More work on #2569 to make test pass again:

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

@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.0-USVFq" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.140" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.Assets/PKSim.Assets.csproj

@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.0-USVFq" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.140" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.BatchTool/PKSim.BatchTool.csproj

@@ -59,8 +59,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-USVFq" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.140" />
     <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="12.0.0-USVFq" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.140" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.0-USVFq" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.140" />
   </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="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Presentation" Version="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-USVFq" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Presentation" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.140" />
     <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/ExpressionProfileToExpressionProfileBuildingBlockMapper.cs

@@ -5,6 +5,8 @@
 using OSPSuite.Core.Domain.Services;
 using PKSim.Assets;
 using PKSim.Core.Model;
+using PKSim.Core.Services;
+using ILazyLoadTask = OSPSuite.Core.Domain.Services.ILazyLoadTask;
 
 namespace PKSim.Core.Mappers
 {
@@ -14,8 +16,8 @@ public interface IExpressionProfileToExpressionProfileBuildingBlockMapper : IPat
 
    public class ExpressionProfileToExpressionProfileBuildingBlockMapper : PathAndValueBuildingBlockMapper<ExpressionProfile, ExpressionProfileBuildingBlock, ExpressionParameter>, IExpressionProfileToExpressionProfileBuildingBlockMapper
    {
-      public ExpressionProfileToExpressionProfileBuildingBlockMapper(IObjectBaseFactory objectBaseFactory, IEntityPathResolver entityPathResolver, IApplicationConfiguration applicationConfiguration, ILazyLoadTask lazyLoadTask) :
-         base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask)
+      public ExpressionProfileToExpressionProfileBuildingBlockMapper(IObjectBaseFactory objectBaseFactory, IEntityPathResolver entityPathResolver, IApplicationConfiguration applicationConfiguration, ILazyLoadTask lazyLoadTask, ICloner cloner) :
+         base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask, cloner)
       {
       }
 

src/PKSim.Core/Mappers/IndividualToIndividualBuildingBlockMapper.cs

@@ -8,6 +8,8 @@
 using PKSim.Assets;
 using PKSim.Core.Model;
 using PKSim.Core.Repositories;
+using PKSim.Core.Services;
+using ILazyLoadTask = OSPSuite.Core.Domain.Services.ILazyLoadTask;
 
 namespace PKSim.Core.Mappers
 {
@@ -21,7 +23,7 @@ public class IndividualToIndividualBuildingBlockMapper : PathAndValueBuildingBlo
       private readonly ICalculationMethodCategoryRepository _calculationMethodCategoryRepository;
 
       public IndividualToIndividualBuildingBlockMapper(IObjectBaseFactory objectBaseFactory, IEntityPathResolver entityPathResolver, IApplicationConfiguration applicationConfiguration,
-         ILazyLoadTask lazyLoadTask, IRepresentationInfoRepository representationInfoRepository, ICalculationMethodCategoryRepository calculationMethodCategoryRepository) : base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask)
+         ILazyLoadTask lazyLoadTask, IRepresentationInfoRepository representationInfoRepository, ICalculationMethodCategoryRepository calculationMethodCategoryRepository, ICloner cloner) : base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask, cloner)
       {
          _representationInfoRepository = representationInfoRepository;
          _calculationMethodCategoryRepository = calculationMethodCategoryRepository;
@@ -32,25 +34,25 @@ protected override IReadOnlyList<IParameter> AllParametersFor(Individual individ
          return individual.GetAllChildren<IParameter>().Where(x => x.GroupName != CoreConstants.Groups.RELATIVE_EXPRESSION).ToList();
       }
 
-      public override IndividualBuildingBlock MapFrom(Individual input)
+      public override IndividualBuildingBlock MapFrom(Individual individual)
       {
-         var buildingBlock = base.MapFrom(input);
-         buildingBlock.Icon = input.Icon;
+         var buildingBlock = base.MapFrom(individual);
+         buildingBlock.Icon = individual.Icon;
 
