Fixes #2569 use individual building block and module from core

Open-Systems-Pharmacology · Mar 22, 2023 · 0a6318a · 0a6318a
1 parent 6386bef
commit 0a6318a
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Showing 27 changed files with 235 additions and 259 deletions.
diff --git a/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj b/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.144" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.144" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.145" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Assets/PKSim.Assets.csproj b/src/PKSim.Assets/PKSim.Assets.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.144" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.144" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.145" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.BatchTool/PKSim.BatchTool.csproj b/src/PKSim.BatchTool/PKSim.BatchTool.csproj
@@ -59,8 +59,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.0.144" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.144" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.145" />
     <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" />

diff --git a/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj b/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj
@@ -27,9 +27,9 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.144" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.145" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.144" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.145" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.CLI/PKSim.CLI.csproj b/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="12.0.144" />
-    <PackageReference Include="OSPSuite.Presentation" Version="12.0.144" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.144" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Presentation" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.145" />
     <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" />

diff --git a/src/PKSim.Core/Mappers/ExpressionProfileToExpressionProfileBuildingBlockMapper.cs b/src/PKSim.Core/Mappers/ExpressionProfileToExpressionProfileBuildingBlockMapper.cs
@@ -2,10 +2,12 @@
 using OSPSuite.Core;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Builder;
+using OSPSuite.Core.Domain.Formulas;
 using OSPSuite.Core.Domain.Services;
 using PKSim.Assets;
 using PKSim.Core.Model;
-using PKSim.Core.Services;
+using static PKSim.Core.CoreConstants.CalculationMethod;
+using IFormulaFactory = PKSim.Core.Model.IFormulaFactory;
 using ILazyLoadTask = OSPSuite.Core.Domain.Services.ILazyLoadTask;
 
 namespace PKSim.Core.Mappers
@@ -16,11 +18,17 @@ public interface IExpressionProfileToExpressionProfileBuildingBlockMapper : IPat
 
    public class ExpressionProfileToExpressionProfileBuildingBlockMapper : PathAndValueBuildingBlockMapper<ExpressionProfile, ExpressionProfileBuildingBlock, ExpressionParameter>, IExpressionProfileToExpressionProfileBuildingBlockMapper
    {
-      public ExpressionProfileToExpressionProfileBuildingBlockMapper(IObjectBaseFactory objectBaseFactory, IEntityPathResolver entityPathResolver, IApplicationConfiguration applicationConfiguration, ILazyLoadTask lazyLoadTask, ICloner cloner) :
-         base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask, cloner)
+      public ExpressionProfileToExpressionProfileBuildingBlockMapper(IObjectBaseFactory objectBaseFactory, IEntityPathResolver entityPathResolver, IApplicationConfiguration applicationConfiguration, ILazyLoadTask lazyLoadTask, IFormulaFactory formulaFactory) :
+         base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask, formulaFactory)
       {
       }
 
+      protected override IFormula TemplateFormulaFor(IParameter parameter, IFormulaCache formulaCache, ExpressionProfile expressionProfile)
+      {
+         //for expression profile, all formula are in the calculation method EXPRESSION_PARAMETERS
+         return _formulaFactory.RateFor(new RateKey(EXPRESSION_PARAMETERS, parameter.Formula.Name), formulaCache);
+      }
+
       protected override IReadOnlyList<IParameter> AllParametersFor(ExpressionProfile expressionProfile)
       {
          return expressionProfile.GetAllChildren<IParameter>();

diff --git a/src/PKSim.Core/Mappers/IndividualToIndividualBuildingBlockMapper.cs b/src/PKSim.Core/Mappers/IndividualToIndividualBuildingBlockMapper.cs
@@ -3,12 +3,14 @@
 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.Extensions;
 using PKSim.Assets;
 using PKSim.Core.Model;
 using PKSim.Core.Repositories;
 using PKSim.Core.Services;
+using IFormulaFactory = PKSim.Core.Model.IFormulaFactory;
 using ILazyLoadTask = OSPSuite.Core.Domain.Services.ILazyLoadTask;
 
 namespace PKSim.Core.Mappers
@@ -21,12 +23,39 @@ public class IndividualToIndividualBuildingBlockMapper : PathAndValueBuildingBlo
    {
       private readonly IRepresentationInfoRepository _representationInfoRepository;
       private readonly ICalculationMethodCategoryRepository _calculationMethodCategoryRepository;
+      private readonly IParameterQuery _parameterQuery;
 
