protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_compoundProperties, _project);
// Adds an incorrect compound process selection
_snapshot.Processes = new List <CompoundProcessSelection>(_snapshot.Processes)
{
new CompoundProcessSelection()
}.ToArray();
_simulation = A.Fake <Simulation>();
_simulationSubject = A.Fake <ISimulationSubject>();
A.CallTo(() => _simulationSubject.MoleculeByName("CYP3A4")).Returns(new IndividualEnzyme {
Name = "CYP3A4"
});
A.CallTo(() => _simulation.BuildingBlock <ISimulationSubject>()).Returns(_simulationSubject);
var newModelCompoundProperties = new Model.CompoundProperties {
Compound = _compoundProperties.Compound
};
_compoundProperties.CompoundGroupSelections.Each(newModelCompoundProperties.AddCompoundGroupSelection);
A.CallTo(() => _simulation.CompoundPropertiesFor(_snapshot.Name)).Returns(newModelCompoundProperties);
_context = new CompoundPropertiesContext(_project, _simulation);
}
protected override Task Context()
{
_parameterIdentificationConfigurationMapper = A.Fake <ParameterIdentificationConfigurationMapper>();
_outputMappingMapper = A.Fake <OutputMappingMapper>();
_identificationParameterMapper = A.Fake <IdentificationParameterMapper>();
_parameterIdentificationAnalysisMapper = A.Fake <ParameterIdentificationAnalysisMapper>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_logger = A.Fake <IOSPSuiteLogger>();
_project = new PKSimProject();
_snapshotContext = new SnapshotContext(_project, ProjectVersions.Current);
_simulation = new IndividualSimulation().WithName("S1");
_project.AddBuildingBlock(_simulation);
_parameterIdentification = new ModelParameterIdentification();
_snapshotParameterIndentificationConfiguration = new ParameterIdentificationConfiguration();
_snapshotOutputMapping = new Snapshots.OutputMapping();
_outputMapping = new OutputMapping();
_parameterIdentification.AddSimulation(_simulation);
_parameterIdentification.AddOutputMapping(_outputMapping);
_identificationParameter = new IdentificationParameter {
Name = "IP"
};
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_snapshotIdentificationParameter = new Snapshots.IdentificationParameter();
_snapshotParameterIdentificationAnalysis = new ParameterIdentificationAnalysis();
_parameterIdentificationAnalysis = A.Fake <ISimulationAnalysis>();
_parameterIdentification.AddAnalysis(_parameterIdentificationAnalysis);
sut = new ParameterIdentificationMapper(
_parameterIdentificationConfigurationMapper,
_outputMappingMapper,
_identificationParameterMapper,
_parameterIdentificationAnalysisMapper,
_objectBaseFactory,
_logger
);
A.CallTo(() => _parameterIdentificationConfigurationMapper.MapToSnapshot(_parameterIdentification.Configuration)).Returns(_snapshotParameterIndentificationConfiguration);
A.CallTo(() => _outputMappingMapper.MapToSnapshot(_outputMapping)).Returns(_snapshotOutputMapping);
A.CallTo(() => _identificationParameterMapper.MapToSnapshot(_identificationParameter)).Returns(_snapshotIdentificationParameter);
A.CallTo(() => _parameterIdentificationAnalysisMapper.MapToSnapshot(_parameterIdentificationAnalysis)).Returns(_snapshotParameterIdentificationAnalysis);
return(_completed);
}
public IEventMapping MapFrom(EventMappingDTO eventMappingDTO, PKSim.Core.Model.Simulation simulation)
{
var templateEventId = eventMappingDTO.Event.Id;
var templateEvent = _buildingBlockRepository.All().FindById(templateEventId);
//in that case, event is a simulation event, we need to retrieve the template event
if (templateEvent == null)
{
var usedEvent = simulation.UsedBuildingBlockById(templateEventId);
templateEventId = usedEvent.TemplateId;
}
var eventMapping = eventMappingDTO.EventMapping;
