public void CalculateBioavailabilityFor(Simulation simulation, string compoundName)
{
var individualSimulation = simulation as IndividualSimulation;
if (individualSimulation == null)
{
return;
}
var compound = simulation.Compounds.FindByName(compoundName);
//BA calculated with a Simple IV with 15 min infusion
var simpleIvProtocol = _protocolFactory.Create(ProtocolMode.Simple, ApplicationTypes.Intravenous)
.WithName("Simple IV for Bioavailability")
.DowncastTo <SimpleProtocol>();
simpleIvProtocol.Parameter(Constants.Parameters.INFUSION_TIME).Value = 15;
var simulationSingleDosingItem = singleDosingItem(simulation, compound);
simpleIvProtocol.Dose.DisplayUnit = simulationSingleDosingItem.Dose.DisplayUnit;
simpleIvProtocol.Dose.Value = simulationSingleDosingItem.Dose.Value;
simpleIvProtocol.StartTime.Value = simulationSingleDosingItem.StartTime.Value;
var ivSimulation = _globalPKAnalysisRunner.RunForBioavailability(simpleIvProtocol, individualSimulation, compound);
var venousBloodCurve = ivSimulation.DataRepository.VenousBloodColumn(compoundName);
var pkVenousBlood = _pkAnalysisTask.CalculateFor(ivSimulation, venousBloodCurve).PKAnalysis;
individualSimulation.CompoundPKFor(compoundName).AucIV = pkParameterValue(pkVenousBlood, Constants.PKParameters.AUC_inf);
}
private IEnumerable <object> pkAnalysisFor(Simulation simulation, CurveChart chart, OSPSuiteTracker buildTracker)
{
var report = new List <object>();
var globalPKAnalysis = _globalPKAnalysisTask.CalculateGlobalPKAnalysisFor(new[] { simulation });
updateDisplayUnits(globalPKAnalysis, PresentationSettingsFor(chart, PresenterConstants.PresenterKeys.GlobalPKAnalysisPresenter));
var globalPKAnalysisTable = _globalPKAnalysisToDataTableMapper.MapFrom(globalPKAnalysis);
if (globalPKAnalysisTable.Rows.Count > 0)
{
report.Add(buildTracker.GetStructureElementRelativeToLast(PKSimConstants.UI.GlobalPKAnalyses, 1));
report.Add(globalPKAnalysisTable);
}
var curvesToDisplay = chart.Curves.ForPKAnalysis();
var pkAnalyses = _pkAnalysisTask.CalculateFor(new[] { simulation }, curvesToDisplay.Select(c => c.yData)).ToList();
updateDisplayUnits(pkAnalyses, PresentationSettingsFor(chart, PresenterConstants.PresenterKeys.IndividualPKParametersPresenter));
var pkAnalysesTable = _pkAnalysisToDataTableMapper.MapFrom(pkAnalyses, curvesToDisplay);
var pkAnalysesForReport = new PKAnalysesTable(pkAnalysesTable);
report.Add(buildTracker.GetStructureElementRelativeToLast(PKSimConstants.UI.PKAnalyses, 1));
report.Add(pkAnalysesForReport);
return(report);
}
public void CalculatePKAnalysis(IPopulationDataCollector populationDataCollector, ChartData <TimeProfileXValue, TimeProfileYValue> timeProfileChartData)
{
_allAnalyses.Clear();
_populationDataCollector = populationDataCollector;
_allPKAnalyses = _pkAnalysesTask.CalculateFor(populationDataCollector, timeProfileChartData);
_allAnalyses.AddRange(_allPKAnalyses);
LoadPreferredUnitsForPKAnalysis();
BindToPKAnalysis();
}
private IEnumerable <object> pkAnalysisFor(PopulationPKAnalyses populationPKAnalyses, OSPSuiteTracker buildTracker)
{
var report = new List <object>();
var pkAnalyses = _pkAnalysisTask.CalculateFor(populationPKAnalyses.DataCollector, populationPKAnalyses.ChartData).ToList();
updateDisplayUnits(pkAnalyses, PresentationSettingsFor(populationPKAnalyses.PopulationAnalysisChart, PresenterConstants.PresenterKeys.PopulationPKAnalysisPresenter));
var pkAnalysesTable = _pkAnalysisToDataTableMapper.MapFrom(pkAnalyses);
var pkAnalysesForReport = new PKAnalysesTable(pkAnalysesTable);
report.Add(buildTracker.GetStructureElementRelativeToLast(PKSimConstants.UI.PKAnalyses, 1));
