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Fixes #2439 Misleading info in global POP PK Analysis if no parameter… #2459

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Dec 7, 2022
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Fixes #2439 Misleading info in global POP PK Analysis if no parameter… #2459

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b62e4db
Fixes #2439 Misleading info in global POP PK Analysis if no parameter…
rwmcintosh Dec 5, 2022
203031b
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rwmcintosh Dec 6, 2022
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8 changes: 5 additions & 3 deletions src/PKSim.Core/Model/SchemaItem.cs
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Expand Up @@ -52,10 +52,12 @@ public string TargetOrgan

public bool NeedsFormulation => ApplicationType.NeedsFormulation;

public bool IsOral => ApplicationType==ApplicationTypes.Oral;
public bool IsOral => ApplicationType == ApplicationTypes.Oral;

public bool IsUserDefined => ApplicationType == ApplicationTypes.UserDefined;

public bool IsIV => ApplicationType == ApplicationTypes.Intravenous || ApplicationType == ApplicationTypes.IntravenousBolus;

public bool IsUserDefined => ApplicationType==ApplicationTypes.UserDefined;

public virtual IParameter StartTime => this.Parameter(Constants.Parameters.START_TIME);

public virtual IParameter Dose => this.Parameter(CoreConstants.Parameters.INPUT_DOSE);
Expand Down
51 changes: 21 additions & 30 deletions src/PKSim.Core/Services/PKAnalysesTask.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,7 @@
using static PKSim.Core.CoreConstants.PKAnalysis;
using static PKSim.Core.CoreConstants.Species;
using static PKSim.Core.CoreConstants.Units;
using Compound = PKSim.Core.Model.Compound;
using IParameterFactory = PKSim.Core.Model.IParameterFactory;
using PKAnalysis = PKSim.Core.Model.PKAnalysis;

namespace PKSim.Core.Services
{
Expand Down Expand Up @@ -110,7 +108,7 @@ public PKAnalysesTask(ILazyLoadTask lazyLoadTask,
IStatisticalDataCalculator statisticalDataCalculator,
IRepresentationInfoRepository representationInfoRepository,
IParameterFactory parameterFactory, IProtocolToSchemaItemsMapper protocolToSchemaItemsMapper, IProtocolFactory protocolFactory,
IGlobalPKAnalysisRunner globalPKAnalysisRunner, IVSSCalculator vssCalculator, IInteractionTask interactionTask, ICloner cloner, IEntityPathResolver entityPathResolver) :
IGlobalPKAnalysisRunner globalPKAnalysisRunner, IVSSCalculator vssCalculator, IInteractionTask interactionTask, ICloner cloner, IEntityPathResolver entityPathResolver) :
base(lazyLoadTask, pkValuesCalculator, pkParameterRepository, pkCalculationOptionsFactory)
{
_lazyLoadTask = lazyLoadTask;
Expand Down Expand Up @@ -145,10 +143,7 @@ public PopulationSimulationPKAnalyses CalculateFor(PopulationSimulation populati
{
var globalPKAnalysesForIndividuals = new Cache<int, GlobalPKAnalysis>();
var analyses = base.CalculateFor(populationSimulation, populationSimulation.Results,
individualId =>
{
updateBodyWeightForIndividual(bodyWeightParameter, allBodyWeights, individualId);
},
individualId => { updateBodyWeightForIndividual(bodyWeightParameter, allBodyWeights, individualId); },
(individualId, options, compoundName) =>
{
var globalPKAnalysis = globalPkAnalysisForIndividual(globalPKAnalysesForIndividuals, individualId);
Expand Down Expand Up @@ -234,6 +229,7 @@ private static CompoundPKContext createCompoundPKContext(Compound compound, Indi
compoundPK.AddDDIAucInf(individualId, individualSimulation.AucDDI[compound.Name]);
compoundPK.AddDDICMax(individualId, individualSimulation.CMaxDDI[compound.Name]);
}

return compoundPKContext;
}

Expand All @@ -247,7 +243,7 @@ private Container createCompoundContainer(PopulationSimulation populationSimulat
var compoundContainer = new Container().WithName(compoundName);
populationSimulation.PKAnalyses.AllPKParametersFor(compoundName).Each(quantityPKParameter =>
{
double? defaultValue = new SortedFloatArray(quantityPKParameter.ValuesAsArray, alreadySorted:false).Median();
double? defaultValue = new SortedFloatArray(quantityPKParameter.ValuesAsArray, alreadySorted: false).Median();
if (double.IsNaN(defaultValue.Value))
defaultValue = null;

