protected override void Context() { base.Context(); _dataRepository = DomainHelperForSpecs.ObservedData( "TOTO", _dimensionTask.DimensionByName(Constants.Dimension.TIME), _dimensionTask.DimensionByName(Constants.Dimension.MOLAR_CONCENTRATION), "OBS_COL" ); _obsColumn = _dataRepository.Columns.FindByName("OBS_COL"); }
protected override void Context() { base.Context(); A.CallTo(() => _dataRepositoryTask.ExportToCsvAsync(A <IEnumerable <DataColumn> > ._, _fileName, A <DataColumnExportOptions> ._)) .Invokes(x => _exportOptions = x.GetArgument <DataColumnExportOptions>(2)); _dataColumn = DomainHelperForSpecs.ObservedData().FirstDataColumn(); _dataColumn.Name = "TOTO"; A.CallTo(() => _quantityDisplayPathMapper.DisplayPathAsStringFor(_simulation, _dataColumn, false)).Returns("NEW NAME"); }
protected override void Context() { _observedData = DomainHelperForSpecs.ObservedData("TOTO"); _outputMapping = new OutputMapping { WeightedObservedData = new WeightedObservedData(_observedData) { Id = 5 } }; _outputMappingDTO = new OutputMappingDTO(_outputMapping); sut = new WeightedObservedDataFormatter(_outputMappingDTO); }
protected override void Context() { base.Context(); sut = new ResidualCalculatorForOnlyObservedData(_timeGridRestrictor, _dimensionFactory); _outputMapping.Scaling = Scalings.Linear; _outputMapping2 = A.Fake <OutputMapping>(); A.CallTo(() => _outputMapping2.FullOutputPath).Returns(_fullOutputPath); _observedData2 = DomainHelperForSpecs.ObservedData().WithName("OBS2"); _outputMapping2.WeightedObservedData = new WeightedObservedData(_observedData2); _outputMappings.Add(_outputMapping2); }
protected override void Context() { base.Context(); _dataRepository = DomainHelperForSpecs.ObservedData(); _sim1 = new IndividualSimulation { Name = "Sim1" }; _sim2 = new IndividualSimulation { Name = "Sim2" }; _sim1.AddUsedObservedData(_dataRepository); A.CallTo(() => _project.AllUsersOfObservedData).Returns(new [] { _sim1, _sim2, }); }
protected override void Context() { base.Context(); _dataRepository = DomainHelperForSpecs.ObservedData(); _sim1 = new IndividualSimulation { Name = "Sim1" }; _sim2 = new IndividualSimulation { Name = "Sim2" }; _sim1.AddUsedObservedData(_dataRepository); _project.AddBuildingBlock(_sim1); _project.AddBuildingBlock(_sim2); }
protected override void Context() { _presentationSettingsTask = A.Fake <IPresentationSettingsTask>(); _view = A.Fake <IParameterIdentificationMultipleRunsAnalysisView>(); _chartEditorAndDisplayPresenter = A.Fake <IChartEditorAndDisplayPresenter>(); _curveNamer = A.Fake <ICurveNamer>(); _pathElementsMapper = A.Fake <IDataColumnToPathElementsMapper>(); _chartTemplatingTask = A.Fake <IChartTemplatingTask>(); _dimensionFactory = A.Fake <IDimensionFactory>(); _displayUnitRetriever = A.Fake <IDisplayUnitRetriever>(); _chartEditorLayoutTask = A.Fake <IChartEditorLayoutTask>(); _projectRetreiver = A.Fake <IProjectRetriever>(); _chartPresenterContext = A.Fake <ChartPresenterContext>(); A.CallTo(() => _chartPresenterContext.EditorAndDisplayPresenter).Returns(_chartEditorAndDisplayPresenter); A.CallTo(() => _chartPresenterContext.CurveNamer).Returns(_curveNamer); A.CallTo(() => _chartPresenterContext.DataColumnToPathElementsMapper).Returns(_pathElementsMapper); A.CallTo(() => _chartPresenterContext.TemplatingTask).Returns(_chartTemplatingTask); A.CallTo(() => _chartPresenterContext.PresenterSettingsTask).Returns(_presentationSettingsTask); A.CallTo(() => _chartPresenterContext.DimensionFactory).Returns(_dimensionFactory); A.CallTo(() => _chartPresenterContext.EditorLayoutTask).Returns(_chartEditorLayoutTask); A.CallTo(() => _chartPresenterContext.ProjectRetriever).Returns(_projectRetreiver); sut = new ParameterIdentificationTimeProfileChartPresenter(_view, _chartPresenterContext, _displayUnitRetriever); _timeProfileAnalysis = new ParameterIdentificationTimeProfileChart(); _outputMapping1 = A.Fake <OutputMapping>(); _outputMapping2 = A.Fake <OutputMapping>(); _observedData1 = DomainHelperForSpecs.ObservedData(); _observedData2 = DomainHelperForSpecs.ObservedData(); A.CallTo(() => _outputMapping1.WeightedObservedData).Returns(new WeightedObservedData(_observedData1)); A.CallTo(() => _outputMapping2.WeightedObservedData).Returns(new WeightedObservedData(_observedData2)); _parameterIdentification = new ParameterIdentification(); _parameterIdentification.AddOutputMapping(_outputMapping1); _parameterIdentification.AddOutputMapping(_outputMapping2); _parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>(); _parameterIdentification.AddResult(_parameterIdentificationRunResult); _optimizationRunResult = new OptimizationRunResult(); _parameterIdentificationRunResult.BestResult = _optimizationRunResult; _parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>(); _parameterIdentification.AddResult(_parameterIdentificationRunResult); _optimizationRunResult2 = new OptimizationRunResult(); _parameterIdentificationRunResult.BestResult = _optimizationRunResult2; }
protected override void Context() { _view = A.Fake <IEditTimeProfileAnalysisChartView>(); _timeProfilerChartPresenter = A.Fake <ITimeProfileChartPresenter>(); _timeProfileChartDataCreator = A.Fake <ITimeProfileChartDataCreator>(); _populationSimulationAnalysisStarter = A.Fake <IPopulationSimulationAnalysisStarter>(); _populationAnalysisTask = A.Fake <IPopulationAnalysisTask>(); _colorGenerator = A.Fake <IColorGenerator>(); _observedDataTask = A.Fake <IObservedDataTask>(); _pkAnalysisPresenter = A.Fake <IPopulationPKAnalysisPresenter>(); _dimensionRepository = A.Fake <IDimensionRepository>(); _presenterSettingsTask = A.Fake <IPresentationSettingsTask>(); sut = new EditTimeProfileAnalysisChartPresenter(_view, _timeProfilerChartPresenter, _timeProfileChartDataCreator, _populationSimulationAnalysisStarter, _populationAnalysisTask, _colorGenerator, _observedDataTask, _pkAnalysisPresenter, _dimensionRepository, _presenterSettingsTask); _timeProfileAnalysisChart = new TimeProfileAnalysisChart(); _populationStatisticalAnalysis = new PopulationStatisticalAnalysis(); _timeProfileAnalysisChart.PopulationAnalysis = _populationStatisticalAnalysis; _populationDataCollector = A.Fake <IPopulationDataCollector>(); sut.InitializeAnalysis(_timeProfileAnalysisChart, _populationDataCollector); _observedDataRepository = DomainHelperForSpecs.ObservedData(); var data = new DragDropInfo( new List <ITreeNode> { new ObservedDataNode(new ClassifiableObservedData { Subject = _observedDataRepository }) } ); _dragEventArgs = new DragEventArgs(new DataObject(data), 0, 0, 0, DragDropEffects.All, DragDropEffects.All); _chartData = new ChartData <TimeProfileXValue, TimeProfileYValue>(null, null); var concentrationDimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs(); var yAxis = new AxisData(concentrationDimension, concentrationDimension.DefaultUnit, Scalings.Linear); _paneData = new PaneData <TimeProfileXValue, TimeProfileYValue>(yAxis); _chartData.AddPane(_paneData); A.CallTo(_timeProfileChartDataCreator).WithReturnType <ChartData <TimeProfileXValue, TimeProfileYValue> >().Returns(_chartData); var outputField = new PopulationAnalysisOutputField { Dimension = DomainHelperForSpecs.MassConcentrationDimensionForSpecs() }; _populationStatisticalAnalysis.Add(outputField); A.CallTo(() => _dimensionRepository.MergedDimensionFor(A <NumericFieldContext> ._)).Returns(concentrationDimension); }
protected override void Context() { _dialogCreator = A.Fake <IDialogCreator>(); _context = A.Fake <IOSPSuiteExecutionContext>(); _dataRepositoryTask = A.Fake <IDataRepositoryExportTask>(); _containerTask = A.Fake <IContainerTask>(); _objectTypeResolver = A.Fake <IObjectTypeResolver>(); sut = new ObservedDataTaskForSpecs(_dialogCreator, _context, _dataRepositoryTask, _containerTask, _objectTypeResolver); _obsData1 = DomainHelperForSpecs.ObservedData("OBS1"); _obsData2 = DomainHelperForSpecs.ObservedData("OBS2"); A.CallTo(() => _context.Project.AllUsersOfObservedData).Returns(_allUserOfObservedData); }
