Fixes #1312

Open-Systems-Pharmacology · Oct 16, 2023 · 63dfd44 · 63dfd44
1 parent bc4f3ef
commit 63dfd44
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Showing 3 changed files with 15 additions and 14 deletions.
diff --git a/src/OSPSuite.Core/Domain/Mappers/NeighborhoodBuilderToNeighborhoodMapper.cs b/src/OSPSuite.Core/Domain/Mappers/NeighborhoodBuilderToNeighborhoodMapper.cs
@@ -51,11 +51,11 @@ public NeighborhoodBuilderToNeighborhoodMapper(
       public Neighborhood MapFrom(NeighborhoodBuilder neighborhoodBuilder, IEnumerable<string> moleculeNames,
          IEnumerable<string> moleculeNamesWithCopyPropertiesRequired, ModelConfiguration modelConfiguration)
       {
-         var (model, simulationConfiguration, replacementContext) = modelConfiguration;
+         var (model, simulationBuilder, replacementContext) = modelConfiguration;
 
          var neighborhood = _objectBaseFactory.Create<Neighborhood>();
          neighborhood.UpdatePropertiesFrom(neighborhoodBuilder, _cloneManagerForModel);
-         simulationConfiguration.AddBuilderReference(neighborhood, neighborhoodBuilder);
+         simulationBuilder.AddBuilderReference(neighborhood, neighborhoodBuilder);
          neighborhood.FirstNeighbor = resolveReference(model, neighborhoodBuilder.FirstNeighborPath, replacementContext);
          neighborhood.SecondNeighbor = resolveReference(model, neighborhoodBuilder.SecondNeighborPath, replacementContext);
 
@@ -66,23 +66,24 @@ public Neighborhood MapFrom(NeighborhoodBuilder neighborhoodBuilder, IEnumerable
          if (neighborhoodBuilder.MoleculeProperties != null)
          {
             moleculeNames.Each(moleculeName => neighborhood.Add(
-               createMoleculePropertiesFor(neighborhoodBuilder, moleculeName, moleculeNamesWithCopyPropertiesRequired, simulationConfiguration, replacementContext)));
+               createMoleculePropertiesFor(neighborhoodBuilder, moleculeName, moleculeNamesWithCopyPropertiesRequired, modelConfiguration)));
          }
 
          //Add neighborhood parameter to the neighborhood (clone the existing parameter)
-         neighborhoodBuilder.Parameters.Each(param => neighborhood.Add(_parameterMapper.MapFrom(param, simulationConfiguration)));
+         neighborhoodBuilder.Parameters.Each(param => neighborhood.Add(_parameterMapper.MapFrom(param, simulationBuilder)));
          return neighborhood;
       }
 
       private IContainer resolveReference(IModel model, ObjectPath objectPath, ReplacementContext replacementContext)
       {
          var objectPathInModel = _keywordReplacerTask.CreateModelPathFor(objectPath, replacementContext);
-         return objectPathInModel.Resolve<IContainer>(replacementContext.RootContainer);
+         return objectPathInModel.Resolve<IContainer>(model.Root);
       }
 
       private IContainer createMoleculePropertiesFor(NeighborhoodBuilder neighborhoodBuilder,
-         string moleculeName, IEnumerable<string> moleculeNamesWithCopyPropertiesRequired, SimulationBuilder simulationBuilder, ReplacementContext replacementContext)
+         string moleculeName, IEnumerable<string> moleculeNamesWithCopyPropertiesRequired, ModelConfiguration modelConfiguration)
       {
+         var (_, simulationBuilder, replacementContext) = modelConfiguration;
          //Create a new model container from the neighborhood container 
          var moleculePropertiesContainer = _containerMapper.MapFrom(neighborhoodBuilder.MoleculeProperties, simulationBuilder);
          moleculePropertiesContainer.ContainerType = ContainerType.Molecule;

