject();
_individual = new Individual {
Name = "IND", Id = "IND"
};
_compound = new Compound {
Name = "COMP", Id = "COMP"
};
_observerSet = new ObserverSet {
Name = "OBS_SET", Id = "OBS_SET"
};
_protocol = new SimpleProtocol {
Name = "PROT", Id = "PROT"
};
_inductionProcess = new InductionProcess().WithName("Interaction process");
_compound.AddProcess(_inductionProcess);
_event = new PKSimEvent {
Name = "Event"
};
_population = new RandomPopulation()
{
Name = "POP"
};
_observedData = new DataRepository("OBS_ID").WithName("OBS");
_project.AddBuildingBlock(_individual);
_project.AddBuildingBlock(_compound);
_project.AddBuildingBlock(_event);
_project.AddBuildingBlock(_population);
_project.AddBuildingBlock(_observerSet);
_project.AddObservedData(_observedData);
_simulationProperties = new SimulationProperties
{
ModelProperties = new ModelProperties
{
ModelConfiguration = new ModelConfiguration {
ModelName = "4Comp"
}
}
};
_interactionSelection = new InteractionSelection {
ProcessName = _inductionProcess.Name
};
_noInteractionSelection = new InteractionSelection {
MoleculeName = "CYP2D6"
};
_simulationProperties.InteractionProperties.AddInteraction(_interactionSelection);
_simulationProperties.InteractionProperties.AddInteraction(_noInteractionSelection);
_settings = new SimulationSettings();
_rootContainer = new Container().WithName("Sim");
_model = new OSPSuite.Core.Domain.Model {
Root = _rootContainer
};
_individualSimulation = new IndividualSimulation
{
Name = "S1",
Properties = _simulationProperties,
SimulationSettings = _settings,
Description = "Simulation Description",
Model = _model
};
_simulationTimeProfile = new SimulationTimeProfileChart();
_snapshotSimulationTimeProfile = new CurveChart();
_individualSimulation.AddAnalysis(_simulationTimeProfile);
A.CallTo(() => _curveChartMapper.MapToSnapshot(_simulationTimeProfile)).Returns(_snapshotSimulationTimeProfile);
_populationSimulation = new PopulationSimulation
{
Properties = _simulationProperties,
SimulationSettings = _settings,
Model = _model
};
_advancedParameterCollection = new AdvancedParameterCollection();
_populationSimulationAnalysisChart = new BoxWhiskerAnalysisChart();
_populationSimulation.SetAdvancedParameters(_advancedParameterCollection);
_populationSimulation.AddAnalysis(_populationSimulationAnalysisChart);
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_snapshotPopulationAnalysisChart = new Snapshots.PopulationAnalysisChart();
A.CallTo(() => _populationAnalysisChartMapper.MapToSnapshot(_populationSimulationAnalysisChart)).Returns(_snapshotPopulationAnalysisChart);
_snapshotInteraction = new CompoundProcessSelection();
A.CallTo(() => _processMappingMapper.MapToSnapshot(_interactionSelection)).Returns(_snapshotInteraction);
_snapshotInteraction.CompoundName = _compound.Name;
_snapshotInteraction.Name = _inductionProcess.Name;
_noSelectionSnapshotInteraction = new CompoundProcessSelection();
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noInteractionSelection)).Returns(_noSelectionSnapshotInteraction);
_noSelectionSnapshotInteraction.MoleculeName = _noInteractionSelection.MoleculeName;
_compoundProperties = new CompoundProperties();
_snapshotCompoundProperties = new Snapshots.CompoundProperties {
Name = _compound.Name
};
_individualSimulation.Properties.AddCompoundProperties(_compoundProperties);
_eventMapping = new EventMapping();
_individualSimulation.EventProperties.AddEventMapping(_eventMapping);
_observerSetMapping = new ObserverSetMapping();
_individualSimulation.ObserverSetProperties.AddObserverSetMapping(_observerSetMapping);
A.CallTo(() => _compoundPropertiesMapper.MapToSnapshot(_compoundProperties, _project)).Returns(_snapshotCompoundProperties);
_eventSelection = new EventSelection
{
Name = _event.Name,
};
_observerSetSelection = new ObserverSetSelection
{
Name = _observerSet.Name,
};
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual,
Altered = true
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("CompTemplateId", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("ProtTemplateId", PKSimBuildingBlockType.Protocol)
{
BuildingBlock = _protocol
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("ObserveSetTemplateId", PKSimBuildingBlockType.ObserverSet)
{
BuildingBlock = _observerSet
});
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("PopTemplateId", PKSimBuildingBlockType.Population)
{
BuildingBlock = _population
});
_individualSimulation.AddUsedObservedData(_observedData);
A.CallTo(() => _eventMappingMapper.MapToSnapshot(_eventMapping, _project)).Returns(_eventSelection);
A.CallTo(() => _observerSetMappingMapper.MapToSnapshot(_observerSetMapping, _project)).Returns(_observerSetSelection);
_outputSelectionSnapshot = new OutputSelections();
A.CallTo(() => _outputSelectionMapper.MapToSnapshot(_individualSimulation.OutputSelections)).Returns(_outputSelectionSnapshot);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotInteraction, _inductionProcess)).Returns(_interactionSelection);
return(_completed);
}
