public void Compute(IMoBiSimulation simulation)
{
var buildConfiguration = _buildConfigurationFactory.CreateFromReferencesUsedIn(simulation.MoBiBuildConfiguration);
buildConfiguration.ShowProgress = false;
_logger.AddDebug("Creating new simulation from loaded building blocks");
var results = _modelConstructor.CreateModelFrom(buildConfiguration, "BatchRun");
if (results.IsInvalid)
{
_logger.AddWarning(results.ValidationResult.Messages.SelectMany(x => x.Details).ToString());
}
var newSimulation = new MoBiSimulation
{
BuildConfiguration = buildConfiguration,
Model = results.Model,
Id = "Sim"
};
_context.Register(newSimulation);
_logger.AddDebug("Running simulation");
_simModelManager.RunSimulation(newSimulation);
}
public IMoBiCommand CreateBuildConfigurationBaseOn(IMoBiSimulation simulation, IBuildingBlock templateBuildingBlock)
{
//we create a build configuration where all current building block are referencing template building blocks
BuildConfiguration = _buildConfigurationFactory.CreateFromReferencesUsedIn(simulation.MoBiBuildConfiguration, templateBuildingBlock);
var tmpSimulation = new MoBiSimulation()
{
DiagramManager = _diagramManagerFactory.Create <ISimulationDiagramManager>(),
BuildConfiguration = BuildConfiguration,
Creation = simulation.Creation,
Name = simulation.Name,
};
edit(tmpSimulation);
_view.Caption = AppConstants.Captions.ConfigureSimulation(simulation.Name);
_view.Display();
if (_view.Canceled)
{
return(new MoBiEmptyCommand());
}
//Set the selected MSV AND PSV as per user inputs
UpdateStartValueInfo <IMoleculeStartValuesBuildingBlock, IMoleculeStartValue>(BuildConfiguration.MoleculeStartValuesInfo, SelectedMoleculeStartValues);
UpdateStartValueInfo <IParameterStartValuesBuildingBlock, IParameterStartValue>(BuildConfiguration.ParameterStartValuesInfo, SelectedParameterStartValues);
return(_commands);
}
public void should_be_able_to_read_all_files_and_run_the_most()
{
var directories = new DirectoryInfo(_directory).EnumerateDirectories();
var messages = new List <string>();
foreach (var directory in directories)
{
_sbmlTask = IoC.Resolve <ISbmlTask>().DowncastTo <SbmlTask>();
var caseName = directory.Name;
Debug.Print(caseName);
var fileName = Path.Combine(directory.FullName, $"{caseName}-sbml-l3v1.xml");
var context = IoC.Resolve <IMoBiContext>();
context.NewProject();
var project = context.CurrentProject;
IMoBiCommand command;
try
{
command = _sbmlTask.ImportModelFromSbml(fileName, project);
}
catch (Exception e)
{
messages.Add($"Import: {caseName} {e.Message}:");
continue;
}
if (command.IsEmpty())
{
messages.Add($"Import: {caseName}");
continue;
}
addjEmptyBBIfneeded(project);
addSettings(project, Path.Combine(directory.FullName, $"{caseName}-settings.txt"));
var buildConfigurtion = genreateBuildConfiguration(project);
var result = _modelConstructor.CreateModelFrom(buildConfigurtion, caseName);
if (result.IsInvalid)
{
messages.Add(caseName);
continue;
}
var simulation = new MoBiSimulation {
BuildConfiguration = buildConfigurtion, Model = result.Model
};
var simModelManager = new SimModelManager(_simModelExporter, new SimModelSimulationFactory(),
new DataFactory(IoC.Resolve <IMoBiDimensionFactory>(), new SBMLTestDataNamingService(), IoC.Resolve <IObjectPathFactory>(), IoC.Resolve <IDisplayUnitRetriever>(), IoC.Resolve <IDataRepositoryTask>()));
var runResults = simModelManager.RunSimulation(simulation);
if (!runResults.Success)
{
messages.Add(caseName);
continue;
}
var dt = _dateRepositoryTask.ToDataTable(runResults.Results);
dt.First().ExportToCSV(Path.Combine(directory.FullName, $"{caseName}-result_mobi.csv"));
_sbmlTask = null;
}
messages.Count.ShouldBeEqualTo(0, messages.ToString("\n"));
}
protected override void Context()
{
base.Context();
var m1 = new Model().WithName("S1");
var m2 = new Model().WithName("S1");
var bc1 = A.Fake <IMoBiBuildConfiguration>();
var bc2 = A.Fake <IMoBiBuildConfiguration>();
var reactionInfo1 = new ReactionBuildingBlockInfo
{
BuildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithName("R1"),
TemplateBuildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithName("R1")
};
