Fixes #2302 bug influx (#2327)

* WIP #2302 add failing tests

* Update database

* Fixes #2302 bug influx

* Fixes #2302 bug influx

* Fixes #2310 remove global column

* Fixes #2310 remove global column

* Make test pass again

* Fixes #2302 bug influx

src/PKSim.Core/CoreConstants.cs

@@ -776,7 +776,8 @@ public static class ORM
          public const string VIEW_SCHEMA_ITEMS = "VIEW_SCHEMA_ITEM_CONTAINERS";
          public const string VIEW_OBSERVERS = "VIEW_OBSERVERS";
          public const string VIEW_OBSERVER_DESCRIPTOR_CONDITIONS = "VIEW_OBSERVER_DESCRIPTOR_CONDITIONS";
-         public const string VIEW_INDIVIDUAL_ACTIVE_TRANSPORTS = "VIEW_INDIVIDUAL_ACTIVE_TRANSPORTS";
+         public const string VIEW_KNOWN_TRANSPORTER_CONTAINERS = "VIEW_KNOWN_TRANSPORTER_CONTAINERS";
+         public const string VIEW_KNOWN_TRANSPORTERS = "VIEW_KNOWN_TRANSPORTERS";
          public const string VIEW_PROTEIN_SYNONYMS = "VIEW_PROTEIN_SYNONYMS";
          public const string VIEW_PARAMETER_RHS = "VIEW_PARAMETER_RHS";
          public const string VIEW_CALCULATION_METHODS = "VIEW_CALCULATION_METHODS";

src/PKSim.Core/Model/TransporterContainerTemplate.cs

@@ -1,8 +1,9 @@
 using OSPSuite.Core.Domain;
+using PKSim.Core.Snapshots.Services;
 
 namespace PKSim.Core.Model
 {
-   public class TransporterContainerTemplate : WithSynonyms
+   public class TransporterContainerTemplate
    {
       /// <summary>
       ///    Gene associated with the template
@@ -15,20 +16,16 @@ public class TransporterContainerTemplate : WithSynonyms
       public string Species { get; set; }
 
       /// <summary>
-      ///    Organ where the transporter is defined
-      /// </summary>
-      public string OrganName { get; set; }
-
-      /// <summary>
-      ///    Compartment of the organ named OrganName where the transporter is defined
+      ///    Transporter type => Direction of transport
       /// </summary>
-      public string CompartmentName { get; set; }
+      public TransportType TransportType { get; set; }
 
       /// <summary>
-      ///    Transporter type => Direction of transport
+      ///    Organ where the transporter is defined
       /// </summary>
-      public TransportType TransportType { get; set; }
+      public string ContainerName { get; set; }
 
-      public override string Name => Gene;
+      //Default membrane location of this specific transport. This will override the default definition for TransportType
+      public MembraneLocation MembraneLocation { get; set; }
    }
 }

src/PKSim.Core/Model/TransporterTemplate.cs

@@ -0,0 +1,24 @@
+using OSPSuite.Core.Domain;
+
+namespace PKSim.Core.Model
+{
+   public class TransporterTemplate : WithSynonyms
+   {
+      /// <summary>
+      ///    Gene associated with the template
+      /// </summary>
+      public string Gene { get; set; }
+
+      /// <summary>
+      ///    Species for which the template is defined
+      /// </summary>
+      public string Species { get; set; }
+
+      /// <summary>
+      ///    Transporter type => Direction of transport
+      /// </summary>
+      public TransportType TransportType { get; set; }
+
+      public override string Name => Gene;
+   }
+}

src/PKSim.Core/Model/WithSynonyms.cs

@@ -8,28 +8,23 @@ public abstract class WithSynonyms
    {
       private readonly List<string> _allSynonyms = new List<string>();
 
-
       public void AddSynonym(string synonym)
       {
          _allSynonyms.Add(synonym);
       }
 
-
-      public IReadOnlyList<string> Synonyms
-      {
-         get { return _allSynonyms; }
-      }
+      public IReadOnlyList<string> Synonyms => _allSynonyms;
 
       public bool IsTemplateFor(string name)
       {
          return areSame(Name, name) || _allSynonyms.Any(s => areSame(s, name));
       }
 