eventMapping.TemplateEventId = templateEventId;
return(eventMapping);
}
protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_compoundProperties, _project);
_simulation = A.Fake <Simulation>();
var newModelCompoundProperties = new Model.CompoundProperties {
Compound = _compoundProperties.Compound
};
_compoundProperties.CompoundGroupSelections.Each(newModelCompoundProperties.AddCompoundGroupSelection);
A.CallTo(() => _simulation.CompoundPropertiesFor(_snapshot.Name)).Returns(newModelCompoundProperties);
_context = new CompoundPropertiesContext(_project, _simulation);
}
public EventMappingDTO MapFrom(IEventMapping eventMapping, PKSim.Core.Model.Simulation simulation)
{
var eventMappingDTO = new EventMappingDTO(eventMapping);
eventMappingDTO.StartTimeParameter = _parameterDTOMapper.MapFrom(eventMapping.StartTime, eventMappingDTO, x => x.StartTime, x => x.StartTimeParameter);
var templateEvent = _buildingBlockRepository.All <PKSim.Core.Model.PKSimEvent>().FindById(eventMapping.TemplateEventId);
var usedEvent = simulation.UsedBuildingBlockByTemplateId(eventMapping.TemplateEventId);
//simulation was already using an event based on template. Retrieved the building block used
if (usedEvent != null)
{
templateEvent = _buildingBlockInSimulationManager.TemplateBuildingBlockUsedBy <PKSim.Core.Model.PKSimEvent>(usedEvent);
}
eventMappingDTO.Event = templateEvent;
return(eventMappingDTO);
}
protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_compoundProperties, _project);
_simulation = A.Fake <Simulation>();
var newModelCompoundProperties = new Model.CompoundProperties {
Compound = _compoundProperties.Compound
};
_compoundProperties.CompoundGroupSelections.Each(newModelCompoundProperties.AddCompoundGroupSelection);
A.CallTo(() => _simulation.CompoundPropertiesFor(_snapshot.Name)).Returns(newModelCompoundProperties);
_context = new SnapshotContextWithSimulation(_simulation, _baseSnapshotContext);
_snapshot.Alternatives[0].AlternativeName = "UNKNOWN";
}
protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_compoundProperties, _project);
_simulation = A.Fake <Simulation>();
_simulationSubject = A.Fake <ISimulationSubject>();
A.CallTo(() => _simulationSubject.MoleculeByName("CYP3A4")).Returns(null);
A.CallTo(() => _simulation.BuildingBlock <ISimulationSubject>()).Returns(_simulationSubject);
var newModelCompoundProperties = new Model.CompoundProperties {
Compound = _compoundProperties.Compound
};
_compoundProperties.CompoundGroupSelections.Each(newModelCompoundProperties.AddCompoundGroupSelection);
A.CallTo(() => _simulation.CompoundPropertiesFor(_snapshot.Name)).Returns(newModelCompoundProperties);
_context = new SnapshotContextWithSimulation(_simulation, _baseSnapshotContext);
}
public static void AddModelToSimulation(Simulation simulation)
{
var simModelConstructor = IoC.Resolve <ISimulationConstructor>();
simModelConstructor.AddModelToSimulation(simulation);
}
public ClassifiableSimulation AddSimulationClassificationFor(Simulation simulation)
{
return(AddClassisificationFor <ClassifiableSimulation, Simulation>(simulation));
}
public void SelectDefaultOutputFor(Simulation simulation)
{
_simulationSettingsRetriever.CreatePKSimDefaults(simulation);
}
public void RunSimulation(Simulation simulation)
{
var simnulationEngine = _simulationEngineFactory.Create <IndividualSimulation>();
simnulationEngine.Run(simulation.DowncastTo <IndividualSimulation>());
}
protected override void Context()
{
base.Context();
_activeSimulation = A.Fake <PKSim.Core.Model.Simulation>();
A.CallTo(() => _activeSubjectRetriever.Active <PKSim.Core.Model.Simulation>()).Returns(_activeSimulation);
}