2640 export initial conditions for expressions as part of the expression profile

src/PKSim.Assets.Images/PKSim.Assets.Images.csproj

@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.186" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.188" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.Assets/PKSim.Assets.csproj

@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.186" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.188" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.BatchTool/PKSim.BatchTool.csproj

@@ -59,8 +59,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.186" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.188" />
     <PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />

src/PKSim.CLI.Core/PKSim.CLI.Core.csproj

@@ -27,9 +27,9 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.186" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.188" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.186" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.188" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.CLI/PKSim.CLI.csproj

@@ -61,9 +61,9 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.8.0" />
     <PackageReference Include="Microsoft.Extensions.Logging.Console" Version="3.1.0" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Presentation" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.186" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Presentation" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.188" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />

src/PKSim.Core/Mappers/MoleculeToQueryExpressionSettingsMapper.cs

@@ -33,7 +33,7 @@ public QueryExpressionSettings MapFrom(IndividualMolecule molecule, ISimulationS
       public QueryExpressionSettings MapFrom(ExpressionProfileBuildingBlock expressionProfileBuildingBlock)
       {
          var expressionContainers = expressionProfileBuildingBlock.
-            Where(x => x.Value.HasValue && x.HasExpressionName()).
+            ExpressionParameters.Where(x => x.Value.HasValue && x.HasExpressionName()).
             Select(expressionContainerInfoForExpressionParameter).ToList();
 
          return new QueryExpressionSettings(expressionContainers, string.Empty, expressionProfileBuildingBlock.MoleculeName);

src/PKSim.Core/Model/Compound.cs

@@ -93,12 +93,12 @@ public virtual ParameterAlternativeGroup ParameterAlternativeGroup(string parame
       public virtual IEnumerable<CompoundProcess> AllProcesses() => AllProcesses<CompoundProcess>();
 
       /// <summary>
-      ///    Returns <c>true</c> if at least one proces is defined in the compound otherwise false
+      ///    Returns <c>true</c> if at least one process is defined in the compound otherwise false
       /// </summary>
       public virtual bool HasProcesses() => HasProcesses<CompoundProcess>();
 
       /// <summary>
-      ///    Returns <c>true</c> if at least one proces of type <typeparamref name="TCompoundProcess"/> is defined in the compound otherwise false
+      ///    Returns <c>true</c> if at least one process of type <typeparamref name="TCompoundProcess"/> is defined in the compound otherwise false
       /// </summary>
       public virtual bool HasProcesses<TCompoundProcess>() where TCompoundProcess : CompoundProcess => AllProcesses<TCompoundProcess>().Any();
 

src/PKSim.Core/Model/PartialProcess.cs

@@ -23,7 +23,7 @@ public override void UpdatePropertiesFrom(IUpdatable sourceObject, ICloneManager
       }
 
       /// <summary>
-      ///    Name of the molecule responsible for triggering the processs
+      ///    Name of the molecule responsible for triggering the process
       /// </summary>
       public string MoleculeName
       {

src/PKSim.Core/Model/SimulationFactory.cs

@@ -200,8 +200,8 @@ public Simulation CreateForVSS(Protocol protocol, Individual individual, Compoun
       {
          //we create a clone here to ensure that a name is set in the compound
          var vssCompound = _cloner.Clone(compound).WithName("VSS COMPOUND");
-         var simulation = CreateFrom(individual, new[] {vssCompound}, _modelPropertiesTask.DefaultFor(individual.OriginData));
-         _simulationBuildingBlockUpdater.UpdateMultipleUsedBuildingBlockInSimulationFromTemplate(simulation, new[] {protocol}, PKSimBuildingBlockType.Protocol);
+         var simulation = CreateFrom(individual, new[] { vssCompound }, _modelPropertiesTask.DefaultFor(individual.OriginData));
+         _simulationBuildingBlockUpdater.UpdateMultipleUsedBuildingBlockInSimulationFromTemplate(simulation, new[] { protocol }, PKSimBuildingBlockType.Protocol);
          _simulationModelCreator.CreateModelFor(simulation);
          return simulation;
       }

src/PKSim.Core/PKSim.Core.csproj

@@ -31,10 +31,10 @@
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.186" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.186" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.188" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.188" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