-      public abstract string Name { get;  }
+      public abstract string Name { get; }
 
       private bool areSame(string name1, string name2)
       {
          return string.Equals(name1, name2, StringComparison.OrdinalIgnoreCase);
-      }  
+      }
    }
 }

src/PKSim.Core/Repositories/ITransporterContainerTemplateRepository.cs

@@ -8,38 +8,12 @@ namespace PKSim.Core.Repositories
    public interface ITransporterContainerTemplateRepository : IStartableRepository<TransporterContainerTemplate>
    {
       /// <summary>
-      /// Returns the default <see cref="TransportType"/> defined for a transporter named <paramref name="transporterName"/> 
-      /// and for the species named <paramref name="speciesName"/>
-      /// </summary>
-      /// <param name="speciesName">Species where the transporter will be defined</param>
-      /// <param name="transporterName">Transporter name (e.g. user input)</param>
-      TransportType TransportTypeFor(string speciesName, string transporterName);
-
-      /// <summary>
-      /// Returns true if a template was defined for a transporter named <paramref name="transporterName"/> for the species named <paramref name="speciesName"/> 
-      /// otherwise false;
-      /// </summary>
-      bool HasTransporterTemplateFor(string speciesName, string transporterName);
-
-      /// <summary>
-      /// Returns the default transporter templates defined for the concrete location <paramref name="containerName"/> and for a specific gene. 
+      /// Returns the default transporter template container defined for the concrete location <paramref name="containerName"/> and for a specific gene. 
       /// </summary>
       /// <param name="speciesName">Species where the transporter will be defined</param>
       /// <param name="containerName">Concrete transporter location (e.g Kidney, Liver etc...)</param>
       /// <param name="geneName">Specific gene for which templates should be returned</param>
-      IEnumerable<TransporterContainerTemplate> TransportersFor(string speciesName, string containerName, string geneName);
-
+      TransporterContainerTemplate TransporterContainerTemplateFor(string speciesName, string containerName, string geneName);
 
-      /// <summary>
-      /// Returns the default transporter templates defined for the concrete location <paramref name="containerName"/> 
-      /// </summary>
-      /// <param name="speciesName">Species where the transporter will be defined</param>
-      /// <param name="containerName">Concrete transporter location (e.g Kidney, Liver etc...)</param>
-      IEnumerable<TransporterContainerTemplate> TransportersFor(string speciesName, string containerName);
-
-      /// <summary>
-      /// Returns the name of all transporters defined in the PKSim Database (template transporters and their synonyms)
-      /// </summary>
-      IReadOnlyList<string> AllTransporterNames { get; }
    }
 }

src/PKSim.Core/Repositories/ITransporterTemplateRepository.cs

@@ -0,0 +1,32 @@
+using System.Collections.Generic;
+using OSPSuite.Core.Domain;
+using OSPSuite.Utility.Collections;
+using PKSim.Core.Model;
+
+namespace PKSim.Core.Repositories
+{
+   public interface ITransporterTemplateRepository : IStartableRepository<TransporterTemplate>
+   {
+      /// <summary>
+      ///    Returns the name of all transporters defined in the PKSim Database (template transporters and their synonyms)
+      /// </summary>
+      IReadOnlyList<string> AllTransporterNames { get; }
+
+      /// <summary>
+      ///    Returns the <see cref="TransportType" /> defined for a transporter named <paramref name="transporterName" />
+      ///    and for the species named <paramref name="speciesName" /> or default if nothing is defined in the database (TransportType.Efflux)
+      /// </summary>
+      /// <param name="speciesName">Species where the transporter will be defined</param>
+      /// <param name="transporterName">Transporter name (e.g. user input)</param>
+      TransportType TransportTypeOrDefaultFor(string speciesName, string transporterName);
+
+      /// <summary>
+      ///    Returns true if a template was defined for a transporter named <paramref name="transporterName" /> for the species
+      ///    named <paramref name="speciesName" />
+      ///    otherwise false;
+      /// </summary>
+      bool HasTransporterTemplateFor(string speciesName, string transporterName);
+
+      TransporterTemplate TransporterTemplateFor(string speciesName, string transporterName);
+   }
+} 

src/PKSim.Core/Repositories/UsedMoleculeRepository.cs

@@ -15,18 +15,18 @@ public class UsedMoleculeRepository : IUsedMoleculeRepository
       private readonly IPKSimProjectRetriever _projectRetriever;
       private readonly IOntogenyRepository _ontogenyRepository;
       private readonly IMoleculeParameterRepository _moleculeParameterRepository;
-      private readonly ITransporterContainerTemplateRepository _transporterContainerTemplateRepository;
+      private readonly ITransporterTemplateRepository _transporterTemplateRepository;
 
