Fixes #1920 create neighborhood builder with path instead of containe…

…r: (#1922)

* Fixes #1920 create neighborhood builder with path instead of container:

* Fixes #1920 create neighborhood builder with path instead of container

* add icons

* add icons

src/OSPSuite.Assets.Images/ApplicationIcons.cs

@@ -497,6 +497,7 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon PKSimModulesFolder = AddNamedIcon("PKSimModulesFolder"); // TODO add icon svg file. Presently just a copy of Folder svg
       public static readonly ApplicationIcon ExtensionModulesFolder = AddNamedIcon("ExtensionModulesFolder"); // TODO add icon svg file. Presently just a copy of Folder svg
       public static readonly ApplicationIcon Module = AddNamedIcon("Module"); // TODO add icon svg file. Presently just a copy of BBExplorer svg
+      public static readonly ApplicationIcon Neighborhood = AddNamedIcon("OSPSuite", "Neighborhood"); // TODO add icon svg file. Presently just a copy of BBExplorer svg
 
       // All icons should go at the end of the preceding list, before this delimiting icon - EmptyIcon
       private static ApplicationIcon createEmptyIcon() => new ApplicationIcon((SvgImage) null);

src/OSPSuite.Assets/UIConstants.cs

@@ -2267,7 +2267,7 @@ public static class ObjectTypes
       public static readonly string Formula = "Formula";
       public static readonly string Simulation = "Simulation";
       public static readonly string ExplicitFormula = "Formula";
-      public static readonly string NeighborhoodBuilder = "Neighborhood";
+      public static readonly string Neighborhood = "Neighborhood";
       public static readonly string PassiveTransportBuilder = "Passive Transport";
       public static readonly string ActiveTransportBuilder = "Active Transport";
       public static readonly string TransportBuilder = "Transport";
@@ -2286,7 +2286,7 @@ public static class ObjectTypes
       public static readonly string SumFormula = "Sum Formula";
       public static readonly string Quantities = "Quantities";
       public static readonly string Model = "Model";
-      public static readonly string MoleculeList = "Moleculelist";
+      public static readonly string MoleculeList = "Molecule List";
       public static readonly string SolverProperty = "Solver Property";
       public static readonly string SimulationSettings = "Simulation Settings";
       public static readonly string OutputSelections = "Output Selections";

src/OSPSuite.Core/Comparison/NeighborhoodBaseDiffBuilder.cs

@@ -1,45 +1,75 @@
 using OSPSuite.Assets;
 using OSPSuite.Core.Domain;
+using OSPSuite.Core.Domain.Builder;
 using OSPSuite.Core.Domain.Services;
 
 namespace OSPSuite.Core.Comparison
 {
-   public class NeighborhoodBaseDiffBuilder : DiffBuilder<INeighborhoodBase>
+   public abstract class NeighborhoodBaseDiffBuilder<TNeighborhood> : DiffBuilder<TNeighborhood> where TNeighborhood : class, IContainer
    {
       private readonly ContainerDiffBuilder _containerDiffBuilder;
-      private readonly IEntityPathResolver _entityPathResolver;
 
-      public NeighborhoodBaseDiffBuilder(ContainerDiffBuilder containerDiffBuilder, IEntityPathResolver entityPathResolver)
+      protected NeighborhoodBaseDiffBuilder(ContainerDiffBuilder containerDiffBuilder)
       {
          _containerDiffBuilder = containerDiffBuilder;
-         _entityPathResolver = entityPathResolver;
       }
 
-      public override void Compare(IComparison<INeighborhoodBase> comparison)
+      public override void Compare(IComparison<TNeighborhood> comparison)
       {
          _containerDiffBuilder.Compare(comparison);
          compareNeighbors(comparison);
       }
 
-      private void compareNeighbors(IComparison<INeighborhoodBase> comparison)
+      private void compareNeighbors(IComparison<TNeighborhood> comparison)
       {
-         var firstNeigbor1Path = _entityPathResolver.PathFor(comparison.Object1.FirstNeighbor);
-         var secondNeigbor1Path = _entityPathResolver.PathFor(comparison.Object1.SecondNeighbor);
-         var firstNeigbor2Path = _entityPathResolver.PathFor(comparison.Object2.FirstNeighbor);
-         var secondNeigbor2Path = _entityPathResolver.PathFor(comparison.Object2.SecondNeighbor);
+         var (firstNeighbor1Path, secondNeighbor1Path, firstNeighbor2Path, secondNeighbor2Path) = GetNeighborsComparisonPath(comparison);
 