diff --git a/src/OSPSuite.Core/Domain/Services/ObserverBuilderTask.cs b/src/OSPSuite.Core/Domain/Services/ObserverBuilderTask.cs
@@ -48,11 +48,11 @@ public void CreateObservers(ModelConfiguration modelConfiguration)
          try
          {
             foreach (var observerBuilder in observers.OfType<AmountObserverBuilder>())
-               createAmountObserver(observerBuilder, replacementContext, presentMolecules);
+               createAmountObserver(observerBuilder, presentMolecules, replacementContext);
 
 
             foreach (var observerBuilder in observers.OfType<ContainerObserverBuilder>())
-               createContainerObserver(observerBuilder, replacementContext, presentMolecules);
+               createContainerObserver(observerBuilder, presentMolecules, replacementContext);
          }
          finally
          {
@@ -77,7 +77,7 @@ private IEnumerable<MoleculeBuilder> moleculeBuildersValidFor(MoleculeList molec
       ///    in the spatial structure of the model.
       ///    Typical example: "Concentration"-Observer (M/V)
       /// </summary>
-      private void createAmountObserver(AmountObserverBuilder observerBuilder, ReplacementContext replacementContext, IEnumerable<MoleculeBuilder> presentMolecules)
+      private void createAmountObserver(AmountObserverBuilder observerBuilder, IEnumerable<MoleculeBuilder> presentMolecules, ReplacementContext replacementContext)
       {
          var moleculeNamesForObserver = moleculeBuildersValidFor(observerBuilder.MoleculeList, presentMolecules)
             .Select(x => x.Name).ToList();
@@ -100,7 +100,7 @@ private void createAmountObserver(AmountObserverBuilder observerBuilder, Replace
       ///    of the model.
       ///    Typical example is average drug concentration in an organ
       /// </summary>
-      private void createContainerObserver(ContainerObserverBuilder observerBuilder, ReplacementContext replacementContext, IEnumerable<MoleculeBuilder> presentMolecules)
+      private void createContainerObserver(ContainerObserverBuilder observerBuilder, IEnumerable<MoleculeBuilder> presentMolecules, ReplacementContext replacementContext)
       {
          var moleculeBuildersForObserver = moleculeBuildersValidFor(observerBuilder.MoleculeList, presentMolecules).ToList();
          //retrieve a list here to avoid endless loop if observers criteria is not well defined

diff --git a/tests/OSPSuite.Core.Tests/Domain/KeywordReplacerTaskSpecs.cs b/tests/OSPSuite.Core.Tests/Domain/KeywordReplacerTaskSpecs.cs
@@ -9,7 +9,7 @@
 
 namespace OSPSuite.Core.Domain
 {
-   internal abstract class concern_for_KeywordReplacerTask : ContextSpecification<IKeywordReplacerTask>
+   public abstract class concern_for_KeywordReplacerTask : ContextSpecification<IKeywordReplacerTask>
    {
       protected string _modelName;
       protected FormulaUsablePath _objPathFirstNeighbor;
@@ -33,7 +33,7 @@ protected override void Context()
       }
    }
 
-   internal class When_replacing_the_keyword_in_a_reaction : concern_for_KeywordReplacerTask
+   public class When_replacing_the_keyword_in_a_reaction : concern_for_KeywordReplacerTask
    {
       private Reaction _reaction;
 
@@ -65,7 +65,7 @@ public void should_have_replace_the_organism_keyword_with_the_global_path_to_the
       }
    }
 
-   internal class When_replacing_the_keyword_in_a_molecule_properties_container : concern_for_KeywordReplacerTask
+   public class When_replacing_the_keyword_in_a_molecule_properties_container : concern_for_KeywordReplacerTask
    {
       private IContainer _moleculeContainer;
       private string _moleculeName;
@@ -102,7 +102,7 @@ public void should_have_replace_the_organism_keyword_with_the_global_path_to_the
       }
    }
 
-   internal class When_replacing_keywords_in_a_parameter_defined_in_a_global_molecule_container : concern_for_KeywordReplacerTask
+   public class When_replacing_keywords_in_a_parameter_defined_in_a_global_molecule_container : concern_for_KeywordReplacerTask
    {
       private IParameter _parameter;
       private IContainer _rootContainer;