       public UsedMoleculeRepository(
-         IPKSimProjectRetriever projectRetriever, 
+         IPKSimProjectRetriever projectRetriever,
          IOntogenyRepository ontogenyRepository,
          IMoleculeParameterRepository moleculeParameterRepository,
-         ITransporterContainerTemplateRepository transporterContainerTemplateRepository)
+         ITransporterTemplateRepository transporterTemplateRepository)
       {
          _projectRetriever = projectRetriever;
          _ontogenyRepository = ontogenyRepository;
          _moleculeParameterRepository = moleculeParameterRepository;
-         _transporterContainerTemplateRepository = transporterContainerTemplateRepository;
+         _transporterTemplateRepository = transporterTemplateRepository;
       }
 
       public IEnumerable<string> All()
@@ -57,9 +57,10 @@ private IEnumerable<string> allPredefinedMolecules()
          //We use human as it has the most predefined molecules in the DB
          return _ontogenyRepository.AllFor(CoreConstants.Species.HUMAN).Select(x => x.Name)
             .Union(_moleculeParameterRepository.All().Select(x => x.MoleculeName))
-            .Union(_transporterContainerTemplateRepository.AllTransporterNames)
+            .Union(_transporterTemplateRepository.AllTransporterNames)
             .OrderBy(x => x);
       }
+
       private IEnumerable<TBuildingBlock> allLoadedBuildingBlocks<TBuildingBlock>() where TBuildingBlock : class, IPKSimBuildingBlock
       {
          return _projectRetriever.Current.All<TBuildingBlock>(x => x.IsLoaded);

src/PKSim.Core/Services/TransportContainerUpdater.cs

@@ -1,11 +1,14 @@
-using System.Linq;
+using System;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Extensions;
 using OSPSuite.Utility.Events;
+using OSPSuite.Utility.Extensions;
 using PKSim.Core.Events;
 using PKSim.Core.Model;
 using PKSim.Core.Model.Extensions;
 using PKSim.Core.Repositories;
+using PKSim.Core.Snapshots.Services;
+using static PKSim.Core.CoreConstants.Parameters;
 
 namespace PKSim.Core.Services
 {
@@ -15,61 +18,62 @@ public interface ITransportContainerUpdater
       ///    Update the default transporter settings using the template defined in the database based on the
       ///    <paramref name="transporterName" />/>
       /// </summary>
-      void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, string transporterName) ;
+      void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, string transporterName);
 
-      void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, TransportType transportType) ;
+      void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, TransportType transportType);
    }
 
    public class TransportContainerUpdater : ITransportContainerUpdater
    {
       private readonly ITransporterContainerTemplateRepository _transporterContainerTemplateRepository;
+      private readonly ITransporterTemplateRepository _transporterTemplateRepository;
       private readonly IEventPublisher _eventPublisher;
 
       public TransportContainerUpdater(
          ITransporterContainerTemplateRepository transporterContainerTemplateRepository,
+         ITransporterTemplateRepository transporterTemplateRepository,
          IEventPublisher eventPublisher)
       {
          _transporterContainerTemplateRepository = transporterContainerTemplateRepository;
+         _transporterTemplateRepository = transporterTemplateRepository;
          _eventPublisher = eventPublisher;
       }
 
       public void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, string transporterName)
       {
          var speciesName = simulationSubject.Species.Name;
-         transporter.TransportType = _transporterContainerTemplateRepository.TransportTypeFor(speciesName, transporterName);
+         var transportType = _transporterTemplateRepository.TransportTypeOrDefaultFor(speciesName, transporterName);
+         transporter.TransportType = transportType;
+
+         if (!_transporterTemplateRepository.HasTransporterTemplateFor(speciesName, transporterName))
+         {
+            //No template was found for the given name. Raise event warning
+            _eventPublisher.PublishEvent(new NoTransporterTemplateAvailableEvent(transporter));
+            return;
+         }
+
 
          foreach (var transporterContainer in simulationSubject.AllMoleculeContainersFor<TransporterExpressionContainer>(transporter))
          {
-            //there is a db template
             var transporterTemplate = _transporterContainerTemplateRepository
-               .TransportersFor(speciesName, transporterContainer.LogicalContainerName, transporterName)
-               .FirstOrDefault();
+               .TransporterContainerTemplateFor(speciesName, transporterContainer.LogicalContainerName, transporterName);
 