protected override async Task Context() { await base.Context(); _runOptions.Validate = true; _expectedOutputPath = Path.Combine(_qualificationConfiguration.OutputFolder, PROJECT_NAME); _expectedObsDataPath = _qualificationConfiguration.ObservedDataFolder; DirectoryHelper.DirectoryExists = s => string.Equals(s, _expectedOutputPath); DirectoryHelper.DeleteDirectory = (s, b) => _deletedDirectory = s; _observedData = DomainHelperForSpecs.ObservedData().WithName("OBS"); _project.AddObservedData(_observedData); }
protected override void Context() { base.Context(); _solubilityDataRepository = DomainHelperForSpecs.ObservedData("SolubilityTable"); A.CallTo(() => _formulaFactory.CreateTableFormula(A <bool> ._)).Returns(new TableFormula { UseDerivedValues = true }); A.CallTo(() => _dataImporter.ImportDataSets( A <IReadOnlyList <MetaDataCategory> > .Ignored, A <IReadOnlyList <ColumnInfo> > .Ignored, A <DataImporterSettings> .Ignored, A <string> .Ignored)).Returns((new List <DataRepository>() { _solubilityDataRepository }, null)); }
protected override void Context() { _eventPublisher = A.Fake <IEventPublisher>(); _view = A.Fake <IParameterIdentificationWeightedObservedDataCollectorView>(); _applicationController = A.Fake <IApplicationController>(); sut = new ParameterIdentificationWeightedObservedDataCollectorPresenter(_view, _applicationController, _eventPublisher); _parameterIdentification = new ParameterIdentification(); _weightedObservedData = new WeightedObservedData(DomainHelperForSpecs.ObservedData()); _outputMapping = new OutputMapping { WeightedObservedData = _weightedObservedData }; _parameterIdentification.AddOutputMapping(_outputMapping); _presenter = A.Fake <IParameterIdentificationWeightedObservedDataPresenter>(); A.CallTo(() => _applicationController.Start <IParameterIdentificationWeightedObservedDataPresenter>()).Returns(_presenter); }
protected override void Context() { _view = A.Fake <IParameterIdentificationSingleRunAnalysisView>(); _chartEditorAndDisplayPresenter = A.Fake <IChartEditorAndDisplayPresenter>(); _curveNamer = A.Fake <ICurveNamer>(); _dataColumnToPathElementsMapper = A.Fake <IDataColumnToPathElementsMapper>(); _chartTemplatingTask = A.Fake <IChartTemplatingTask>(); _presentationSettingsTask = A.Fake <IPresentationSettingsTask>(); _dimensionFactory = A.Fake <IDimensionFactory>(); _predictedVsObservedService = A.Fake <IPredictedVsObservedChartService>(); _chartEditorLayoutTask = A.Fake <IChartEditorLayoutTask>(); _projectRetreiver = A.Fake <IProjectRetriever>(); _chartPresenterContext = A.Fake <ChartPresenterContext>(); A.CallTo(() => _chartPresenterContext.EditorAndDisplayPresenter).Returns(_chartEditorAndDisplayPresenter); A.CallTo(() => _chartPresenterContext.CurveNamer).Returns(_curveNamer); A.CallTo(() => _chartPresenterContext.DataColumnToPathElementsMapper).Returns(_dataColumnToPathElementsMapper); A.CallTo(() => _chartPresenterContext.TemplatingTask).Returns(_chartTemplatingTask); A.CallTo(() => _chartPresenterContext.PresenterSettingsTask).Returns(_presentationSettingsTask); A.CallTo(() => _chartPresenterContext.DimensionFactory).Returns(_dimensionFactory); A.CallTo(() => _chartPresenterContext.EditorLayoutTask).Returns(_chartEditorLayoutTask); A.CallTo(() => _chartPresenterContext.ProjectRetriever).Returns(_projectRetreiver); _observationData = DomainHelperForSpecs.ObservedData(); _simulationData = DomainHelperForSpecs.IndividualSimulationDataRepositoryFor("Simulation"); _noDimensionColumnForSimulation = _simulationData.FirstDataColumn(); _predictedVsObservedChart = new ParameterIdentificationPredictedVsObservedChart().WithAxes(); _parameterIdentification = A.Fake <ParameterIdentification>(); sut = new ParameterIdentificationPredictedVsObservedChartPresenter(_view, _chartPresenterContext, _predictedVsObservedService); _parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>(); A.CallTo(() => _parameterIdentification.Results).Returns(new[] { _parameterIdentificationRunResult }); _residualResults = new ResidualsResult(); _optimizationRunResult = new OptimizationRunResult { ResidualsResult = _residualResults, SimulationResults = new List <DataRepository> { _simulationData } }; _parameterIdentificationRunResult.BestResult = _optimizationRunResult; sut.InitializeAnalysis(_predictedVsObservedChart); }