bc1.ReactionsInfo = reactionInfo1;
var reactionInfo2 = new ReactionBuildingBlockInfo
{
BuildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithName("R2"),
TemplateBuildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithName("R2")
};
bc2.ReactionsInfo = reactionInfo2;
var sim1 = new MoBiSimulation {
BuildConfiguration = bc1, Model = m1
}.WithName("S1");
var sim2 = new MoBiSimulation {
BuildConfiguration = bc2, Model = m2
}.WithName("S1");
_object1 = sim1;
_object2 = sim2;
}
protected override void Context()
{
base.Context();
_cloneManager = A.Fake <ICloneManager>();
_simulationDiagramManager = A.Fake <ISimulationDiagramManager>();
_moBiSimulation = new MoBiSimulation {
DiagramManager = _simulationDiagramManager
};
}
protected override void Context()
{
base.Context();
_observedData = new DataRepository("OBS1");
_simulationResults = new DataRepository("RES");
_simmulation = new MoBiSimulation().WithId("ID");
_simmulation.Results = _simulationResults;
_project.AddSimulation(_simmulation);
_project.AddObservedData(_observedData);
}
public IMoBiSimulation CreateFrom(IMoBiBuildConfiguration buildConfiguration, IModel model)
{
var moBiSimulation = new MoBiSimulation()
{
DiagramManager = _diagramManagerFactory.Create <ISimulationDiagramManager>(),
BuildConfiguration = buildConfiguration,
Model = model,
Creation = _creationMetaDataFactory.Create(),
HasChanged = true,
Id = _idGenerator.NewId(),
};
_simulationParameterOriginIdUpdater.UpdateSimulationId(moBiSimulation);
return(moBiSimulation);
}
protected override void Context()
{
base.Context();
_currentResult = new DataRepository("id1");
_historicResult = new DataRepository("id2");
_repositories = new List <DataRepository> {
_currentResult, _historicResult
};
_moBiSimulation = new MoBiSimulation {
Results = _currentResult
};
_moBiSimulation.HistoricResults.Add(_historicResult);
_project.AddSimulation(_moBiSimulation);
A.CallTo(_dialogCreator).WithReturnType <ViewResult>().Returns(ViewResult.Yes);
}
protected override void Context()
{
base.Context();
var m1 = new Model().WithName("S1");
var m2 = new Model().WithName("S1");
var bc1 = A.Fake <IMoBiBuildConfiguration>();
var bc2 = A.Fake <IMoBiBuildConfiguration>();
var sim1 = new MoBiSimulation {
BuildConfiguration = bc1, Model = m1
}.WithName("S1");
var sim2 = new MoBiSimulation {
BuildConfiguration = bc2, Model = m2
}.WithName("S1");
_object1 = sim1;
_object2 = sim2;
}
protected override void Context()
{
base.Context();
_simulation = new MoBiSimulation();
_simModelManager = A.Fake <ISimModelManager>();
_outputSelections = new OutputSelections();
_drug = new MoleculeBuilder().WithName("DRUG");
_drug.AddParameter(new Parameter().WithName(AppConstants.Parameters.MOLECULAR_WEIGHT).WithFormula(new ConstantFormula(400)));
_outputSelections.AddOutput(new QuantitySelection("A", QuantityType.Drug));
_simulation.BuildConfiguration = new MoBiBuildConfiguration
{
SimulationSettings = new SimulationSettings
{
OutputSelections = _outputSelections
},
Molecules = new MoleculeBuildingBlock
{
_drug
}
};
A.CallTo(() => _simModelManagerFactory.Create()).Returns(_simModelManager);
_oldResults = new DataRepository("OLD");
_simulation.Results = _oldResults;
_newResults = new DataRepository("NEW");
_simulationResults = new SimulationRunResults(success: true, warnings: Enumerable.Empty <SolverWarning>(), results: _newResults);
A.CallTo(() => _simModelManager.RunSimulation(_simulation)).Returns(_simulationResults);
var baseGrid = new BaseGrid("Time", DomainHelperForSpecs.TimeDimension);
_concentrationColumn = new DataColumn("Drug", DomainHelperForSpecs.ConcentrationDimension, baseGrid);
_fractionColumn = new DataColumn("Fraction", DomainHelperForSpecs.FractionDimension, baseGrid);
_newResults.Add(_concentrationColumn);
_newResults.Add(_fractionColumn);
A.CallTo(() => _keyPathMapper.MoleculeNameFrom(_concentrationColumn)).Returns(_drug.Name);
}
protected override void Because()
{
var testSimulation = new MoBiSimulation().WithName("Sim");
_forbiddenNames = sut.For(testSimulation);
}
public void Visit(MoBiSimulation simulation)
{
enableActiveSimulationItems = true;
}