private async Task <InteractionSelection> interactionSelectionFrom(CompoundProcessSelection snapshotInteraction, ISimulationSubject simulationSubject, PKSimProject project)
{
var process = findProcess(project, snapshotInteraction, simulationSubject);
if (process == null)
{
return(null);
}
var processSelection = await _processMappingMapper.MapToModel(snapshotInteraction, process);
return(processSelection.DowncastTo <InteractionSelection>());
}
private async Task <InteractionSelection> interactionSelectionFrom(CompoundProcessSelection snapshotInteraction, PKSimProject project)
{
var process = findProcess(project, snapshotInteraction);
if (process == null)
{
_logger.AddWarning(PKSimConstants.Error.ProcessNotFoundInCompound(snapshotInteraction.Name, snapshotInteraction.CompoundName));
return(null);
}
var processSelection = await _processMappingMapper.MapToModel(snapshotInteraction, process);
return(processSelection.DowncastTo <InteractionSelection>());
}
private Model.CompoundProcess notSelectedProcessFrom(CompoundProcessSelection snapshotCompoundProcessSelection, ISimulationSubject simulationSubject)
{
//Partial process
var moleculeName = snapshotCompoundProcessSelection.MoleculeName;
var systemicProcessType = snapshotCompoundProcessSelection.SystemicProcessType;
//this should be a specific process
if (!string.IsNullOrEmpty(systemicProcessType))
{
return new NotSelectedSystemicProcess {
SystemicProcessType = SystemicProcessTypes.ById(systemicProcessType)
}
}
;
if (string.IsNullOrEmpty(moleculeName))
{
return(null);
}
var molecule = simulationSubject.MoleculeByName(moleculeName);
if (molecule == null)
{
return(null);
}
switch (molecule)
{
case IndividualTransporter _:
return(new TransportPartialProcess {
MoleculeName = moleculeName
});
case IndividualEnzyme _:
return(new EnzymaticProcess {
MoleculeName = moleculeName
});
case IndividualOtherProtein _:
return(new SpecificBindingPartialProcess {
MoleculeName = moleculeName
});
}
return(null);
}
private Model.CompoundProcess findProcess(PKSimProject project, CompoundProcessSelection snapshotInteraction, ISimulationSubject simulationSubject)
{
var compoundProcess = project.BuildingBlockByName <Model.Compound>(snapshotInteraction.CompoundName)
?.ProcessByName(snapshotInteraction.Name);
if (compoundProcess != null)
{
return(compoundProcess);
}
//No process found and a name was specified. This is a snapshot that is corrupted
if (!string.IsNullOrEmpty(snapshotInteraction.Name))
{
_logger.AddWarning(PKSimConstants.Error.ProcessNotFoundInCompound(snapshotInteraction.Name, snapshotInteraction.CompoundName));
return(null);
}
//This might be a process that was deselected explicitly by the user
var molecule = simulationSubject.MoleculeByName(snapshotInteraction.MoleculeName);
return(molecule == null ? null : new NoInteractionProcess {
MoleculeName = molecule.Name
});
}
private async Task addProcessToProcessSelection(CompoundProcessesSelection compoundProcessesSelection, CompoundProcessSelection snapshotCompoundProcessSelection, Model.CompoundProcess process, SnapshotContext snapshotContext)
{
var processSelectionGroup = selectionGroupFor(compoundProcessesSelection, process);
var processContext = new CompoundProcessSnapshotContext(process, snapshotContext);
var processSelection = await _processMappingMapper.MapToModel(snapshotCompoundProcessSelection, processContext);
processSelectionGroup.AddProcessSelection(processSelection);
}
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);
}
private async Task addProcessToProcessSelection(CompoundProcessesSelection compoundProcessesSelection, CompoundProcessSelection compoundProcessSelection, Model.CompoundProcess process)
{
var processSelectionGroup = selectionGroupFor(compoundProcessesSelection, process);
var processSelection = await _processMappingMapper.MapToModel(compoundProcessSelection, process);
processSelectionGroup.AddProcessSelection(processSelection);
}
protected override Task Context()
{
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMappingMapper = A.Fake <ProcessMappingMapper>();
_logger = A.Fake <ILogger>();
_project = new PKSimProject();
_calculationMethodSnapshot = new CalculationMethodCache();
sut = new CompoundPropertiesMapper(_calculationMethodCacheMapper, _processMappingMapper, _logger);
_compoundGroupSelectionOneAlternative = new CompoundGroupSelection
{
AlternativeName = "ALT1",
GroupName = "ALTERNATIVE_GROUP_1"
};
_compoundGroupSelectionTwoAlternatives = new CompoundGroupSelection
{
AlternativeName = "ALT2",
GroupName = "ALTERNATIVE_GROUP_2"
};
_compound = new Compound
{
Name = "COMP",
};
_protocol = new SimpleProtocol
{
Name = "PROTOCOL"
};
_parameterAlternativeGroupWithOneAlternative = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionOneAlternative.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionTwoAlternatives.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT1"