src/PKSim.Core/Services/EventBuildingBlockCreator.cs

@@ -42,7 +42,7 @@ public EventBuildingBlockCreator(IObjectBaseFactory objectBaseFactory,
          ICloneManagerForBuildingBlock cloneManagerForBuildingBlock,
          IParameterIdUpdater parameterIdUpdater,
          IParameterSetUpdater parameterSetUpdater,
-         IEventGroupRepository eventGroupRepository, 
+         IEventGroupRepository eventGroupRepository,
          IParameterDefaultStateUpdater parameterDefaultStateUpdater)
       {
          _objectBaseFactory = objectBaseFactory;
@@ -85,7 +85,7 @@ private void createNonApplicationEvents()
          var eventBuildingBlockInfos = (from eventMapping in _simulation.EventProperties.EventMappings
                let usedBuildingBlock = _simulation.UsedBuildingBlockByTemplateId(eventMapping.TemplateEventId)
                let eventBuildingBlock = usedBuildingBlock.BuildingBlock.DowncastTo<PKSimEvent>()
-               select new {eventBuildingBlock.Id, eventBuildingBlock.TemplateName, eventBuildingBlock.Name})
+               select new { eventBuildingBlock.Id, eventBuildingBlock.TemplateName, eventBuildingBlock.Name })
             .Distinct();
 
          // create event groups for each used event-building block
@@ -229,15 +229,15 @@ private static void setParticleRadiusDistributionParametersToLockedAndInvisible(
          CoreConstants.Parameters.ParticleDistributionStructuralParameters.Each(paramName => formulationBuilder.Parameter(paramName).Editable = false);
 
          // second, set some parameters to not visible depending on settings
-         var parameterNamesToBeInvisible = new List<string> { Constants.Parameters.PARTICLE_DISPERSE_SYSTEM};
+         var parameterNamesToBeInvisible = new List<string> { Constants.Parameters.PARTICLE_DISPERSE_SYSTEM };
 
-         var numberOfBins = (int) formulationBuilder.Parameter(Constants.Parameters.NUMBER_OF_BINS).Value;
+         var numberOfBins = (int)formulationBuilder.Parameter(Constants.Parameters.NUMBER_OF_BINS).Value;
 
          if (numberOfBins == 1)
             parameterNamesToBeInvisible.AddRange(CoreConstants.Parameters.HiddenParameterForMonodisperse);
          else
          {
-            var particlesDistributionType = (int) formulationBuilder.Parameter(Constants.Parameters.PARTICLE_SIZE_DISTRIBUTION).Value;
+            var particlesDistributionType = (int)formulationBuilder.Parameter(Constants.Parameters.PARTICLE_SIZE_DISTRIBUTION).Value;
 
             if (particlesDistributionType == CoreConstants.Parameters.PARTICLE_SIZE_DISTRIBUTION_NORMAL)
                parameterNamesToBeInvisible.AddRange(CoreConstants.Parameters.HiddenParameterForPolydisperseNormal);

src/PKSim.Core/Services/MoleculesAndReactionsCreator.cs

@@ -10,7 +10,6 @@
 using PKSim.Core.Model;
 using PKSim.Core.Repositories;
 using IMoleculeBuilderFactory = PKSim.Core.Model.IMoleculeBuilderFactory;
-using ModelConfiguration = PKSim.Core.Model.ModelConfiguration;
 
 namespace PKSim.Core.Services
 {
@@ -187,8 +186,8 @@ private void addAdditionalStaticMolecules(string modelName, CompoundProperties c
 
       private string moleculeNameFor(string moleculeName, string compoundName)
       {
-         return moleculeName.ReplaceKeywords(new[] {CoreConstants.Molecule.Drug, CoreConstants.Molecule.DrugFcRnComplexTemplate},
-            new[] {compoundName, CoreConstants.Molecule.DrugFcRnComplexName(compoundName)});
+         return moleculeName.ReplaceKeywords(new[] { CoreConstants.Molecule.Drug, CoreConstants.Molecule.DrugFcRnComplexTemplate },
+            new[] { compoundName, CoreConstants.Molecule.DrugFcRnComplexName(compoundName) });
       }
 
       private void addIndividualMolecules(IEnumerable<CompoundProperties> compoundPropertiesList)