-      public IndividualToIndividualBuildingBlockMapper(IObjectBaseFactory objectBaseFactory, IEntityPathResolver entityPathResolver, IApplicationConfiguration applicationConfiguration,
-         ILazyLoadTask lazyLoadTask, IRepresentationInfoRepository representationInfoRepository, ICalculationMethodCategoryRepository calculationMethodCategoryRepository, ICloner cloner) : base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask, cloner)
+      public IndividualToIndividualBuildingBlockMapper(IObjectBaseFactory objectBaseFactory,
+         IEntityPathResolver entityPathResolver,
+         IApplicationConfiguration applicationConfiguration,
+         ILazyLoadTask lazyLoadTask,
+         IRepresentationInfoRepository representationInfoRepository,
+         ICalculationMethodCategoryRepository calculationMethodCategoryRepository,
+         IFormulaFactory formulaFactory,
+         IParameterQuery parameterQuery) : base(objectBaseFactory, entityPathResolver, applicationConfiguration, lazyLoadTask, formulaFactory)
       {
          _representationInfoRepository = representationInfoRepository;
          _calculationMethodCategoryRepository = calculationMethodCategoryRepository;
+         _parameterQuery = parameterQuery;
+      }
+
+      protected override IFormula TemplateFormulaFor(IParameter parameter, IFormulaCache formulaCache, Individual individual)
+      {
+         bool isMetaDataForParameter(ParameterMetaData p) => p.BuildingBlockType == PKSimBuildingBlockType.Individual && string.Equals(p.ParameterName, parameter.Name);
+
+
+         //for individual, the CM to use depends on the CM available in the origin data as well as the container where the parameter resides.
+         var calculationMethods = individual.OriginData.AllCalculationMethods().AllNames();
+
+         var parameterRate = _parameterQuery.ParameterRatesFor(parameter.ParentContainer, calculationMethods, isMetaDataForParameter).ToList();
+
+         //this is not possible?
+         if (parameterRate.Count != 1)
+            return null;
+
+         var cloneFormula = _formulaFactory.RateFor(parameterRate[0], formulaCache);
+         cloneFormula.ObjectPaths.Each(x => x.Remove(Constants.ROOT));
+         return cloneFormula;
       }
 
       protected override IReadOnlyList<IParameter> AllParametersFor(Individual individual)

diff --git a/src/PKSim.Core/Mappers/PathAndValueBuildingBlockMapper.cs b/src/PKSim.Core/Mappers/PathAndValueBuildingBlockMapper.cs
@@ -6,11 +6,9 @@
 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;
+using IFormulaFactory = PKSim.Core.Model.IFormulaFactory;
 
 namespace PKSim.Core.Mappers
 {
@@ -21,8 +19,8 @@ public interface IPathAndValueBuildingBlockMapper<in TPKSimBuildingBlock, out TB
    public interface IPathAndValueBuildingBlockMapper<in TPKSimBuildingBlock, out TBuildingBlock, out TBuilder> : IPathAndValueBuildingBlockMapper<TPKSimBuildingBlock, TBuildingBlock>
    {
       /// <summary>
-      /// Map the parameter to the underlying builder parameter.
-      /// Note that formula or value will not be set. Only common parameter properties
+      ///    Map the parameter to the underlying builder parameter.
+      ///    Note that formula or value will not be set. Only common parameter properties
       /// </summary>
       TBuilder MapParameter(IParameter parameter);
    }
@@ -35,24 +33,24 @@ public abstract class PathAndValueBuildingBlockMapper<TPKSimBuildingBlock, TBuil
       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);
+      private readonly IFormulaCache _formulaCache = new BuildingBlockFormulaCache();
+      protected readonly IFormulaFactory _formulaFactory;
 
       protected PathAndValueBuildingBlockMapper(
          IObjectBaseFactory objectBaseFactory,
          IEntityPathResolver entityPathResolver,
          IApplicationConfiguration applicationConfiguration,
          ILazyLoadTask lazyLoadTask,
-         ICloner cloner)
+         IFormulaFactory formulaFactory)
       {
          _objectBaseFactory = objectBaseFactory;
          _entityPathResolver = entityPathResolver;
          _applicationConfiguration = applicationConfiguration;
          _lazyLoadTask = lazyLoadTask;
-         _cloner = cloner;
+         _formulaFactory = formulaFactory;
       }
 
       protected TBuildingBlock CreateBaseObject(TPKSimBuildingBlock pkSimBuildingBlock)
@@ -74,15 +72,16 @@ public virtual TBuilder MapParameter(IParameter parameter)
          return builderParameter;
       }
 