-         if (firstNeigbor1Path.Equals(firstNeigbor2Path) && secondNeigbor1Path.Equals(secondNeigbor2Path) ||
-             firstNeigbor1Path.Equals(secondNeigbor2Path) && secondNeigbor1Path.Equals(firstNeigbor2Path))
+         if (firstNeighbor1Path.Equals(firstNeighbor2Path) && secondNeighbor1Path.Equals(secondNeighbor2Path) ||
+             firstNeighbor1Path.Equals(secondNeighbor2Path) && secondNeighbor1Path.Equals(firstNeighbor2Path))
             return;
 
          comparison.Add(new PropertyValueDiffItem
          {
             CommonAncestor = comparison.Object1,
-            FormattedValue1 = Captions.Diff.ConnectionBetween(firstNeigbor1Path, secondNeigbor1Path),
-            FormattedValue2 = Captions.Diff.ConnectionBetween(firstNeigbor2Path, secondNeigbor2Path),
+            FormattedValue1 = Captions.Diff.ConnectionBetween(firstNeighbor1Path, secondNeighbor1Path),
+            FormattedValue2 = Captions.Diff.ConnectionBetween(firstNeighbor2Path, secondNeighbor2Path),
             PropertyName = Captions.Diff.Connection,
-            Description = Captions.Diff.PropertyDiffers(Captions.Diff.Connection, Captions.Diff.ConnectionBetween(firstNeigbor1Path, secondNeigbor1Path), Captions.Diff.ConnectionBetween(firstNeigbor2Path, secondNeigbor2Path))
+            Description = Captions.Diff.PropertyDiffers(Captions.Diff.Connection, Captions.Diff.ConnectionBetween(firstNeighbor1Path, secondNeighbor1Path), Captions.Diff.ConnectionBetween(firstNeighbor2Path, secondNeighbor2Path))
          });
       }
+
+      protected abstract (ObjectPath firstNeighbor1Path, ObjectPath secondNeighbor1Path, ObjectPath firstNeighbor2Path, ObjectPath secondNeighbor2Path) GetNeighborsComparisonPath(IComparison<TNeighborhood> comparison);
+   }
+
+   public class NeighborhoodBuilderDiffBuilder : NeighborhoodBaseDiffBuilder<NeighborhoodBuilder>
+   {
+      public NeighborhoodBuilderDiffBuilder(ContainerDiffBuilder containerDiffBuilder) : base(containerDiffBuilder)
+      {
+      }
+
+      protected override (ObjectPath firstNeighbor1Path, ObjectPath secondNeighbor1Path, ObjectPath firstNeighbor2Path, ObjectPath secondNeighbor2Path) GetNeighborsComparisonPath(IComparison<NeighborhoodBuilder> comparison)
+      {
+         return (comparison.Object1.FirstNeighborPath, comparison.Object1.SecondNeighborPath, comparison.Object2.FirstNeighborPath, comparison.Object2.SecondNeighborPath);
+      }
+   }
+
+   public class NeighborhoodDiffBuilder : NeighborhoodBaseDiffBuilder<Neighborhood>
+   {
+      private readonly IEntityPathResolver _entityPathResolver;
+
+      public NeighborhoodDiffBuilder(ContainerDiffBuilder containerDiffBuilder, IEntityPathResolver entityPathResolver) : base(containerDiffBuilder)
+      {
+         _entityPathResolver = entityPathResolver;
+      }
+
+      protected override (ObjectPath firstNeighbor1Path, ObjectPath secondNeighbor1Path, ObjectPath firstNeighbor2Path, ObjectPath secondNeighbor2Path) GetNeighborsComparisonPath(IComparison<Neighborhood> comparison)
+      {
+         var firstNeighbor1Path = _entityPathResolver.ObjectPathFor(comparison.Object1.FirstNeighbor);
+         var secondNeighbor1Path = _entityPathResolver.ObjectPathFor(comparison.Object1.SecondNeighbor);
+         var firstNeighbor2Path = _entityPathResolver.ObjectPathFor(comparison.Object2.FirstNeighbor);
+         var secondNeighbor2Path = _entityPathResolver.ObjectPathFor(comparison.Object2.SecondNeighbor);
+
+         return (firstNeighbor1Path, secondNeighbor1Path, firstNeighbor2Path, secondNeighbor2Path);
+      }
    }
 }