src/PKSim.Core/Services/PKAnalysesTask.cs

@@ -369,13 +369,13 @@ private IContainer calculateGlobalPKAnalysisFor(Simulation simulation, string co
             vssPlasma.Value *= bioAvailabilityValue;
             vdPlasma.Value *= bioAvailabilityValue;
             totalPlasmaCL.Value *= bioAvailabilityValue;
-            fractionAbsorbedWarningParameters.AddRange(new[] {vssPlasma, vdPlasma});
-            pkValues.AddRange(new[] {vssPlasma, vdPlasma, totalPlasmaCL, bioAvailability});
+            fractionAbsorbedWarningParameters.AddRange(new[] { vssPlasma, vdPlasma });
+            pkValues.AddRange(new[] { vssPlasma, vdPlasma, totalPlasmaCL, bioAvailability });
          }
          else
          {
-            fractionAbsorbedWarningParameters.AddRange(new[] {vssPlasmaOverF, vdPlasmaOverF});
-            pkValues.AddRange(new[] {vssPlasmaOverF, vdPlasmaOverF, totalPlasmaCLOverF, bioAvailability});
+            fractionAbsorbedWarningParameters.AddRange(new[] { vssPlasmaOverF, vdPlasmaOverF });
+            pkValues.AddRange(new[] { vssPlasmaOverF, vdPlasmaOverF, totalPlasmaCLOverF, bioAvailability });
          }
 
 
@@ -427,9 +427,9 @@ private static QuantityPKParameter quantityPKParameterFor(ICache<int, GlobalPKAn
          if (firstParameter == null)
             return new QuantityPKParameter();
 
-         var quantityPKParameter = new QuantityPKParameter {Dimension = firstParameter.Dimension, Name = firstParameter.Name, QuantityPath = quantityPath};
+         var quantityPKParameter = new QuantityPKParameter { Dimension = firstParameter.Dimension, Name = firstParameter.Name, QuantityPath = quantityPath };
 
-         pKValuesForPKParameter.Each(pKValue => { quantityPKParameter.SetValue(pKValuesForPKParameter.IndexOf(pKValue), (float) pKValue.Value); });
+         pKValuesForPKParameter.Each(pKValue => { quantityPKParameter.SetValue(pKValuesForPKParameter.IndexOf(pKValue), (float)pKValue.Value); });
          return quantityPKParameter;
       }
 
@@ -535,7 +535,7 @@ 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)
@@ -581,7 +581,7 @@ public void CalculateDDIRatioFor(Simulation simulation)
 
                // First calculate the compound context. We will know the AucInf and CMax when DDI is turned off
                CalculateFor(ddiPopulationSimulation, ddiCompoundPKContext);
-               var parameterNames = new[] {AUCRatio, C_maxRatio};
+               var parameterNames = new[] { AUCRatio, C_maxRatio };
 
                // From the ddi context, create the context from the original simulation and the ddi simulation for calculating ddi ratio parameters
                var contextForPopulationSimulation = createContextForPopulationSimulation(ddiCompoundPKContext, mapFromDDISimulationCompoundPK, compoundName, populationSimulation, parameterNames);
@@ -632,14 +632,14 @@ private CompoundPKContext createContextForPopulationSimulation(CompoundPKContext
 
       private CompoundPK mapFromBioavailabilityCompoundPK(CompoundPK bioAvailabilitySimulationCompoundPK)
       {
-         var compoundPK = new CompoundPK {CompoundName = bioAvailabilitySimulationCompoundPK.CompoundName};
+         var compoundPK = new CompoundPK { CompoundName = bioAvailabilitySimulationCompoundPK.CompoundName };
          bioAvailabilitySimulationCompoundPK.AllBioAvailabilityAucInf.KeyValues.Each(bioAvailability => { compoundPK.AddBioavailability(bioAvailability.Key, bioAvailability.Value); });
          return compoundPK;
       }
 
       private CompoundPK mapFromDDISimulationCompoundPK(CompoundPK ddiSimulationCompoundPK)
       {
-         var compoundPK = new CompoundPK {CompoundName = ddiSimulationCompoundPK.CompoundName};
+         var compoundPK = new CompoundPK { CompoundName = ddiSimulationCompoundPK.CompoundName };
          ddiSimulationCompoundPK.AllDDIAucInf.KeyValues.Each(aucInf => compoundPK.AddDDIAucInf(aucInf.Key, aucInf.Value));
          ddiSimulationCompoundPK.AllDDICMax.KeyValues.Each(cMax => compoundPK.AddDDICMax(cMax.Key, cMax.Value));
          return compoundPK;
@@ -732,7 +732,7 @@ public IEnumerable<PopulationPKAnalysis> CalculateFor(IPopulationDataCollector p
             return pkAnalyses; // there are no analyses to calculate
 
