public TBuildingBlock FindByName <TBuildingBlock>(string name) where TBuildingBlock : class, IPKSimBuildingBlock
{
var bb = _project.All <TBuildingBlock>().FindByName(name);
Load(bb);
return(bb);
}
protected override void Context()
{
var workspace = A.Fake <ICoreWorkspace>();
_project = A.Fake <PKSimProject>();
workspace.Project = _project;
A.CallTo(() => _project.All(PKSimBuildingBlockType.Template)).Returns(_allBuildingBlocks);
A.CallTo(() => _project.All <Simulation>()).Returns(new[] { _simulation });
sut = IoC.Resolve <SimulationsReporter>();
}
public void should_return_a_project_with_the_expected_building_blocks()
{
_newProject.All <Compound>().ShouldContain(_compound);
_newProject.All <PKSimEvent>().ShouldContain(_event);
_newProject.All <Formulation>().ShouldContain(_formulation);
_newProject.All <Protocol>().ShouldContain(_protocol);
_newProject.All <Population>().ShouldContain(_population);
_newProject.All <ObserverSet>().ShouldContain(_observerSet);
_newProject.All <ExpressionProfile>().ShouldContain(_expressionProfile);
_newProject.All <Individual>().ShouldContain(_individual);
}
private void mapQualificationStepPropertiesToModel(IQualificationStep qualificationStep, SnapshotQualificationStep snapshot, PKSimProject project)
{
switch (qualificationStep)
{
case RunParameterIdentificationQualificationStep runParameterIdentification:
var parameterIdentification = project.AllParameterIdentifications.FindByName(snapshot.Subject);
if (parameterIdentification == null)
{
throw new SnapshotOutdatedException(PKSimConstants.Error.CouldNotFindParameterIdentification(snapshot.Subject));
}
runParameterIdentification.ParameterIdentification = parameterIdentification;
break;
case RunSimulationQualificationStep runSimulationQualificationStep:
var simulation = project.All <Model.Simulation>().FindByName(snapshot.Subject);
if (simulation == null)
{
throw new SnapshotOutdatedException(PKSimConstants.Error.CouldNotFindSimulation(snapshot.Subject));
}
runSimulationQualificationStep.Simulation = simulation;
break;
default:
throw new ArgumentException(PKSimConstants.Error.NotMappingDefinedForQualificationStep(qualificationStep.GetType().Name));
}
}
public async Task <SimulationExport[]> ExportSimulationsIn(PKSimProject project, ExportRunOptions exportRunOptions)
{
var nameOfSimulationsToExport = (exportRunOptions.Simulations ?? Enumerable.Empty <string>()).ToList();
if (!nameOfSimulationsToExport.Any())
{
nameOfSimulationsToExport.AddRange(project.All <Simulation>().AllNames());
}
var simulationExports = new List <SimulationExport>();
//sequential for now
foreach (var simulationName in nameOfSimulationsToExport)
{
var simulation = project.BuildingBlockByName <Simulation>(simulationName);
if (simulation == null)
{
_logger.AddWarning($"Simulation '{simulationName}' was not found in project '{project.Name}'", project.Name);
continue;
}
simulationExports.Add((await ExportSimulation(simulation, exportRunOptions, project)));
}
return(simulationExports.ToArray());
}
private SimulationQuantitySelection outputSelectionFrom(string outputFullPath, PKSimProject project)
{
var outputPath = new ObjectPath(outputFullPath.ToPathArray());
if (outputPath.Count == 0)
{
return(null);
}
var simulationName = outputPath[0];
var simulation = project.All <Model.Simulation>().FindByName(simulationName);
if (simulation == null)
{
_logger.AddWarning(PKSimConstants.Error.CouldNotFindSimulation(simulationName));
return(null);
}
outputPath.RemoveAt(0);
var output = simulation.Model.Root.EntityAt <IQuantity>(outputPath.ToArray());
if (output == null)
{
_logger.AddWarning(PKSimConstants.Error.CouldNotFindOutputInSimulation(outputPath, simulationName));
return(null);
}
return(new SimulationQuantitySelection(simulation, new QuantitySelection(outputPath, output.QuantityType)));
}
public void UpdateProjectAfterSave(PKSimProject project)
{
foreach (var simulation in project.All <Simulation>())
{
simulation.ResultsHaveChanged = false;
}
}
protected override void Context()