src/OSPSuite.Core/Converters/v12/Converter110To120.cs

@@ -0,0 +1,68 @@
+using System.Xml.Linq;
+using OSPSuite.Core.Domain;
+using OSPSuite.Core.Domain.Builder;
+using OSPSuite.Core.Serialization;
+using OSPSuite.Core.Serialization.Exchange;
+using OSPSuite.Utility.Extensions;
+using OSPSuite.Utility.Visitor;
+
+namespace OSPSuite.Core.Converters.v12
+{
+   public class Converter110To120 : IObjectConverter,
+      IVisitor<ISpatialStructure>,
+      IVisitor<SimulationTransfer>,
+      IVisitor<IModelCoreSimulation>,
+      IVisitor<IBuildConfiguration>
+   {
+      private readonly IObjectPathFactory _objectPathFactory;
+      private bool _converted;
+
+      public Converter110To120(IObjectPathFactory objectPathFactory)
+      {
+         _objectPathFactory = objectPathFactory;
+      }
+
+      public bool IsSatisfiedBy(int version) => version == PKMLVersion.V11_0;
+
+      public (int convertedToVersion, bool conversionHappened) Convert(object objectToUpdate)
+      {
+         _converted = false;
+         performConversion(objectToUpdate);
+         return (PKMLVersion.V12_0, _converted);
+      }
+
+      public (int convertedToVersion, bool conversionHappened) ConvertXml(XElement element)
+      {
+         return (PKMLVersion.V12_0, false);
+      }
+
+      private void performConversion(object objectToUpdate) => this.Visit(objectToUpdate);
+
+      public void Visit(ISpatialStructure spatialStructure)
+      {
+         spatialStructure.Neighborhoods.Each(updateNeighborsPathIn);
+      }
+
+      private void updateNeighborsPathIn(NeighborhoodBuilder neighborhoodBuilder)
+      {
+         neighborhoodBuilder.FirstNeighborPath = _objectPathFactory.CreateAbsoluteObjectPath(neighborhoodBuilder.FirstNeighbor);
+         neighborhoodBuilder.SecondNeighborPath = _objectPathFactory.CreateAbsoluteObjectPath(neighborhoodBuilder.SecondNeighbor);
+         _converted = true;
+      }
+
+      public void Visit(SimulationTransfer simulationTransfer)
+      {
+         Visit(simulationTransfer.Simulation);
+      }
+
+      public void Visit(IModelCoreSimulation modelCoreSimulation)
+      {
+         Visit(modelCoreSimulation.BuildConfiguration);
+      }
+
+      public void Visit(IBuildConfiguration buildConfiguration)
+      {
+         Visit(buildConfiguration.SpatialStructure);
+      }
+   }
+}

src/OSPSuite.Core/Domain/Builder/NeighborhoodBuilder.cs

@@ -1,49 +1,65 @@
 using System.Collections.Generic;
+using OSPSuite.Core.Domain.Services;
 
 namespace OSPSuite.Core.Domain.Builder
 {
-   public interface INeighborhoodBuilder : INeighborhoodBase
+   public interface INeighborhoodBase : IContainer
    {
-      IContainer MoleculeProperties { get; }
-      IEnumerable<IParameter> Parameters { get; }
-      void AddParameter(IParameter newParameter);
-      void RemoveParameter(IParameter parameterToRemove);
-      bool IsConnectedTo(IContainer container);
+      /// <summary>
+      ///    First neighbor in the neighborhood.
+      /// </summary>
+      IContainer FirstNeighbor { get; }
+
+      /// <summary>
+      ///    Second neighbor in the neighborhood.
+      /// </summary>
+      IContainer SecondNeighbor { get; }
    }
 
-   public class NeighborhoodBuilder : Container, INeighborhoodBuilder
+   public class NeighborhoodBuilder : Container, INeighborhoodBase
    {
+      //We define a property set for the first neighbor only to be compatible with serialization prior to v12
       public IContainer FirstNeighbor { get; set; }
+
+      //We define a property set for the second neighbor only to be compatible with serialization prior to v12
       public IContainer SecondNeighbor { get; set; }
 
+      public ObjectPath FirstNeighborPath { get; set; }
+      public ObjectPath SecondNeighborPath { get; set; }
+
       public NeighborhoodBuilder()
       {
          ContainerType = ContainerType.Neighborhood;
       }
 
-      public IContainer MoleculeProperties
-      {
-         get { return this.GetSingleChildByName<IContainer>(Constants.MOLECULE_PROPERTIES); }
-      }
+      public IContainer MoleculeProperties => this.Container(Constants.MOLECULE_PROPERTIES);
 