          var allColumns = timeProfileChartData.Panes.SelectMany(x => x.Curves).SelectMany(x =>
-               columnsFor(x, populationDataCollector).Select(column => new {curveData = x, column}))
+               columnsFor(x, populationDataCollector).Select(column => new { curveData = x, column }))
             .Where(c => c.column.IsConcentration());
 
          var columnsByMolecules = allColumns.GroupBy(x => x.column.MoleculeName());
@@ -775,7 +775,7 @@ public IEnumerable<IndividualPKAnalysis> CalculateFor(IReadOnlyList<Simulation>
 
       private IEnumerable<DataColumn> columnsFor(CurveData<TimeProfileXValue, TimeProfileYValue> curveData, IPopulationDataCollector populationDataCollector)
       {
-         var baseGrid = new BaseGrid(Constants.TIME, curveData.XAxis.Dimension) {Values = curveData.XValues.Select(x => x.X).ToList()};
+         var baseGrid = new BaseGrid(Constants.TIME, curveData.XAxis.Dimension) { Values = curveData.XValues.Select(x => x.X).ToList() };
 
          if (curveData.IsRange())
          {
@@ -785,14 +785,14 @@ private IEnumerable<DataColumn> columnsFor(CurveData<TimeProfileXValue, TimeProf
                new DataColumn(lowerRange, curveData.YAxis.Dimension, baseGrid)
                {
                   Values = curveData.YValues.Select(y => y.LowerValue).ToList(),
-                  DataInfo = {MolWeight = populationDataCollector.MolWeightFor(curveData.QuantityPath)},
-                  QuantityInfo = {Path = curveData.QuantityPath.ToPathArray()}
+                  DataInfo = { MolWeight = populationDataCollector.MolWeightFor(curveData.QuantityPath) },
+                  QuantityInfo = { Path = curveData.QuantityPath.ToPathArray() }
                },
                new DataColumn(upperRange, curveData.YAxis.Dimension, baseGrid)
                {
                   Values = curveData.YValues.Select(y => y.UpperValue).ToList(),
-                  DataInfo = {MolWeight = populationDataCollector.MolWeightFor(curveData.QuantityPath)},
-                  QuantityInfo = {Path = curveData.QuantityPath.ToPathArray()}
+                  DataInfo = { MolWeight = populationDataCollector.MolWeightFor(curveData.QuantityPath) },
+                  QuantityInfo = { Path = curveData.QuantityPath.ToPathArray() }
                }
             };
          }
@@ -802,8 +802,8 @@ 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() }
             }
          };
       }
@@ -813,7 +813,7 @@ public IndividualPKAnalysis CalculateFor(Simulation simulation, DataColumn dataC
          if (dataColumn == null)
             return new NullIndividualPKAnalysis();
 
-         return CalculateFor(new[] {simulation}, new[] {dataColumn}).FirstOrDefault() ?? new NullIndividualPKAnalysis();
+         return CalculateFor(new[] { simulation }, new[] { dataColumn }).FirstOrDefault() ?? new NullIndividualPKAnalysis();
       }
 
       private PKValues calculatePK(DataColumn column, PKCalculationOptions options)
@@ -890,13 +890,13 @@ public PKAnalysis CreatePKAnalysisFromValues(PKValues pkValues, Simulation simul
       /// </returns>
       private (string lowerRange, string upperRange) rangeDescriptions(string text)
       {
-         var splitStrings = text.Split(new[] {"Range"}, StringSplitOptions.None);
+         var splitStrings = text.Split(new[] { "Range" }, StringSplitOptions.None);
          var match = splitStrings.Length == 2;
 
          if (!match)
             return (text, text);
 
-         var upperAndLowerRange = splitStrings.Last().Split(new[] {"to"}, StringSplitOptions.RemoveEmptyEntries).Select(x => x.Trim()).ToArray();
+         var upperAndLowerRange = splitStrings.Last().Split(new[] { "to" }, StringSplitOptions.RemoveEmptyEntries).Select(x => x.Trim()).ToArray();
 
          return ($"{splitStrings[0]}{upperAndLowerRange[0]}", $"{splitStrings[0]}{upperAndLowerRange[1]}");
       }
@@ -945,7 +945,7 @@ private string correctNameFromMetric(string originalText, bool multipleValues, b
             suffix = isLowerValue ? lowerRange : upperRange;
          }
 
-         return (new[] {captionPrefix, suffix}).ToCaption();
+         return (new[] { captionPrefix, suffix }).ToCaption();
       }
 
       private CurveData<TimeProfileXValue, TimeProfileYValue> buildCurveData(QuantityPKParameter quantityPKParameter, string caption)