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.DiseaseState, input.OriginData.DiseaseState?.DisplayName);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Species, input.Species?.DisplayName);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Gender, input.OriginData.Gender?.DisplayName);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Age, input.OriginData.Age);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.GestationalAge, input.OriginData.GestationalAge);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Height, input.OriginData.Height);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.BMI, input.OriginData.BMI);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Weight, input.OriginData.Weight);
-         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Population, input.OriginData.Population?.DisplayName);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.DiseaseState, individual.OriginData.DiseaseState?.DisplayName);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Species, individual.Species?.DisplayName);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Gender, individual.OriginData.Gender?.DisplayName);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Age, individual.OriginData.Age);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.GestationalAge, individual.OriginData.GestationalAge);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Height, individual.OriginData.Height);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.BMI, individual.OriginData.BMI);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Weight, individual.OriginData.Weight);
+         addOriginDataToBuildingBlock(buildingBlock, PKSimConstants.UI.Population, individual.OriginData.Population?.DisplayName);
 
-         input.OriginData.AllCalculationMethods().Where(cm => _calculationMethodCategoryRepository.HasMoreThanOneOption(cm, input.Species))
+         individual.OriginData.AllCalculationMethods().Where(cm => _calculationMethodCategoryRepository.HasMoreThanOneOption(cm, individual.Species))
             .Each(x => addCalculationMethodOriginDataToBuildingBlock(buildingBlock, x));
 
-         buildingBlock.OriginData.ValueOrigin = input.OriginData.ValueOrigin.Clone();
+         buildingBlock.OriginData.ValueOrigin = individual.OriginData.ValueOrigin.Clone();
 
          return buildingBlock;
       }
@@ -79,7 +81,7 @@ private void addOriginDataToBuildingBlock(IndividualBuildingBlock buildingBlock,
          if (string.IsNullOrEmpty(value))
             return;
 
-         buildingBlock.OriginData.AddOriginDataItem(new OriginDataItem { Name = key, Value = value });
+         buildingBlock.OriginData.AddOriginDataItem(new OriginDataItem {Name = key, Value = value});
       }
    }
 }

src/PKSim.Core/Mappers/PathAndValueBuildingBlockMapper.cs

@@ -1,36 +1,51 @@
 using System.Collections.Generic;
+using System.Linq;
 using OSPSuite.Core;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Builder;
 using OSPSuite.Core.Domain.Formulas;
 using OSPSuite.Core.Domain.Services;
 using OSPSuite.Utility;
 using OSPSuite.Utility.Collections;
+using OSPSuite.Utility.Extensions;
 using PKSim.Core.Model;
+using PKSim.Core.Services;
+using ILazyLoadTask = OSPSuite.Core.Domain.Services.ILazyLoadTask;
 
 namespace PKSim.Core.Mappers
 {
-   public interface IPathAndValueBuildingBlockMapper<in T, out TBuildingBlock> : IMapper<T, TBuildingBlock>
+   public interface IPathAndValueBuildingBlockMapper<in TPKSimBuildingBlock, out TBuildingBlock> : IMapper<TPKSimBuildingBlock, TBuildingBlock>
    {
    }
 
-   public abstract class PathAndValueBuildingBlockMapper<T, TBuildingBlock, TBuilder> : IPathAndValueBuildingBlockMapper<T, TBuildingBlock> where T : PKSimBuildingBlock where TBuildingBlock : PathAndValueEntityBuildingBlockFromPKSim<TBuilder> where TBuilder : PathAndValueEntity
+   public abstract class PathAndValueBuildingBlockMapper<TPKSimBuildingBlock, TBuildingBlock, TBuilder> : IPathAndValueBuildingBlockMapper<TPKSimBuildingBlock, TBuildingBlock> where TPKSimBuildingBlock : PKSimBuildingBlock where TBuildingBlock : PathAndValueEntityBuildingBlockFromPKSim<TBuilder>
+      where TBuilder : PathAndValueEntity
    {
       protected IObjectBaseFactory _objectBaseFactory;
       protected IEntityPathResolver _entityPathResolver;
       protected IApplicationConfiguration _applicationConfiguration;
       private readonly ILazyLoadTask _lazyLoadTask;
+      private readonly ICloner _cloner;
+
+      //Cache used to store all formula that can be cached. This is required to avoid having the same formula defined multiple times in the building block
+      //note that a clone of the original formula is added to the cache so that it can be modified if required
       private readonly Cache<string, IFormula> _formulaCache = new Cache<string, IFormula>(x => x.Name);
 