{
_projectRetriever = A.Fake <IProjectRetriever>();
_project = A.Fake <PKSimProject>();
_individual1 = new Individual();
_individual2 = new Individual();
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
A.CallTo(() => _project.All <Individual>()).Returns(new[] { _individual1, _individual2 });
sut = new BuildingBlockRepository(_projectRetriever);
}
private void addSimulation(string simulationName, ModelParameterIdentification parameterIdentification, PKSimProject project)
{
var simulation = project.All <Model.Simulation>().FindByName(simulationName);
if (simulation == null)
{
_logger.AddWarning(PKSimConstants.Error.CouldNotFindSimulation(simulationName));
return;
}
parameterIdentification.AddSimulation(simulation);
}
public ProjectMetaData MapFrom(PKSimProject project)
{
var projectMetaData = new ProjectMetaData();
project.All <IPKSimBuildingBlock>().Each(x => projectMetaData.AddBuildingBlock(mapFrom(x)));
project.AllSimulationComparisons.Each(x => projectMetaData.AddSimulationComparison(mapFrom(x)));
project.AllParameterIdentifications.Each(x => projectMetaData.AddParameterIdentification(mapFrom(x)));
project.AllSensitivityAnalyses.Each(x => projectMetaData.AddSensitivityAnalysis(mapFrom(x)));
project.AllObservedData.Each(x => projectMetaData.AddObservedData(mapFrom(x)));
projectMetaData.Name = project.Name;
projectMetaData.Description = project.Description;
projectMetaData.Content.Data = _serializationManager.Serialize(project);
_metaData = null;
return(projectMetaData);
}
private ParameterSelection parameterSelectionFrom(string parameterFullPath, PKSimProject project)
{
var parameterPath = new ObjectPath(parameterFullPath.ToPathArray());
if (parameterPath.Count == 0)
{
return(null);
}
var simulationName = parameterPath[0];
var simulation = project.All <Model.Simulation>().FindByName(simulationName);
if (simulation == null)
{
_logger.AddWarning(PKSimConstants.Error.CouldNotFindSimulation(simulationName));
return(null);
}
parameterPath.RemoveAt(0);
return(new ParameterSelection(simulation, parameterPath));
}
private async Task exportSimulations(PKSimProject project, ExportRunOptions exportRunOptions)
{
var nameOfSimulationsToExport = (exportRunOptions.Simulations ?? Enumerable.Empty <string>()).ToList();
if (!nameOfSimulationsToExport.Any())
{
nameOfSimulationsToExport.AddRange(project.All <Simulation>().AllNames());
}
//sequential for now
foreach (var simulationName in nameOfSimulationsToExport)
{
var simulation = project.BuildingBlockByName <Simulation>(simulationName);
if (simulation == null)
{
_logger.AddWarning($"Simulation '{simulationName}' was not found in project '{project.Name}'");
continue;
}
await exportSimulation(simulation, exportRunOptions);
}
}
public IPKSimProject MapFrom(ProjectMetaData projectMetaData)
{
var project = new PKSimProject
{
Name = projectMetaData.Name,
Description = projectMetaData.Description
};
//Observed data needs to be loaded first into project
projectMetaData.AllObservedData.Each(x => project.AddObservedData(mapFrom(x)));
projectMetaData.BuildingBlocks.Each(x => project.AddBuildingBlock(mapFrom(x)));
//we need a shared context for all object referencing observed data and simulations
using (var context = _serializationContextFactory.Create(project.AllObservedData, project.All <ISimulation>()))
{
var localContext = context;
projectMetaData.ParameterIdentifications.Each(x => project.AddParameterIdentification(mapFrom(x, localContext)));
projectMetaData.SensitivityAnalyses.Each(x => project.AddSensitivityAnalysis(mapFrom(x, localContext)));
}
projectMetaData.SimulationComparisons.Each(x => project.AddSimulationComparison(mapFrom(x)));
//Once reference to dynamic meta data was added, deserialize the project itself
_serializationManager.Deserialize(project, projectMetaData.Content.Data);
//if the project DB Version is the same as the current project, the project did not change
if (projectMetaData.Version == ProjectVersions.Current)
{
project.HasChanged = false;
}
return(project);
}