Expand Down Expand Up @@ -319,7 +315,7 @@ private IContainer calculateGlobalPKAnalysisFor(Simulation simulation, Compound
var vssPlasmaOverF = createParameter(VssPlasmaOverF, bloodPlasmaPK[Vss], VolumePerBodyWeight);
var vdPlasma = createParameter(VdPlasma, bloodPlasmaPK[Vd], VolumePerBodyWeight);
var vdPlasmaOverF = createParameter(VdPlasmaOverF, bloodPlasmaPK[Vd], VolumePerBodyWeight);
if(simulation is IndividualSimulation)
if (simulation is IndividualSimulation)
vssPhysChem = createParameter(VssPhysChem, calculateVSSPhysChemFor(simulation, compoundName), VolumePerBodyWeight);

var totalPlasmaCL = createParameter(TotalPlasmaCL, bloodPlasmaPK[PKParameters.CL], FlowPerWeight);
Expand All @@ -346,7 +342,7 @@ private IContainer calculateGlobalPKAnalysisFor(Simulation simulation, Compound
if (isIntravenous(schemaItem))
{
container.AddChildren(vssPlasma, vdPlasma, totalPlasmaCL);
if(vssPhysChem != null)
if (vssPhysChem != null)
container.Add(vssPhysChem);

return container;
Expand Down Expand Up @@ -398,13 +394,7 @@ private static IEnumerable<QuantityPKParameter> mapQuantityPKParametersFromIndiv
// use the first in series as a template to retrieve from all individual results.
// The list of parameters should be identical for all the individual global analyses.
var aPKAnalysis = globalIndividualPKParameterCache.FirstOrDefault();
aPKAnalysis?.AllPKParameters.GroupBy(moleculeNameFrom).Each(group =>
{
group.Each(pKParameter =>
{
quantityPKList.Add(quantityPKParameterFor(globalIndividualPKParameterCache, pKParameter, group.Key));
});
});
aPKAnalysis?.AllPKParameters.GroupBy(moleculeNameFrom).Each(group => { group.Each(pKParameter => { quantityPKList.Add(quantityPKParameterFor(globalIndividualPKParameterCache, pKParameter, group.Key)); }); });
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This looks very hard to read. Why is this all on one line suddenly?

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ah, shoot. That's a Resharper.

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fixed


return quantityPKList;
}
Expand Down Expand Up @@ -530,9 +520,8 @@ public void CalculateBioavailabilityFor(Simulation simulation, string compoundNa
// We know this is a valid cast because it is cloned from simulation
var populationSimulation = simulation.DowncastTo<PopulationSimulation>();
CalculateFor(ivPopulationSimulation, ivCompoundPKContext);
var contextForPopulationSimulation = createContextForPopulationSimulation(ivCompoundPKContext, mapFromBioavailabilityCompoundPK, compoundName, populationSimulation, new []{Bioavailability});
var contextForPopulationSimulation = createContextForPopulationSimulation(ivCompoundPKContext, mapFromBioavailabilityCompoundPK, compoundName, populationSimulation, new[] { Bioavailability });
populationSimulation.PKAnalyses = CalculateFor(populationSimulation, contextForPopulationSimulation);

}
else if (ivSimulation is IndividualSimulation ivIndividualSimulation)
{
Expand Down Expand Up @@ -648,20 +637,20 @@ private bool isMultipleOral(Simulation simulation, Compound compound)
return allSchemaItems.Any() && allSchemaItems.All(isOral);
}

private static bool isOral(ISchemaItem schemaItem)
private static bool isOral(SchemaItem schemaItem)
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Why this chnage from Interface to not interface?

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I implemented a bool property on SchemaItem that matches 'IsOral' and 'IsUserDefined' (IsIV) and like those ones, I did not pull them up to interface. I'm pretty sure all those conversions are local in this class.

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I am wondering if we need the ISchemaItem at all. Another day