-      private TBuilder mapBuilderParameter(IParameter parameter)
+      private TBuilder mapBuilderParameter(IParameter parameter, TPKSimBuildingBlock pkSimBuildingBlock)
       {
          var builderParameter = MapParameter(parameter);
 
          // Add the formula to the building block formula cache if the formula can be cached
          var parameterValue = getParameterValue(parameter);
          var valueChanged = parameter.ValueDiffersFromDefault();
+         var formula = parameter.Formula;
 
-         switch (parameter.Formula)
+         switch (formula)
          {
             case ConstantFormula _:
                builderParameter.Value = parameterValue;
@@ -98,13 +97,10 @@ private TBuilder mapBuilderParameter(IParameter parameter)
                return builderParameter;
 
             default:
-               if (isFormulaCachable(parameter))
+               if (formula.IsCachable())
                {
-                  if (!_formulaCache.Contains(parameter.Formula.Name))
-                     _formulaCache.Add(cloneFormulaForExport(parameter));
-
-                  //Set the formula no matter what
-                  builderParameter.Formula = _formulaCache[parameter.Formula.Name];
+                  var templateFormula = retrieveTemplateFormulaFromCache(parameter, pkSimBuildingBlock);
+                  builderParameter.Formula = templateFormula;
                }
 
                // Only set the value of the parameter using a formula if it was indeed set
@@ -115,17 +111,20 @@ private TBuilder mapBuilderParameter(IParameter parameter)
          }
       }
 
-      private IFormula cloneFormulaForExport(IParameter parameter)
+      private IFormula retrieveTemplateFormulaFromCache(IParameter parameter, TPKSimBuildingBlock pkSimBuildingBlock)
       {
-         var cloneFormula = _cloner.Clone(parameter.Formula);
-         cloneFormula.ObjectPaths.Each(x => x.Remove(Constants.ROOT));
-         return cloneFormula;
+         var formulaName = parameter.Formula.Name;
+         if (_formulaCache.Contains(formulaName))
+            return _formulaCache[formulaName];
+
+         //This will add the formula top the cache 
+         var templateFormula = TemplateFormulaFor(parameter, _formulaCache, pkSimBuildingBlock);
+         //We need to remove the ROOT keyword when exporting to PKML structure 
+         templateFormula?.ObjectPaths.Each(x => x.Remove(Constants.ROOT));
+         return templateFormula;
       }
 
-      private static bool isFormulaCachable(IParameter parameter)
-      {
-         return parameter.Formula != null && parameter.Formula.IsCachable();
-      }
+      protected abstract IFormula TemplateFormulaFor(IParameter parameter, IFormulaCache formulaCache, TPKSimBuildingBlock pkSimBuildingBlock);
 
       private static double getParameterValue(IParameter parameter)
       {
@@ -134,7 +133,7 @@ private static double getParameterValue(IParameter parameter)
 
       protected void MapAllParameters(TPKSimBuildingBlock sourcePKSimBuildingBlock, TBuildingBlock buildingBlock)
       {
-         var allBuilderParameters = AllParametersFor(sourcePKSimBuildingBlock).Select(mapBuilderParameter);
+         var allBuilderParameters = AllParametersFor(sourcePKSimBuildingBlock).Select(x=>mapBuilderParameter(x, sourcePKSimBuildingBlock));
          allBuilderParameters.Where(x => x != null).Each(buildingBlock.Add);
 