protected override void Context() { _view = A.Fake <IDataBrowserView>(); sut = new DataBrowserPresenter(_view); sut.SetDisplayQuantityPathDefinition(x => new PathElements { { PathElement.Name, new PathElementDTO { DisplayName = x.Name } } }); A.CallTo(() => _view.BindTo(A <IEnumerable <DataColumnDTO> > ._)) .Invokes(x => _allDataColumnDTOs = x.GetArgument <IEnumerable <DataColumnDTO> >(0).ToList()); _obsData1 = DomainHelperForSpecs.ObservedData("OBS1"); _column1 = _obsData1.FirstDataColumn(); _obsData2 = DomainHelperForSpecs.ObservedData("OBS2"); _column2 = _obsData2.FirstDataColumn(); }
protected override void Context() { base.Context(); _bestColumn = DomainHelperForSpecs.ObservedData().FirstDataColumn(); _currentColumn = DomainHelperForSpecs.ObservedData().FirstDataColumn(); _bestResult = A.Fake <OptimizationRunResult>(); _currentResult = A.Fake <OptimizationRunResult>(); sut.EditParameterIdentification(_parameterIdentification); sut.SelectedOutput = A.Fake <OutputMapping>(); A.CallTo(() => _bestResult.SimulationResultFor(A <string> ._)).Returns(_bestColumn); A.CallTo(() => _currentResult.SimulationResultFor(A <string> ._)).Returns(_currentColumn); _runState = A.Fake <ParameterIdentificationRunState>(); A.CallTo(() => _runState.BestResult).Returns(_bestResult); A.CallTo(() => _runState.CurrentResult).Returns(_currentResult); }
protected override async Task Context() { await base.Context(); _expectedOutputPath = Path.Combine(_qualificationConfiguration.OutputFolder, PROJECT_NAME); DirectoryHelper.DirectoryExists = s => string.Equals(s, _expectedOutputPath); DirectoryHelper.DeleteDirectory = (s, b) => _deletedDirectory = s; _simulationName = "S1"; _simulation = new Simulation { Name = _simulationName }; _individualSimulation = new IndividualSimulation { Name = _simulationName }; _input = new Input { Project = PROJECT_NAME, Name = _simulationName, SectionId = 2, Type = PKSimBuildingBlockType.Simulation, SectionLevel = 5 }; _expectedSimulationPath = Path.Combine(_expectedOutputPath, _simulationName); _simulationExport = new SimulationMapping { Project = PROJECT_NAME, Simulation = _simulationName, Path = _expectedSimulationPath }; _simulationExports = new[] { _simulationExport }; A.CallTo(() => _exportSimulationRunner.ExportSimulationsIn(_project, A <ExportRunOptions> ._)) .Invokes(x => _exportOptions = x.GetArgument <ExportRunOptions>(1)) .Returns(_simulationExports); _observedData = DomainHelperForSpecs.ObservedData().WithName("OBS"); _project.AddObservedData(_observedData); _projectSnapshot.Simulations = new[] { _simulation }; _expectedObservedDataXlsFullPath = Path.Combine(_qualificationConfiguration.ObservedDataFolder, $"{_observedData.Name}{Constants.Filter.XLSX_EXTENSION}"); _expectedObservedDataCsvFullPath = Path.Combine(_qualificationConfiguration.ObservedDataFolder, $"{_observedData.Name}{Constants.Filter.CSV_EXTENSION}"); _expectedInputFullPath = Path.Combine(_qualificationConfiguration.InputsFolder, PROJECT_NAME, PKSimBuildingBlockType.Simulation.ToString(), $"{_simulationName}{CoreConstants.Filter.MARKDOWN_EXTENSION}"); A.CallTo(() => _jsonSerializer.Serialize(A <QualificationMapping> ._, _qualificationConfiguration.MappingFile)) .Invokes(x => _mapping = x.GetArgument <QualificationMapping>(0)); _project.AddBuildingBlock(_individualSimulation); _qualificationConfiguration.Inputs = new[] { _input }; _qualificationConfiguration.Simulations = new[] { _simulationName, }; _runOptions.Run = true; }