{
if (schemaItem == null)
return false;

return schemaItem.ApplicationType == ApplicationTypes.Oral;
}

private static bool isIntravenous(ISchemaItem schemaItem)
private static bool isIntravenous(SchemaItem schemaItem)
{
if (schemaItem == null)
return false;

return schemaItem.ApplicationType == ApplicationTypes.Intravenous || schemaItem.ApplicationType == ApplicationTypes.IntravenousBolus;
return schemaItem.IsIV;
}

private ApplicationType applicationTypeFor(Simulation simulation, Compound compound)
Expand All @@ -673,17 +662,17 @@ private ApplicationType applicationTypeFor(Simulation simulation, Compound compo
return numberOfApplications > 1 ? ApplicationType.Multiple : ApplicationType.Empty;
}

private ISchemaItem singleDosingItem(Simulation simulation, Compound compound)
private SchemaItem singleDosingItem(Simulation simulation, Compound compound)
{
//this may be null for compound created by metabolization process only
return schemaItemsFrom(simulation, compound).FirstOrDefault();
}

private IReadOnlyList<ISchemaItem> schemaItemsFrom(Simulation simulation, Compound compound)
private IReadOnlyList<SchemaItem> schemaItemsFrom(Simulation simulation, Compound compound)
{
var protocol = simulation.CompoundPropertiesFor(compound).ProtocolProperties.Protocol;
if (protocol == null)
return new List<ISchemaItem>();
return new List<SchemaItem>();

return _protocolToSchemaItemsMapper.MapFrom(protocol);
}
Expand Down Expand Up @@ -778,8 +767,8 @@ private IEnumerable<DataColumn> columnsFor(CurveData<TimeProfileXValue, TimeProf
new DataColumn(curveData.Caption, curveData.YAxis.Dimension, baseGrid)
{
Values = curveData.YValues.Select(y => y.Y).ToList(),
DataInfo = {MolWeight = populationDataCollector.MolWeightFor(curveData.QuantityPath)},
QuantityInfo = {Path = curveData.QuantityPath.ToPathArray()}
DataInfo = { MolWeight = populationDataCollector.MolWeightFor(curveData.QuantityPath) },
QuantityInfo = { Path = curveData.QuantityPath.ToPathArray() }
}
};
}
Expand Down Expand Up @@ -857,11 +846,13 @@ public PKAnalysis CreatePKAnalysisFromValues(PKValues pkValues, Simulation simul
}

/// <summary>
/// Returns the range strings when the <paramref name="text"/> contains 'Range 2.5% to 97.5%' language
/// Returns the range strings when the <paramref name="text" /> contains 'Range 2.5% to 97.5%' language
/// </summary>
/// <param name="text">The text being split</param>
/// <returns>The individual range descriptions as a tuple containing low range and high range.
/// If the string cannot be split on 'Range', returns the original text in both members of the tuple</returns>
/// <returns>
/// The individual range descriptions as a tuple containing low range and high range.
/// If the string cannot be split on 'Range', returns the original text in both members of the tuple
/// </returns>
private (string lowerRange, string upperRange) rangeDescriptions(string text)
{
var splitStrings = text.Split(new[] { "Range" }, StringSplitOptions.None);
Expand Down
41 changes: 28 additions & 13 deletions src/PKSim.Presentation/Presenters/Simulations/GlobalPKAnalysisPresenter.cs
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@@ -1,21 +1,22 @@
using System;
using System.Collections.Generic;
using System.Linq;
using PKSim.Assets;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.UnitSystem;
using OSPSuite.Core.Services;
using OSPSuite.Presentation.Core;
using OSPSuite.Presentation.Presenters;
using OSPSuite.Presentation.Services;
using OSPSuite.Utility.Extensions;
using PKSim.Assets;
using PKSim.Core;
using PKSim.Core.Mappers;
using PKSim.Core.Model;
using PKSim.Core.Repositories;
using PKSim.Core.Services;
using PKSim.Presentation.DTO.Mappers;
using PKSim.Presentation.DTO.Simulations;
using PKSim.Presentation.Views.Simulations;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.UnitSystem;
using OSPSuite.Core.Services;
using OSPSuite.Presentation.Core;
using OSPSuite.Presentation.Presenters;
using OSPSuite.Presentation.Services;

namespace PKSim.Presentation.Presenters.Simulations
{
Expand All @@ -29,6 +30,7 @@ public interface IGlobalPKAnalysisPresenter : IPresenter<IGlobalPKAnalysisView>,
void CalculateDDIRatioFor(string compoundName);
string DisplayNameFor(string parameterName);
bool HasParameters();
bool CanCalculateGlobalPK();
}

public class GlobalPKAnalysisPresenter : AbstractSubPresenter<IGlobalPKAnalysisView, IGlobalPKAnalysisPresenter>, IGlobalPKAnalysisPresenter
Expand All @@ -43,15 +45,17 @@ public class GlobalPKAnalysisPresenter : AbstractSubPresenter<IGlobalPKAnalysisV
private GlobalPKAnalysisDTO _globalPKAnalysisDTO;
private DefaultPresentationSettings _settings;
private readonly IPresentationSettingsTask _presentationSettingsTask;
private readonly IProtocolToSchemaItemsMapper _protocolToSchemaItemsMapper;

