Parameter mode etc

src/PKSim.Infrastructure/ORM/FlatObjects/FlatProcessDescriptorCondition.cs

@@ -1,9 +1,14 @@
 namespace PKSim.Infrastructure.ORM.FlatObjects
 {
+   /// <summary>
+   /// Source and Target are used for transport source/target container conditions
+   /// Parent is used e.g. for reactions (parent) container conditions
+   /// </summary>
    public enum ProcessTagType
    {
       Source,
-      Target
+      Target,
+      Parent
    }
 
    public class FlatProcessDescriptorCondition : FlatDescriptorConditionBase

src/PKSim.Infrastructure/ORM/Mappers/FlatProcessToActiveProcessMapper.cs

@@ -69,7 +69,7 @@ private IPKSimProcess createProcessFrom(FlatProcess flatProcess)
          {
             case ProcessActionType.Reaction:
                var reaction = newReaction();
-               addReactionPartnersTo(reaction, flatProcess.Name);
+               addReactionPartnersAndContainerCriteriaTo(reaction, flatProcess.Name);
                return reaction;
             case ProcessActionType.Transport:
                return _entityBaseFactory.Create<PKSimTransport>();
@@ -91,7 +91,7 @@ private PKSimReaction newReaction()
          return _entityBaseFactory.Create<PKSimReaction>();
       }
 
-      private void addReactionPartnersTo(PKSimReaction reaction, string reactionName)
+      private void addReactionPartnersAndContainerCriteriaTo(PKSimReaction reaction, string reactionName)
       {
          var allPartners = (from rp in _reactionPartnerRepository.All()
             where rp.Reaction.Equals(reactionName)
@@ -101,6 +101,20 @@ where rp.Reaction.Equals(reactionName)
          {
             addReactionPartnerTo(reaction, flatReactionPartner);
          }
+
+         var conditions = from pd in _processDescriptorRepository.All()
+            where pd.TagType == ProcessTagType.Parent
+            where pd.Process == reactionName
+            select pd;
+
+         //TODO we should extend the DB structure to allow also InContainer/NotInContainer criteria
+         foreach (var condition in conditions)
+         {
+            if (condition.ShouldHave)
+               reaction.ContainerCriteria.Add(new MatchTagCondition(condition.Tag));
+            else
+               reaction.ContainerCriteria.Add(new NotMatchTagCondition(condition.Tag));
+         }
       }
 
       private void addReactionPartnerTo(PKSimReaction reaction, FlatReactionPartner flatReactionPartner)

tests/PKSim.Tests/IntegrationTests/FlatIndividualParametersNotCommonForAllSpeciesRepositorySpecs.cs

@@ -2,6 +2,8 @@
 using System.Linq;
 using OSPSuite.BDDHelper;
 using OSPSuite.BDDHelper.Extensions;
+using OSPSuite.Core.Domain;
+using PKSim.Core;
 using PKSim.Infrastructure.ORM.FlatObjects;
 using PKSim.Infrastructure.ORM.Repositories;
 
@@ -11,19 +13,30 @@ public abstract class concern_for_FlatIndividualParametersNotCommonForAllSpecies
    {
    }
 
-   public class When_resolving_all_parameters_not_common_for_all_species_as_a_flat_table : concern_for_FlatIndividualParametersNotCommonForAllSpeciesRepository
+   public class
+      When_resolving_all_parameters_not_common_for_all_species_as_a_flat_table :
+      concern_for_FlatIndividualParametersNotCommonForAllSpeciesRepository
    {
       private IEnumerable<FlatIndividualParametersNotCommonForAllSpecies> _result;
+      private IEnumerable<FlatIndividualParametersNotCommonForAllSpecies> _organismParameters;
 
       protected override void Because()
       {
          _result = sut.All();
+         _organismParameters = _result.Where(p => p.ContainerName.Equals("Organism"));
       }
 
       [Observation]
       public void should_retrieve_some_object_from_the_underlying_database()
       {
          _result.Count().ShouldBeGreaterThan(0);
       }
+
+      [Observation]
+      public void should_contain_mean_height()
+      {
+         _organismParameters.Count(p => p.ParameterName.Equals(CoreConstants.Parameters.MEAN_HEIGHT))
+            .ShouldBeEqualTo(1);
+      }
    }
 }

tests/PKSim.Tests/IntegrationTests/FlatParameterInContainsRepositorySpecs.cs

@@ -38,6 +38,13 @@ private bool isOneOfReadOnlyAndIsInputParameters(string parameterName)
          return parameterName.IsOneOf(Constants.Parameters.IS_SMALL_MOLECULE, CoreConstants.Parameters.INPUT_DOSE);
       }
 
+      [Observation]
+      public void all_parameters_should_have_build_mode_global_or_local()
+      {
+         _allParameters.Count(p => p.BuildMode != ParameterBuildMode.Global && p.BuildMode != ParameterBuildMode.Local)
+            .ShouldBeEqualTo(0);
+      }
+
       [Observation]
       public void all_hidden_parameters_should_be_read_only()
       {

tests/PKSim.Tests/IntegrationTests/PKSimParameterStartValuesCreatorSpecs.cs

@@ -75,17 +75,6 @@ public void should_have_created_one_entry_for_the_changed_parameter_in_the_param
          _parameterValues[_parameterPath].Value.ShouldBeEqualTo(10);
       }
 