protected override void Context() { base.Context(); _outputPath = "Liver|Cell|Drug"; _simulation = A.Fake <ISimulation>().WithId("Sim"); _parameterIdentification = new ParameterIdentification(); _output1 = A.Fake <IQuantity>(); var allOutputs = new PathCacheForSpecs <IQuantity> { { _outputPath, _output1 } }; A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation)).Returns(allOutputs); _observedData1 = DomainHelperForSpecs.ObservedData("OBS1"); _observedData2 = DomainHelperForSpecs.ObservedData("OBS2"); _observedData3 = DomainHelperForSpecs.ObservedData("OBS3"); A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation)).Returns(new[] { _observedData1, _observedData2 }); var simulationQuantitySelection = A.Fake <SimulationQuantitySelection>(); A.CallTo(() => simulationQuantitySelection.Path).Returns(_outputPath); _parameterIdentification.AddOutputMapping(new OutputMapping { WeightedObservedData = new WeightedObservedData(_observedData2), OutputSelection = simulationQuantitySelection }); _observedData1.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.MOLECULE, Value = "Drug" }); _observedData1.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.ORGAN, Value = "Liver" }); _observedData1.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.COMPARTMENT, Value = "Cell" }); _observedData3.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.ORGAN, Value = "Kidney" }); }
protected override void Context() { base.Context(); var otherSimulationDataColumn = new DataColumn("Col", DomainHelperForSpecs.ConcentrationDimensionForSpecs(), _simulationDataColumn.BaseGrid) { Values = new[] { 0f, 2.5f, 0.9f, 0.9f, 0.5f }, DataInfo = { Origin = ColumnOrigins.Calculation }, QuantityInfo = new QuantityInfo("Concentration", new[] { "Sim", "Organism", "Liver", "Plasma", "Concentration" }, QuantityType.Drug) }; _simulationResults.Add(otherSimulationDataColumn); _outputMapping2 = A.Fake <OutputMapping>(); A.CallTo(() => _outputMapping2.FullOutputPath).Returns(otherSimulationDataColumn.PathAsString); var observedData2 = DomainHelperForSpecs.ObservedData().WithName("OBS2"); _outputMapping2.WeightedObservedData = new WeightedObservedData(observedData2); _outputMappings.Add(_outputMapping2); sut = new ResidualCalculatorForOnlyObservedData(_timeGridRestrictor, _dimensionFactory); }
protected override void Context() { base.Context(); _simulation = A.Fake <ISimulation>(); _project = A.Fake <IProject>(); _parameterIdentification = new ParameterIdentification(); A.CallTo(() => _executionContext.Project).Returns(_project); A.CallTo(() => _project.AllParameterIdentifications).Returns(new[] { _parameterIdentification }); _parameterIdentification.AddSimulation(_simulation); _initialObjectPath = new ObjectPath("oldName", "path"); var parameterIdentificationRunResult = new ParameterIdentificationRunResult { BestResult = new OptimizationRunResult() }; _simulationDataRepository = DomainHelperForSpecs.SimulationDataRepositoryFor("oldName"); _observationDataRepository = DomainHelperForSpecs.ObservedData(); _observationDataRepository.AllButBaseGrid().Each(x => x.QuantityInfo.Path = _initialObjectPath); _simulationDataRepository.AllButBaseGrid().Each(x => x.QuantityInfo.Path = _initialObjectPath); parameterIdentificationRunResult.BestResult.AddResult(_simulationDataRepository); _residualsResult = new ResidualsResult(); _residualsResult.AddOutputResiduals(_initialObjectPath.PathAsString, _observationDataRepository, new List <Residual> { new Residual(0, 1, 1) }); parameterIdentificationRunResult.BestResult.ResidualsResult = _residualsResult; _parameterIdentification.AddResult(parameterIdentificationRunResult); var outputMapping = new OutputMapping { WeightedObservedData = new WeightedObservedData(_observationDataRepository), OutputSelection = new ParameterSelection(_simulation, _initialObjectPath.PathAsString) }; _parameterIdentification.AddOutputMapping(outputMapping); }