public GlobalPKAnalysisPresenter(IGlobalPKAnalysisView view, IPKAnalysesTask pkAnalysesTask,
IGlobalPKAnalysisToGlobalPKAnalysisDTOMapper globalPKAnalysisDTOMapper, IHeavyWorkManager heavyWorkManager, IRepresentationInfoRepository representationInfoRepository, IPresentationSettingsTask presentationSettingsTask) : base(view)
IGlobalPKAnalysisToGlobalPKAnalysisDTOMapper globalPKAnalysisDTOMapper, IHeavyWorkManager heavyWorkManager, IRepresentationInfoRepository representationInfoRepository, IPresentationSettingsTask presentationSettingsTask, IProtocolToSchemaItemsMapper protocolToSchemaItemsMapper) : base(view)
{
_pkAnalysesTask = pkAnalysesTask;
_globalPKAnalysisDTOMapper = globalPKAnalysisDTOMapper;
_heavyWorkManager = heavyWorkManager;
_representationInfoRepository = representationInfoRepository;
_presentationSettingsTask = presentationSettingsTask;
_protocolToSchemaItemsMapper = protocolToSchemaItemsMapper;
_settings = new DefaultPresentationSettings();
}

Expand All @@ -78,7 +82,7 @@ public bool ShouldCalculateDDIRatio(string compoundName, string parameterName)
shouldCalculateGlobalPKParameter(compoundName, parameterName, CoreConstants.PKAnalysis.C_maxRatio);
}

private bool shouldCalculateGlobalPKParameter(string compoundName, string parameterName,string globalPKParameterName)
private bool shouldCalculateGlobalPKParameter(string compoundName, string parameterName, string globalPKParameterName)
{
if (!string.Equals(parameterName, globalPKParameterName))
return false;
Expand Down Expand Up @@ -119,10 +123,7 @@ private void loadPreferredUnitsForPKAnalysis()

private void updateParameterDisplayUnits(string parameterName)
{
GlobalPKAnalysis.PKParameters(parameterName).Each(parameter =>
{
parameter.DisplayUnit = parameter.Dimension.Unit(_settings.GetSetting(parameterName, DisplayUnitFor(parameterName).Name));
});
GlobalPKAnalysis.PKParameters(parameterName).Each(parameter => { parameter.DisplayUnit = parameter.Dimension.Unit(_settings.GetSetting(parameterName, DisplayUnitFor(parameterName).Name)); });
}

private Simulation firstSimulation => _simulations.FirstOrDefault();
Expand Down Expand Up @@ -164,6 +165,20 @@ public bool HasParameters()
return false;
}

public bool CanCalculateGlobalPK()
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I ran resharper to auto-format so there's some noise in this PR. The gist is we need to calculate when a simulation contains only multiple IV applications of all compounds. If there's only single IV, oral, or a mix we want to show the global panel.

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it this how it was doen for individual simulation?

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for individual, the global is calculated on demand, so if it can calculate a global, the presenter just indicates that the datatable has rows and the view should show the panel.

For populations, you might have to re-run if the results are from an older version because the global would not have been calculated, and will not be calculated just because you show it.

{
return firstSimulation.Compounds.Any(compound =>
{
var schemaItems = _protocolToSchemaItemsMapper.MapFrom(firstSimulation.CompoundPropertiesFor(compound).ProtocolProperties.Protocol);
return !isMultipleIV(schemaItems);
});
}

private bool isMultipleIV(IReadOnlyList<SchemaItem> schemaItems)
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On the other hand, those small methods can really be on one line. no { } etc... makes sense to me

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It's similar. In Individual =>
_view.GlobalPKVisible = _globalPKAnalysisPresenter.HasParameters();

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Fixed

{
return schemaItems.Count(schemaItem => schemaItem.IsIV) > 1;
}

public void LoadSettingsForSubject(IWithId subject)
{
_settings = _presentationSettingsTask.PresentationSettingsFor<DefaultPresentationSettings>(this, subject);
Expand Down
18 changes: 8 additions & 10 deletions src/PKSim.Presentation/Presenters/Simulations/IndividualPKAnalysisPresenter.cs
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Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
using System.Collections.Generic;
using System.Linq;
using OSPSuite.Core.Chart;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Data;
using OSPSuite.Core.Domain.PKAnalyses;
using OSPSuite.Presentation.Presenters;
using OSPSuite.Presentation.Services;
using OSPSuite.Utility.Collections;
using OSPSuite.Utility.Extensions;
using PKSim.Core.Extensions;
Expand All @@ -8,12 +14,6 @@
using PKSim.Presentation.DTO.Mappers;
using PKSim.Presentation.Services;
using PKSim.Presentation.Views.Simulations;
using OSPSuite.Core.Chart;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Data;
using OSPSuite.Core.Domain.PKAnalyses;
using OSPSuite.Presentation.Presenters;
using OSPSuite.Presentation.Services;