});
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT2"
});
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithOneAlternative);
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithTwoAlternatives);
_compoundProperties = new Model.CompoundProperties();
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionOneAlternative);
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionTwoAlternatives);
_compoundProperties.Compound = _compound;
_enzymaticProcess = new EnzymaticProcess {
Name = "EnzymaticProcess"
};
_anotherEnzymaticProcess = new EnzymaticProcess {
Name = "AnotherEnzymaticProcess", MoleculeName = "CYP3A4"
};
_specificBindingProcess = new SpecificBindingPartialProcess {
Name = "SpecificBinding"
};
_gfrTransportProcess = new SystemicProcess {
Name = "Transport", SystemicProcessType = SystemicProcessTypes.GFR
};
_hepaticEnzymaticProcess = new SystemicProcess {
Name = "Plasma Clearance", SystemicProcessType = SystemicProcessTypes.Hepatic
};
_compound.AddProcess(_enzymaticProcess);
_compound.AddProcess(_specificBindingProcess);
_compound.AddProcess(_gfrTransportProcess);
_compound.AddProcess(_hepaticEnzymaticProcess);
_enzymaticPartialProcessSelection = new EnzymaticProcessSelection {
ProcessName = _enzymaticProcess.Name
};
_noEnzymaticSystemicProcessSelection = new SystemicProcessSelection {
ProcessType = SystemicProcessTypes.Hepatic
};
_specificBindingPartialProcessSelection = new ProcessSelection {
ProcessName = _specificBindingProcess.Name
};
_transportSystemicProcessSelection = new SystemicProcessSelection {
ProcessName = _gfrTransportProcess.Name, ProcessType = _gfrTransportProcess.SystemicProcessType,
};
_noEnzymaticPartialProcessSelection = new EnzymaticProcessSelection {
MoleculeName = _anotherEnzymaticProcess.MoleculeName
};
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_enzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_noEnzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddSystemicProcessSelection(_noEnzymaticSystemicProcessSelection);
_compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(_specificBindingPartialProcessSelection);
_compoundProperties.Processes.TransportAndExcretionSelection.AddSystemicProcessSelection(_transportSystemicProcessSelection);
_snapshotProcess1 = new CompoundProcessSelection {
Name = _enzymaticPartialProcessSelection.ProcessName
};
_snapshotProcess2 = new CompoundProcessSelection {
Name = _specificBindingPartialProcessSelection.ProcessName
};
_snapshotProcess3 = new CompoundProcessSelection {
Name = _transportSystemicProcessSelection.ProcessName
};
_snapshotProcess4 = new CompoundProcessSelection {
SystemicProcessType = _noEnzymaticSystemicProcessSelection.ProcessType.SystemicProcessTypeId.ToString()
};
_snapshotProcess5 = new CompoundProcessSelection {
MoleculeName = _noEnzymaticPartialProcessSelection.MoleculeName
};
_formulation = new Formulation
{
Id = "123456"
};
_compoundProperties.ProtocolProperties.Protocol = _protocol;
_compoundProperties.ProtocolProperties.AddFormulationMapping(new FormulationMapping
{
FormulationKey = "F1",
TemplateFormulationId = _formulation.Id
});
_project.AddBuildingBlock(_formulation);
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compoundProperties.CalculationMethodCache)).Returns(_calculationMethodSnapshot);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_enzymaticPartialProcessSelection)).Returns(_snapshotProcess1);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_specificBindingPartialProcessSelection)).Returns(_snapshotProcess2);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_transportSystemicProcessSelection)).Returns(_snapshotProcess3);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticSystemicProcessSelection)).Returns(_snapshotProcess4);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticPartialProcessSelection)).Returns(_snapshotProcess5);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess1, _enzymaticProcess)).Returns(_enzymaticPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess2, _specificBindingProcess)).Returns(_specificBindingPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess3, _gfrTransportProcess)).Returns(_transportSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess4, A <NotSelectedSystemicProcess> ._)).Returns(_noEnzymaticSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess5, A <EnzymaticProcess> ._)).Returns(_noEnzymaticPartialProcessSelection);
return(_completed);
}
private Model.CompoundProcess findProcess(PKSimProject project, CompoundProcessSelection snapshotInteraction)
{
return(project.BuildingBlockByName <Model.Compound>(snapshotInteraction.CompoundName)
?.ProcessByName(snapshotInteraction.Name));
}