-            updateTransporterContainerFromTemplate(transporterContainer, transporterTemplate, transporter.TransportType);
+            updateTransporterContainerFromTemplate(transporterContainer, transporterTemplate, transportType);
          }
-
-         if (_transporterContainerTemplateRepository.HasTransporterTemplateFor(speciesName, transporterName))
-            return;
-
-         //No template was found for the given name. Raise event warning
-         _eventPublisher.PublishEvent(new NoTransporterTemplateAvailableEvent(transporter));
       }
 
       public void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, TransportType transportType)
       {
-         foreach (var transporterContainer in simulationSubject.AllMoleculeContainersFor<TransporterExpressionContainer>(transporter))
-         {
-            updateTransporterContainerFromTemplate(transporterContainer, null, transportType);
-            updateFractionExpressedApical(transporterContainer, transportType);
-         }
+         var allTransporterContainers = simulationSubject.AllMoleculeContainersFor<TransporterExpressionContainer>(transporter);
+         allTransporterContainers.Each(transporterContainer => updateTransporterContainerForTransportType(transporterContainer, transportType));
       }
 
       private void updateFractionExpressedApical(TransporterExpressionContainer transporterContainer, TransportType transportType)
       {
          if (!transportType.IsOneOf(TransportType.Efflux, TransportType.Influx, TransportType.PgpLike))
             return;
-         
-         var fractionExpressedApical = transporterContainer.Parameter(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL);
+
+         var fractionExpressedApical = transporterContainer.Parameter(FRACTION_EXPRESSED_APICAL);
          if (fractionExpressedApical == null)
             return;
 
@@ -82,14 +86,52 @@ private void updateFractionExpressedApical(TransporterExpressionContainer transp
             return;
 
          //Set the value according to the new transport type (Efflux + pgp one, Influx 0) except in mucosa where it is always apical
-         fractionExpressedApical.Value = transporterContainer.IsInMucosa() ? 1 :  transportType == TransportType.Influx ? 0 : 1;
+         fractionExpressedApical.Value = transporterContainer.IsInMucosa() ? 1 : transportType == TransportType.Influx ? 0 : 1;
+      }
+
+      private void updateTransporterContainerFromTemplate(TransporterExpressionContainer transporterContainer, TransporterContainerTemplate transporterContainerTemplate, TransportType transportType)
+      {
+         var transporterTypeToUse = transporterContainerTemplate?.TransportType ?? transportType;
+         //default update based on transport type
+         updateTransporterContainerForTransportType(transporterContainer, transporterTypeToUse);
+
+         //now overwrite if a template container is defined with value specific based on membrane location
+         if (transporterContainerTemplate == null)
+            return;
+
+
+         void setFractionValue(string fractionExpressedParameterName, double value)
+         {
+            var fractionExpressedParameter = transporterContainer.Parameter(fractionExpressedParameterName);
+            if (fractionExpressedParameter == null)
+               return;
+
+            fractionExpressedParameter.Value = value;
+         }
+
+         switch (transporterContainerTemplate.MembraneLocation)
+         {
+            case MembraneLocation.Apical:
+               setFractionValue(FRACTION_EXPRESSED_APICAL, 1);
+               break;
+            case MembraneLocation.Basolateral:
+               setFractionValue(FRACTION_EXPRESSED_APICAL, 0);
+               break;
+            case MembraneLocation.BloodBrainBarrier:
+               setFractionValue(FRACTION_EXPRESSED_AT_BLOOD_BRAIN_BARRIER, 1);
+               break;
+            case MembraneLocation.Tissue:
+               setFractionValue(FRACTION_EXPRESSED_AT_BLOOD_BRAIN_BARRIER, 0);
+               break;
+            default:
+               throw new ArgumentOutOfRangeException();
+         }
       }
 
-      private void updateTransporterContainerFromTemplate(TransporterExpressionContainer expressionContainer,
-         TransporterContainerTemplate transporterContainerTemplate, TransportType defaultTransportType)
+      private void updateTransporterContainerForTransportType(TransporterExpressionContainer transporterContainer, TransportType transportType)
       {
-         var transportType = transporterContainerTemplate?.TransportType ?? defaultTransportType;
-         expressionContainer.TransportDirection = TransportDirections.DefaultDirectionFor(transportType, expressionContainer);
+         transporterContainer.TransportDirection = TransportDirections.DefaultDirectionFor(transportType, transporterContainer);
+         updateFractionExpressedApical(transporterContainer, transportType);
       }
    }
 }

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

@@ -1,16 +1,10 @@
-using OSPSuite.Core.Domain;
-using PKSim.Core.Model;
 using PKSim.Core.Snapshots.Services;
 
 namespace PKSim.Infrastructure.ORM.FlatObjects
 {
-   public class FlatTransporterContainerTemplate
+   public class FlatTransporterContainerTemplate : FlatTransporterTemplate
    {
-      public string Gene { get; set; }
-      public string Species { get; set; }
-      public string OrganName { get; set; }
-      public string CompartmentName { get; set; }
-      public TransportType TransportType { get; set; }
+      public string ContainerName { get; set; }
       public MembraneLocation MembraneLocation { get; set; }
    }
 }