-      protected PathAndValueBuildingBlockMapper(IObjectBaseFactory objectBaseFactory, IEntityPathResolver entityPathResolver, IApplicationConfiguration applicationConfiguration, ILazyLoadTask lazyLoadTask)
+      protected PathAndValueBuildingBlockMapper(
+         IObjectBaseFactory objectBaseFactory,
+         IEntityPathResolver entityPathResolver,
+         IApplicationConfiguration applicationConfiguration,
+         ILazyLoadTask lazyLoadTask,
+         ICloner cloner)
       {
          _objectBaseFactory = objectBaseFactory;
          _entityPathResolver = entityPathResolver;
          _applicationConfiguration = applicationConfiguration;
          _lazyLoadTask = lazyLoadTask;
+         _cloner = cloner;
       }
 
-      protected TBuildingBlock CreateBaseObject(T pkSimBuildingBlock)
+      protected TBuildingBlock CreateBaseObject(TPKSimBuildingBlock pkSimBuildingBlock)
       {
          var buildingBlock = _objectBaseFactory.Create<TBuildingBlock>();
 
@@ -43,12 +58,16 @@ protected TBuildingBlock CreateBaseObject(T pkSimBuildingBlock)
       private TBuilder mapBuilderParameter(IParameter parameter)
       {
          var builderParameter = _objectBaseFactory.Create<TBuilder>();
+         builderParameter.Name = parameter.Name;
+         builderParameter.Path = _entityPathResolver.ObjectPathFor(parameter);
+         builderParameter.Dimension = parameter.Dimension;
+         builderParameter.DisplayUnit = parameter.DisplayUnit;
 
          // Add the formula to the building block formula cache if the formula can be cached
          if (isFormulaCachable(parameter))
          {
             if (!_formulaCache.Contains(parameter.Formula.Name))
-               _formulaCache.Add(parameter.Formula);
+               _formulaCache.Add(cloneFormulaForExport(parameter));
 
             // If the parameter value is different from the default value, set the value only and not the formula
             // If the parameter value is not different from the default, set the formula only and not the value
@@ -63,14 +82,16 @@ private TBuilder mapBuilderParameter(IParameter parameter)
             builderParameter.Value = getParameterValue(parameter);
          }
 
-         builderParameter.Name = parameter.Name;
-
-         builderParameter.Path = _entityPathResolver.ObjectPathFor(parameter);
-         builderParameter.Dimension = parameter.Dimension;
-         builderParameter.DisplayUnit = parameter.DisplayUnit;
          return builderParameter;
       }
 
+      private IFormula cloneFormulaForExport(IParameter parameter)
+      {
+         var cloneFormula = _cloner.Clone(parameter.Formula);
+         cloneFormula.ObjectPaths.Each(x => x.Remove(Constants.ROOT));
+         return cloneFormula;
+      }
+
       private static bool isFormulaCachable(IParameter parameter)
       {
          return parameter.Formula != null && parameter.Formula.IsCachable();
@@ -81,30 +102,23 @@ private static double getParameterValue(IParameter parameter)
          return parameter.TryGetValue().value;
       }
 
-      protected void MapAllParameters(T sourcePKSimBuildingBlock, TBuildingBlock buildingBlock)
+      protected void MapAllParameters(TPKSimBuildingBlock sourcePKSimBuildingBlock, TBuildingBlock buildingBlock)
       {
-         var allParameters = AllParametersFor(sourcePKSimBuildingBlock);
+         var allBuilderParameters = AllParametersFor(sourcePKSimBuildingBlock).Select(mapBuilderParameter);
+         allBuilderParameters.Each(buildingBlock.Add);
 