protected override void Context() { _identification = A.Fake <ParameterIdentification>(); _dimensionFactory = A.Fake <IDimensionFactory>(); _displayUnitRetriever = A.Fake <IDisplayUnitRetriever>(); A.CallTo(_dimensionFactory).WithReturnType <IDimension>().ReturnsLazily(x => x.Arguments.Get <IWithDimension>(0).Dimension); _predictedVsObservedChart = new ParameterIdentificationPredictedVsObservedChart().WithAxes(); _observedConcentrationData = DomainHelperForSpecs.ObservedData(); _concentrationObservationColumn = _observedConcentrationData.FirstDataColumn(); _simulationData = DomainHelperForSpecs.IndividualSimulationDataRepositoryFor("Simulation"); _simulationColumn = _simulationData.FirstDataColumn(); _fractionObservedData = DomainHelperForSpecs.ObservedData(); _fractionObservationColumn = _fractionObservedData.FirstDataColumn(); _fractionObservationColumn.Dimension = DomainHelperForSpecs.NoDimension(); sut = new PredictedVsObservedChartService(_dimensionFactory, _displayUnitRetriever); }
protected override void Context() { _dimensionFactory = A.Fake <IDimensionFactory>(); sut = new CurveChart().WithAxes(); _xAxis = sut.AxisBy(AxisTypes.X); _yAxis = sut.AxisBy(AxisTypes.Y); _obsData1 = DomainHelperForSpecs.ObservedData(); _obsData2 = DomainHelperForSpecs.ObservedData(); _curveOnYAxis = new Curve { yAxisType = AxisTypes.Y }; _curveOnYAxis.SetxData(_obsData1.BaseGrid, _dimensionFactory); _curveOnYAxis.SetyData(_obsData1.FirstDataColumn(), _dimensionFactory); _curveOnY2Axis = new Curve { yAxisType = AxisTypes.Y2 }; _curveOnY2Axis.SetxData(_obsData2.BaseGrid, _dimensionFactory); _curveOnY2Axis.SetyData(_obsData2.FirstDataColumn(), _dimensionFactory); }
protected override void Context() { base.Context(); _dimensionFactory = A.Fake <IDimensionFactory>(); _individualSimulationComparison = new IndividualSimulationComparison(); var dataRepository = DomainHelperForSpecs.ObservedData(); var curve = new Curve(); curve.SetxData(dataRepository.BaseGrid, _dimensionFactory); curve.SetyData(dataRepository.FirstDataColumn(), _dimensionFactory); _individualSimulationComparison.AddCurve(curve); sut.InitializeAnalysis(_individualSimulationComparison); _simulation = A.Fake <IndividualSimulation>(); A.CallTo(() => _simulation.HasResults).Returns(true); var simulationNode = new SimulationNode(new ClassifiableSimulation { Subject = _simulation }); _dropEventArgs = new DragEventArgs(new DataObject(new DragDropInfo(new List <SimulationNode> { simulationNode })), 0, 0, 0, DragDropEffects.All, DragDropEffects.All); }
protected override void Context() { _binIntervalCreator = A.Fake <IBinIntervalsCreator>(); _observedData = DomainHelperForSpecs.ObservedData(); sut = new ResidualDistibutionDataCreator(_binIntervalCreator); }
protected override void Context() { base.Context(); _dataRepository = DomainHelperForSpecs.ObservedData(); }
public override void GlobalContext() { base.GlobalContext(); _observedData = DomainHelperForSpecs.ObservedData(); _sim1 = new IndividualSimulation { Id = "Sim1", Name = "Sim1", IsLoaded = true, Model = new Model { Root = new Container() } }; _sim1.Model.Root.Add(new Container { new Parameter().WithName("P") }.WithName("Liver")); _sim2 = new IndividualSimulation { Id = "Sim2", Name = "Sim2", IsLoaded = true, Model = new Model { Root = new Container() } }; _sim2.Model.Root.Add(new Container { new Parameter().WithName("P") }.WithName("Liver")); _objectBaseRepository = IoC.Resolve <IWithIdRepository>(); var workspace = IoC.Resolve <ICoreWorkspace>(); _project = IoC.Resolve <PKSimProject>(); workspace.Project = _project; _objectBaseRepository.Register(_sim1); _objectBaseRepository.Register(_sim2); _project.AddObservedData(_observedData); _project.AddBuildingBlock(_sim1); _project.AddBuildingBlock(_sim2); _parameterIdentification = new ParameterIdentification(); _parameterIdentification.AddSimulation(_sim1); _parameterIdentification.AddSimulation(_sim2); _outputMapping = new OutputMapping { WeightedObservedData = new WeightedObservedData(_observedData), OutputSelection = new SimulationQuantitySelection(_sim1, new QuantitySelection("A|B", QuantityType.Metabolite)), Weight = 5, Scaling = Scalings.Log }; _outputMapping.WeightedObservedData.Weights[1] = 10; _parameterIdentification.AddOutputMapping(_outputMapping); _identificationParameter = DomainHelperForSpecs.IdentificationParameter(min: 1, max: 10, startValue: 5); _parameterSelection1 = new ParameterSelection(_sim1, new QuantitySelection("Liver|P", QuantityType.Parameter)); _parameterSelection2 = new