report.Add(pkAnalysesForReport);
return(report);
}
public void ShowPKAnalysis(IEnumerable <Simulation> simulations, IEnumerable <Curve> curves)
{
_simulations = simulations.ToList();
_globalPKAnalysisPresenter.CalculatePKAnalysis(_simulations);
var globalPKAnalysis = _globalPKAnalysisPresenter.GlobalPKAnalysis;
var curveList = curves.ToList();
createColumnsWithPKAnalysesFrom(curveList);
_allColumns = _curveCache.Keys.ToList();
_allPKAnalysis = _pkAnalysesTask.CalculateFor(_simulations, _allColumns, globalPKAnalysis).ToList();
_view.GlobalPKVisible = _globalPKAnalysisPresenter.HasParameters();
_view.ShowControls = true;
LoadPreferredUnitsForPKAnalysis();
BindToPKAnalysis();
}
protected override void Context()
{
_exportTask = A.Fake <IPKAnalysisExportTask>();
_pkAnalysesTask = A.Fake <IPKAnalysesTask>();
_view = A.Fake <IPopulationPKAnalysisView>();
_populationPKAnalysisToDTOMapper = A.Fake <IPopulationPKAnalysisToPKAnalysisDTOMapper>();
_populationPKAnalysisToDataTableMapper = A.Fake <IPopulationPKAnalysisToDataTableMapper>();
_pkParameterRepository = A.Fake <IPKParameterRepository>();
_presenterSettingsTask = A.Fake <IPresentationSettingsTask>();
sut = new PopulationPKAnalysisPresenter(_view, _pkAnalysesTask, _exportTask, _populationPKAnalysisToDTOMapper, _pkParameterRepository, _presenterSettingsTask);
_populationDataCollector = A.Fake <IPopulationDataCollector>();
_timeProfileChartData = new ChartData <TimeProfileXValue, TimeProfileYValue>(null, null);
var pane = new PaneData <TimeProfileXValue, TimeProfileYValue>(null)
{
Caption = "TOTO"
};
_curve1 = new TimeProfileCurveData {
Caption = "A", Pane = pane
};
_curve2 = new TimeProfileCurveData {
Caption = "B", Pane = pane
};
_pk1 = new PKAnalysis();
_pk2 = new PKAnalysis();
_allPKanalysis = new List <PopulationPKAnalysis>
{
new PopulationPKAnalysis(_curve1, _pk1),
new PopulationPKAnalysis(_curve2, _pk2),
};
A.CallTo(() => _pkAnalysesTask.CalculateFor(_populationDataCollector, _timeProfileChartData)).Returns(_allPKanalysis);
A.CallTo(() => _view.BindTo(A <PKAnalysisDTO> ._)).Invokes(x => _dataTable = x.GetArgument <PKAnalysisDTO>(0).DataTable);
A.CallTo(() => _populationPKAnalysisToDataTableMapper.MapFrom(A <IReadOnlyList <PopulationPKAnalysis> > ._, true)).Returns(_dataTable);
}
protected override void Context()
{
base.Context();
_context = A.Fake <IExecutionContext>();
_quantityRetriever = A.Fake <IEntitiesInContainerRetriever>();
_populationAnalysisTask = A.Fake <IPKAnalysesTask>();
_pkAnalyses = A.Fake <PopulationSimulationPKAnalyses>();
_quantityCache = new PathCacheForSpecs <IQuantity>();
_quantity1 = new MoleculeAmount();
_quantity2 = new MoleculeAmount();
_quantityCache.Add("PATH1", _quantity1);
_quantityCache.Add("PATH2", _quantity2);
A.CallTo(() => _context.Resolve <IEntitiesInContainerRetriever>()).Returns(_quantityRetriever);
A.CallTo(() => _context.Resolve <IPKAnalysesTask>()).Returns(_populationAnalysisTask);
A.CallTo(() => _quantityRetriever.QuantitiesFrom(_populationSimulation)).Returns(_quantityCache);
A.CallTo(() => _populationAnalysisTask.CalculateFor(_populationSimulation)).Returns(_pkAnalyses);
_allQuantityPaths = new List <string> {
"PATH1", "PATH2"
};
_simulationSettings = new OutputSelections();
A.CallTo(() => _populationSimulation.OutputSelections).Returns(_simulationSettings);
A.CallTo(() => _simulationResults.AllQuantityPaths()).Returns(_allQuantityPaths);
}
public void Synchronize(PopulationSimulation populationSimulation, SimulationResults newResults)
{
populationSimulation.Results = newResults;
populationSimulation.PKAnalyses = _populationPKAnalysesTask.CalculateFor(populationSimulation);
}