-         foreach (var parameter in allParameters)
-         {
-            var builderParameter = mapBuilderParameter(parameter);
-            buildingBlock.Add(builderParameter);
-         }
-
-         foreach (var formula in _formulaCache)
-         {
-            buildingBlock.FormulaCache.Add(formula);
-         }
+         //Formula cache already contains a clone of all formula. We can add as is
+         _formulaCache.Each(buildingBlock.FormulaCache.Add);
       }
 
-      protected abstract IReadOnlyList<IParameter> AllParametersFor(T sourcePKSimBuildingBlock);
+      protected abstract IReadOnlyList<IParameter> AllParametersFor(TPKSimBuildingBlock sourcePKSimBuildingBlock);
 
-      public virtual TBuildingBlock MapFrom(T input)
+      public virtual TBuildingBlock MapFrom(TPKSimBuildingBlock pkSimBuildingBlock)
       {
-         _lazyLoadTask.Load(input);
+         _lazyLoadTask.Load(pkSimBuildingBlock);
 
-         var buildingBlock = CreateBaseObject(input);
-         MapAllParameters(input, buildingBlock);
+         var buildingBlock = CreateBaseObject(pkSimBuildingBlock);
+         MapAllParameters(pkSimBuildingBlock, buildingBlock);
          return buildingBlock;
       }
    }

src/PKSim.Core/Model/PKSimSpatialStructureFactory.cs

@@ -138,9 +138,6 @@ private void addModelStructureTo(IContainer container, OriginData originData, Mo
          }
       }
 
-      protected override ISpatialStructure CreateSpatialStructure()
-      {
-         return _objectBaseFactory.Create<IPKSimSpatialStructure>();
-      }
+      protected override ISpatialStructure CreateSpatialStructure() => _objectBaseFactory.Create<IPKSimSpatialStructure>();
    }
 }

src/PKSim.Core/PKSim.Core.csproj

@@ -30,10 +30,10 @@
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.0-USVFq" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.0-USVFq" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.140" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.140" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

src/PKSim.Core/Services/Cloner.cs

@@ -43,7 +43,7 @@ public Cloner(ICloneManagerForModel cloneManagerForModel, ICloneManagerForBuildi
 
       public T Clone<T>(T objectToClone) where T : class, IUpdatable
       {
-         //formula cache are never used in pksim explicitely. And if need, we access CloneManagerForBuildingBlock
+         //formula cache are never used in pksim explicitly. And if need, we access CloneManagerForBuildingBlock
          _cloneManagerForBuildingBlock.FormulaCache = new FormulaCache();
          return createClone(objectToClone, _cloneManagerForBuildingBlock);
       }

src/PKSim.Core/Services/DistributedParameterToTableParameterConverter.cs

@@ -119,7 +119,7 @@ private void updateAgeParameter(SimulationConfiguration simulationConfiguration)
       {
          var spatialStructure = simulationConfiguration.SpatialStructure;
          //We have only one in PK-Sim
-         var parameterStartValueBuildingBlock = simulationConfiguration.ParameterStartValuesCollection.First();
+         var parameterStartValueBuildingBlock = simulationConfiguration.ParameterStartValues;
          var organism = spatialStructure.TopContainers.FindByName(Constants.ORGANISM);
          var ageParameter = organism.Parameter(CoreConstants.Parameters.AGE);
          var minToYearFactor = _timeDimension.BaseUnitValueToUnitValue(_yearUnit, 1);
@@ -199,7 +199,7 @@ private void createSpatialStructureTableParameters(SimulationConfiguration simul
       private void createOntogenyTableParameters(SimulationConfiguration simulationConfiguration)
       {
          var simulationPopulation = _simulation as PopulationSimulation;
-         var parameterStartValueBuildingBlock = simulationConfiguration.ParameterStartValuesCollection.First();
+         var parameterStartValueBuildingBlock = simulationConfiguration.ParameterStartValues;
          foreach (var molecule in _baseIndividual.AllMolecules().Where(m => m.Ontogeny.IsDefined()))
          {
             var ontogenyFactorPath = _entityPathResolver.ObjectPathFor(molecule.OntogenyFactorParameter);