ParameterSelection(_sim2, new QuantitySelection("Liver|P", QuantityType.Parameter)); _identificationParameter.AddLinkedParameter(_parameterSelection1); _identificationParameter.AddLinkedParameter(_parameterSelection2); _parameterIdentification.AddIdentificationParameter(_identificationParameter); _identificationParameter.Scaling = Scalings.Linear; _parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("AA"); _parameterIdentification.AlgorithmProperties.Add(new ExtendedProperty <double> { Name = "Toto", Value = 5 }); _runResult = new ParameterIdentificationRunResult(); _parameterIdentification.AddResult(_runResult); _parameterIdentification.AddAnalysis(new ParameterIdentificationPredictedVsObservedChart()); _parameterIdentification.AddAnalysis(new ParameterIdentificationTimeProfileChart()); _parameterIdentification.AddAnalysis(new ParameterIdentificationResidualHistogram()); _parameterIdentification.AddAnalysis(new ParameterIdentificationResidualVsTimeChart()); GlobalBecause(); }
protected override void Context() { base.Context(); _dataRepository = DomainHelperForSpecs.ObservedData(); _dataRepository.FirstDataColumn().Dimension = DomainHelperForSpecs.FractionDimensionForSpecs(); }
protected override void Context() { base.Context(); _dataRepository = DomainHelperForSpecs.ObservedData(); A.CallTo(() => _mdiChildPresenter.Subject).Returns(_dataRepository); }
protected override void Context() { _observedData = DomainHelperForSpecs.ObservedData(); sut = new WeightedObservedData(_observedData); }
protected override void Context() { _modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>(); _residualCalculatorFactory = A.Fake <IResidualCalculatorFactory>(); _timeGridUpdater = A.Fake <ITimeGridUpdater>(); _simModelBatchFactory = A.Fake <ISimModelBatchFactory>(); _optimizationAlgorithmMapper = A.Fake <IParameterIdentificationAlgorithmToOptmizationAlgorithmMapper>(); _outputSelectionUpdater = A.Fake <IOutputSelectionUpdater>(); _coreUserSettings = A.Fake <ICoreUserSettings>(); _jacobianMatrixCalculator = A.Fake <IJacobianMatrixCalculator>(); _coreUserSettings.MaximumNumberOfCoresToUse = 2; sut = new ParameterIdentificationRun(_residualCalculatorFactory, _timeGridUpdater, _simModelBatchFactory, _modelCoreSimulationMapper, _optimizationAlgorithmMapper, _outputSelectionUpdater, _coreUserSettings, _jacobianMatrixCalculator); _simulation = A.Fake <ISimulation>(); _parameter1 = A.Fake <IParameter>(); _parameter1.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs(); _parameter1.Value = 15; _parameter2 = A.Fake <IParameter>(); _parameter2.Value = 35; _parameter2.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs(); _parameterIdentification = new ParameterIdentification(); _parameterIdentification.Configuration.LLOQMode = LLOQModes.OnlyObservedData; _parameterIdentification.Configuration.RemoveLLOQMode = RemoveLLOQModes.NoTrailing; _parameterIdentification.AddSimulation(_simulation); _parameterSelection1 = ParameterSelectionFor(_parameter1, "ParameterPath1"); _parameterSelection2 = ParameterSelectionFor(_parameter2, "ParameterPath2"); _identificationParameter = DomainHelperForSpecs.IdentificationParameter("IdParam", min: 10, max: 20, startValue: 15); _identificationParameter.AddLinkedParameter(_parameterSelection1); _identificationParameter.AddLinkedParameter(_parameterSelection2); _modelCoreSimulation = A.Fake <IModelCoreSimulation>(); A.CallTo(() => _modelCoreSimulationMapper.MapFrom(_simulation, true)).Returns(_modelCoreSimulation); _outputMapping = A.Fake <OutputMapping>(); A.CallTo(() => _outputMapping.UsesSimulation(_simulation)).Returns(true); A.CallTo(() => _outputMapping.WeightedObservedData.ObservedData).Returns(DomainHelperForSpecs.ObservedData()); _parameterIdentification.AddOutputMapping(_outputMapping); _simModelBatch = A.Fake <ISimModelBatch>(); A.CallTo(() => _simModelBatchFactory.Create()).Returns(_simModelBatch); _parameterIdentification.AddIdentificationParameter(_identificationParameter); _residualCalculator = A.Fake <IResidualCalculator>(); A.CallTo(_residualCalculatorFactory).WithReturnType <IResidualCalculator>().Returns(_residualCalculator); _algorithm = A.Fake <IOptimizationAlgorithm>(); A.CallTo(() => _optimizationAlgorithmMapper.MapFrom(_parameterIdentification.AlgorithmProperties)).Returns(_algorithm); _cancellationTokenSource = new CancellationTokenSource(); _cancellationToken = _cancellationTokenSource.Token; _runInitializer = A.Fake <IParameterIdentifcationRunInitializer>(); A.CallTo(() => _runInitializer.InitializeRun()).ReturnsAsync(_parameterIdentification); PerformExtraInitializationSteps(); sut.InitializeWith(_runInitializer); }
protected override void Context() { _view = A.Fake <IParameterIdentificationOutputMappingView>(); _observedDataRepository = A.Fake <IObservedDataRepository>(); _entitiesInSimulationRetriever = A.Fake <IEntitiesInSimulationRetriever>(); _outputMappingDTOMapper = A.Fake <IOutputMappingToOutputMappingDTOMapper>(); _simulationQuantitySelectionDTOMapper = A.Fake <IQuantityToSimulationQuantitySelectionDTOMapper>(); _parameterIdentificationTask = A.Fake <IParameterIdentificationTask>(); sut = new ParameterIdentificationOutputMappingPresenter(_view, _entitiesInSimulationRetriever, _observedDataRepository, _outputMappingDTOMapper, _simulationQuantitySelectionDTOMapper, _parameterIdentificationTask); _observedData1 = DomainHelperForSpecs.ObservedData("Obs1").WithName("Obs1"); _weightedObservedData1 = new WeightedObservedData(_observedData1); _observedData2 = DomainHelperForSpecs.ObservedData("Obs2").WithName("Obs2"); _weightedObservedData2 = new WeightedObservedData(_observedData2); _parameterIdentification = new ParameterIdentification(); _simulation1 = A.Fake <ISimulation>().WithId("Id1"); _simulation2 = A.Fake <ISimulation>().WithId("Id2"); _usedObservedData1 = new UsedObservedData { Id = "Obs1" }; _usedObservedData2 = new UsedObservedData { Id = "Obs2" }; A.CallTo(() => _observedDataRepository.All()).Returns(new[] { _observedData1, _observedData2 }); A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation1)).Returns(new[] { _observedData2 }); A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation2)).Returns(new[] { _observedData1, _observedData2 }); _parameterIdentification.AddSimulation(_simulation1); _parameterIdentification.AddSimulation(_simulation2); _quantity1 = A.Fake <IQuantity>(); _quantity2 = A.Fake <IQuantity>(); _output1 = A.Fake <SimulationQuantitySelectionDTO>(); A.CallTo(() => _output1.Simulation).Returns(_simulation1); _output2 = A.Fake <SimulationQuantitySelectionDTO>(); A.CallTo(() => _output2.Simulation).Returns(_simulation2); A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation1)).Returns(new PathCache <IQuantity>(new EntityPathResolverForSpecs()) { { "AA", _quantity1 } }); A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation2)).Returns(new PathCache <IQuantity>(new EntityPathResolverForSpecs()) { { "BB", _quantity2 } }); A.CallTo(() => _simulationQuantitySelectionDTOMapper.MapFrom(_simulation1, _quantity1)).Returns(_output1); A.CallTo(() => _simulationQuantitySelectionDTOMapper.MapFrom(_simulation2, _quantity2)).Returns(_output2); A.CallTo(() => _view.BindTo(A <IEnumerable <OutputMappingDTO> > ._)) .Invokes(x => _allOutputMappingDTOs = x.GetArgument <IEnumerable <OutputMappingDTO> >(0)); sut.EditParameterIdentification(_parameterIdentification); _outputMapping1 = A.Fake <OutputMapping>(); _outputMapping2 = A.Fake <OutputMapping>(); _outputMappingDTO1 = new OutputMappingDTO(_outputMapping1) { Output = _output1 }; _outputMappingDTO2 = new OutputMappingDTO(_outputMapping2) { Output = _output2 }; A.CallTo(() => _outputMapping1.Simulation).Returns(_simulation1); A.CallTo(() => _outputMapping2.Simulation).Returns(_simulation2); A.CallTo(() => _outputMappingDTOMapper.MapFrom(_outputMapping1, A <IEnumerable <SimulationQuantitySelectionDTO> > ._)).Returns(_outputMappingDTO1); A.CallTo(() => _outputMappingDTOMapper.MapFrom(_outputMapping2, A <IEnumerable <SimulationQuantitySelectionDTO> > ._)).Returns(_outputMappingDTO2); }