          //Formula cache already contains a clone of all formula. We can add as is

diff --git a/src/PKSim.Core/Model/Individual.cs b/src/PKSim.Core/Model/Individual.cs
@@ -67,13 +67,24 @@ public Individual() : base(PKSimBuildingBlockType.Individual)
       /// <summary>
       ///    All defined molecules defined in the individual
       /// </summary>
-      public virtual IEnumerable<IndividualMolecule> AllDefinedMolecules() => AllMolecules().Where(x => !x.IsUndefinedMolecule());
+      public virtual IEnumerable<IndividualMolecule> AllDefinedMolecules() => AllMolecules<IndividualMolecule>(x => !x.IsUndefinedMolecule());
+
+      /// <summary>
+      ///    All defined molecules defined in the individual
+      /// </summary>
+      public virtual IEnumerable<IndividualMolecule> AllUndefinedMolecules() => AllMolecules<IndividualMolecule>(x => x.IsUndefinedMolecule());
+
+      /// <summary>
+      ///    All protein of type <typeparamref name="TMolecule" /> in the individual
+      /// </summary>
+      /// <typeparam name="TMolecule"> Type of molecule to be retrieved </typeparam>
+      public virtual IEnumerable<TMolecule> AllMolecules<TMolecule>() where TMolecule : IndividualMolecule => AllMolecules<TMolecule>(x => true);
 
       /// <summary>
       ///    All protein of type <typeparamref name="TMolecule" /> in the individual
       /// </summary>
       /// <typeparam name="TMolecule"> Type of molecule to be retrieved </typeparam>
-      public virtual IEnumerable<TMolecule> AllMolecules<TMolecule>() where TMolecule : IndividualMolecule => GetChildren<TMolecule>();
+      public virtual IEnumerable<TMolecule> AllMolecules<TMolecule>(Func<TMolecule, bool> predicate) where TMolecule : IndividualMolecule => GetChildren(predicate);
 
       public ExpressionProfile ExpressionProfileFor(IndividualMolecule molecule) => AllExpressionProfiles().Find(x => string.Equals(x.MoleculeName, molecule.Name));
 

diff --git a/src/PKSim.Core/PKSim.Core.csproj b/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="12.0.144" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.144" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.144" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.144" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.145" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.145" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

diff --git a/src/PKSim.Core/Services/PKSimParameterStartValuesCreator.cs b/src/PKSim.Core/Services/PKSimParameterStartValuesCreator.cs
@@ -30,10 +30,28 @@ public PKSimParameterStartValuesCreator(
 
       public ParameterStartValuesBuildingBlock CreateFor(SimulationConfiguration simulationConfiguration, Simulation simulation)
       {
-         //default default parameter start values matrix
-         _defaultStartValues = _objectBaseFactory.Create<ParameterStartValuesBuildingBlock>();
-         updateSimulationParameters(simulation);
-         return _defaultStartValues.WithName(simulation.Name);
+         try
+         {
+            //default default parameter start values matrix
+            _defaultStartValues = _objectBaseFactory.Create<ParameterStartValuesBuildingBlock>();
+            var individual = simulation.Individual;
+
+            //set the relative expression values for each molecule undefined molecule of the individual (other will be done in expression profile)
+            individual.AllUndefinedMolecules().Each(molecule => updateMoleculeParametersValues(molecule, individual));
+
+            updateSimulationParameters(simulation);
+            return _defaultStartValues.WithName(simulation.Name);
+         }
+         finally
+         {
+            _defaultStartValues = null;
+         }
+      }
+
+      private void updateMoleculeParametersValues(IndividualMolecule molecule, Individual individual)
+      {
+         var allMoleculeParameters = individual.AllMoleculeParametersFor(molecule);
+         allMoleculeParameters.Each(p => trySetValue(p));
       }
 
       private void updateSimulationParameters(Simulation simulation)
@@ -43,14 +61,10 @@ private void updateSimulationParameters(Simulation simulation)
          if (simulation.Model == null)
             return;
 
+         //TODO: Ensure that the formula will not become a constant after clone
+         //THis was done with  psv.OverrideFormulaWithValue = false;
          var allSimulationParameters = simulation.Model.Root.GetAllChildren<IParameter>(isChangedSimulationParameter);
-         allSimulationParameters.Each(p =>
-         {
-            var psv = trySetValue(p);
-            //Ensure that the formula will not become a constant after clone
-            //TODO
-//            psv.OverrideFormulaWithValue = false;
-         });
+         allSimulationParameters.Each(p => trySetValue(p));
       }
 
       private bool isChangedSimulationParameter(IParameter parameter)