-      [Observation]
-      public void should_have_not_created_entries_for_property_parameter_of_the_enzyme()
-      {
-         var propertyParameters = _enzyme.AllParameters().Where(x => x.BuildMode == ParameterBuildMode.Property).ToList();
-         propertyParameters.Count.ShouldBeGreaterThan(0);
-         propertyParameters.Each(x =>
-         {
-            var parameterPath = _entityPathResolver.ObjectPathFor(x);
-            _parameterValues[parameterPath].ShouldBeNull();
-         });
-      }
    }
 
    public class When_creating_a_parameter_start_value_for_an_individual_and_simulation_where_the_initial_concentration_was_changed_in_the_expression_profile : ContextForSimulationIntegration<IPKSimParameterValuesCreator>

tests/PKSim.Tests/IntegrationTests/SimulationSpecs.cs

@@ -593,9 +593,6 @@ public void should_create_required_molecules_in_sub_compartments_of_tissue_organ
       public void should_create_required_molecules_in_subcompartments_of_endogenous_igg_organ()
       {
          string fcRn = CoreConstants.Molecule.FcRn;
-         const string fcRnKineticsEndosome = "FcRn kinetics endosome";
-         const string fcRnKineticsInterstitial = "FcRn kinetics interstitial";
-         const string fcRnKineticsPlasma = "FcRn kinetics plasma";
          string ligandEndo = CoreConstants.Molecule.LigandEndo;
          string ligandEndoComplex = CoreConstants.Molecule.LigandEndoComplex;
 
@@ -605,19 +602,19 @@ public void should_create_required_molecules_in_subcompartments_of_endogenous_ig
          var plasma = endoIgg.GetSingleChildByName<IContainer>(CoreConstants.Compartment.PLASMA);
          var endoIggPlasmaMoleculeNames = moleculeNamesIn(plasma);
 
-         endoIggPlasmaMoleculeNames.ShouldOnlyContain(fcRn, fcRnKineticsPlasma, ligandEndo, ligandEndoComplex);
+         endoIggPlasmaMoleculeNames.ShouldOnlyContain(fcRn, ligandEndo, ligandEndoComplex);
 
          // interstitial 
          var interstitial = endoIgg.GetSingleChildByName<IContainer>(CoreConstants.Compartment.INTERSTITIAL);
          var endoIggInterstitialMoleculeNames = moleculeNamesIn(interstitial);
 
-         endoIggInterstitialMoleculeNames.ShouldOnlyContain(fcRn, fcRnKineticsInterstitial, ligandEndo, ligandEndoComplex);
+         endoIggInterstitialMoleculeNames.ShouldOnlyContain(fcRn, ligandEndo, ligandEndoComplex);
 
          // endosome
          var endosome = endoIgg.GetSingleChildByName<IContainer>(CoreConstants.Compartment.ENDOSOME);
          var endoIggEndosomeMoleculeNames = moleculeNamesIn(endosome);
 
-         endoIggEndosomeMoleculeNames.ShouldOnlyContain(fcRn, fcRnKineticsEndosome, ligandEndo, ligandEndoComplex);
+         endoIggEndosomeMoleculeNames.ShouldOnlyContain(fcRn, ligandEndo, ligandEndoComplex);
 
          // IgG_Source
          var iggSrc = endoIgg.GetSingleChildByName<IContainer>("IgG_Source");

tests/PKSim.Tests/IntegrationTests/StaticReactionRepositorySpecs.cs

@@ -2,6 +2,7 @@
 using System.Linq;
 using OSPSuite.BDDHelper;
 using OSPSuite.BDDHelper.Extensions;
+using OSPSuite.Utility.Extensions;
 using PKSim.Core;
 using PKSim.Core.Model;
 using PKSim.Core.Repositories;
@@ -11,6 +12,7 @@ namespace PKSim.IntegrationTests
    public abstract class concern_for_StaticReactionRepository : ContextForIntegration<IStaticReactionRepository>
    {
       protected const string _reactionName1 = "FcRn binding tissue";
+      protected const string _reactionPrefix = "FcRn binding drug in ";
    }
 
    public class When_retrieving_all_static_reactions_the_repository : concern_for_StaticReactionRepository
@@ -44,6 +46,7 @@ public void should_return_the_reaction_with_partners()
          _reaction.ShouldNotBeNull();
          _reaction.Educts.Count().ShouldBeGreaterThan(0);
          _reaction.Products.Count().ShouldBeGreaterThan(0);
+         _reaction.ContainerCriteria.Count.ShouldBeEqualTo(0);
       }
    }
 
@@ -61,13 +64,27 @@ protected override void Because()
       [Observation]
       public void four_comp_reactions_list_should_be_empty()
       {
-         _fourCompReactions.Count().ShouldBeEqualTo(0);
+         _fourCompReactions.Count.ShouldBeEqualTo(0);
       }
 
       [Observation]
-      public void two_pores_reactions_list_should_contain_FcRn_binding_endosomal_tissue()
+      public void two_pores_reactions_list_should_contain_FcRn_binding_tissue()
       {
          _twoPoreReactions.Any(r => r.Name.Equals(_reactionName1)).ShouldBeTrue();
       }
+
+      [Observation]
+      public void two_pores_FcRn_binding_tissue_reaction_should_not_have_container_criteria()
+      {
+         _twoPoreReactions.First(r => r.Name.Equals(_reactionName1)).ContainerCriteria.Count.ShouldBeEqualTo(0);
+      }
+
+      [Observation]
+      public void two_pores_endogenousIgg_FcRn_binding_reactions_Should_have_container_criteria()
+      {
+         var reactions = _twoPoreReactions.Where(r => r.Name.StartsWith(_reactionPrefix)).ToList();
+         reactions.Count.ShouldBeEqualTo(3);
+         reactions.Each(r=>r.ContainerCriteria.Count.ShouldBeGreaterThan(0));
+      }
    }
 }