namespace PKSim.Presentation.Presenters.Simulations
{
Expand All @@ -30,15 +30,13 @@ public class IndividualPKAnalysisPresenter : PKAnalysisPresenter<IIndividualPKAn
private IReadOnlyList<Simulation> _simulations;
private readonly ICache<DataColumn, Curve> _curveCache;
private List<DataColumn> _allColumns;
private readonly IGlobalPKAnalysisPresenter _globalPKAnalysisPresenter;
private readonly IIndividualPKAnalysisToPKAnalysisDTOMapper _pKAnalysisToDTOMapper;

public IndividualPKAnalysisPresenter(IIndividualPKAnalysisView view, IPKAnalysesTask pkAnalysesTask, IPKAnalysisExportTask exportTask,
IGlobalPKAnalysisPresenter globalPKAnalysisPresenter, IIndividualPKAnalysisToPKAnalysisDTOMapper pKAnalysisToDTOMapper,
IPKParameterRepository pkParameterRepository, IPresentationSettingsTask presentationSettingsTask) : base(view, pkParameterRepository, presentationSettingsTask)
IPKParameterRepository pkParameterRepository, IPresentationSettingsTask presentationSettingsTask) : base(view, pkParameterRepository, presentationSettingsTask, globalPKAnalysisPresenter)
{
_pkAnalysesTask = pkAnalysesTask;
_globalPKAnalysisPresenter = globalPKAnalysisPresenter;
_exportTask = exportTask;
_view.ShowControls = false;
_curveCache = new Cache<DataColumn, Curve>(onMissingKey: x => null);
Expand All @@ -61,7 +59,7 @@ public void ShowPKAnalysis(IEnumerable<Simulation> simulations, IEnumerable<Curv
createColumnsWithPKAnalysesFrom(curveList);
_allColumns = _curveCache.Keys.ToList();
_allPKAnalysis = _pkAnalysesTask.CalculateFor(_simulations, _allColumns, globalPKAnalysis).ToList();

_view.GlobalPKVisible = _globalPKAnalysisPresenter.HasParameters();

_view.ShowControls = true;
Expand Down
10 changes: 6 additions & 4 deletions src/PKSim.Presentation/Presenters/Simulations/PKAnalysisPresenter.cs
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
using System.Collections.Generic;
using System.Linq;
using OSPSuite.Utility.Extensions;
using PKSim.Core.Model;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.PKAnalyses;
using OSPSuite.Core.Domain.UnitSystem;
using OSPSuite.Presentation.Core;
using OSPSuite.Presentation.Presenters;
using OSPSuite.Presentation.Services;
using OSPSuite.Presentation.Views;
using OSPSuite.Utility.Extensions;
using PKSim.Core.Model;

namespace PKSim.Presentation.Presenters.Simulations
{
Expand All @@ -27,14 +27,16 @@ public abstract class PKAnalysisPresenter<TView, TPresenter> : AbstractSubPresen
private readonly IParameter _undefinedPKParameter;
private DefaultPresentationSettings _settings;
private readonly IPresentationSettingsTask _presentationSettingsTask;
protected IGlobalPKAnalysisPresenter _globalPKAnalysisPresenter;

protected PKAnalysisPresenter(TView view, IPKParameterRepository pkParameterRepository, IPresentationSettingsTask presentationSettingsTask)
protected PKAnalysisPresenter(TView view, IPKParameterRepository pkParameterRepository, IPresentationSettingsTask presentationSettingsTask, IGlobalPKAnalysisPresenter globalPKAnalysisPresenter)
: base(view)
{
_pkParameterRepository = pkParameterRepository;
_presentationSettingsTask = presentationSettingsTask;
_undefinedPKParameter = new PKSimParameter {Dimension = Constants.Dimension.NO_DIMENSION};
_undefinedPKParameter = new PKSimParameter { Dimension = Constants.Dimension.NO_DIMENSION };
_settings = new DefaultPresentationSettings();
_globalPKAnalysisPresenter = globalPKAnalysisPresenter;
}

public void ChangeUnit(string pkParameterName, Unit newUnit)
Expand Down
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