-      public IEnumerable<IParameter> Parameters
-      {
-         get { return GetChildren<IParameter>(); }
-      }
+      public IEnumerable<IParameter> Parameters => GetChildren<IParameter>();
+
+      public void AddParameter(IParameter newParameter) => Add(newParameter);
 
-      public void AddParameter(IParameter newParameter)
+      public void RemoveParameter(IParameter parameterToRemove) => RemoveChild(parameterToRemove);
+
+      public bool IsConnectedTo(ObjectPath containerPath)
       {
-         Add(newParameter);
+         return Equals(FirstNeighborPath, containerPath) || Equals(SecondNeighborPath, containerPath);
       }
 
-      public void RemoveParameter(IParameter parameterToRemove)
+      public void ResolveReference(IContainer container)
       {
-         RemoveChild(parameterToRemove);
+         FirstNeighbor = FirstNeighborPath.Resolve<IContainer>(container);
+         SecondNeighbor = SecondNeighborPath.Resolve<IContainer>(container);
       }
 
-      public bool IsConnectedTo(IContainer container)
+      public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager)
       {
-         return Equals(FirstNeighbor, container) || Equals(SecondNeighbor, container);
+         base.UpdatePropertiesFrom(source, cloneManager);
+         var sourceNeighborhood = source as NeighborhoodBuilder;
+         if (sourceNeighborhood == null)
+            return;
+
+         FirstNeighborPath = sourceNeighborhood.FirstNeighborPath;
+         SecondNeighborPath = sourceNeighborhood.SecondNeighborPath;
       }
    }
 }

src/OSPSuite.Core/Domain/Builder/NeighborhoodBuilderFactory.cs

@@ -9,14 +9,14 @@ public interface INeighborhoodBuilderFactory
       /// Creates a new instance of a <see cref="NeighborhoodBuilder"/>.
       /// </summary>
       ///<returns> the new  <see cref="NeighborhoodBuilder"/></returns>
-      INeighborhoodBuilder Create();
+      NeighborhoodBuilder Create();
       /// <summary>
       /// Creates a new <see cref="NeighborhoodBuilder"/> between <paramref name="firstNeighbor"/> and <paramref name="secondNeighbor"/>.
       /// </summary>
       /// <param name="firstNeighbor">The first neighbor.</param>
       /// <param name="secondNeighbor">The second neighbor.</param>
       ///<returns> the new  <see cref="NeighborhoodBuilder"/></returns>
-      INeighborhoodBuilder CreateBetween(IContainer firstNeighbor, IContainer secondNeighbor);
+      NeighborhoodBuilder CreateBetween(IContainer firstNeighbor, IContainer secondNeighbor);
    }
 
    /// <summary>
@@ -25,35 +25,36 @@ public interface INeighborhoodBuilderFactory
    public class NeighborhoodBuilderFactory : INeighborhoodBuilderFactory
    {
       private readonly IObjectBaseFactory _objectBaseFactory;
+      private readonly IObjectPathFactory _objectPathFactory;
 
       /// <summary>
       /// Initializes a new instance of the <see cref="NeighborhoodBuilderFactory"/> class.
       /// </summary>
-      /// <param name="objectBaseFactory">The object base factory used to create new objects.</param>
-      public NeighborhoodBuilderFactory(IObjectBaseFactory objectBaseFactory)
+      public NeighborhoodBuilderFactory(IObjectBaseFactory objectBaseFactory, IObjectPathFactory objectPathFactory)
       {
          _objectBaseFactory = objectBaseFactory;
+         _objectPathFactory = objectPathFactory;
       }
 
       /// <summary>
       /// Creates a new instance of a <see cref="NeighborhoodBuilder"/>.
       /// </summary>
       ///<returns> the new  <see cref="NeighborhoodBuilder"/></returns>
-      public INeighborhoodBuilder Create()
+      public NeighborhoodBuilder Create()
       {
          var neighborhoodBuilder = CreateNeighborhoodBuilder().WithMode(ContainerMode.Logical);
-         var moelculePropertiers = CreateMoleculeProperties()
+         var moleculeProperties = CreateMoleculeProperties()
             .WithName(Constants.MOLECULE_PROPERTIES)
             .WithMode(ContainerMode.Logical);
 
-         neighborhoodBuilder.Add(moelculePropertiers);
+         neighborhoodBuilder.Add(moleculeProperties);
 
          return neighborhoodBuilder;
       }
 
-      protected INeighborhoodBuilder CreateNeighborhoodBuilder()
+      protected NeighborhoodBuilder CreateNeighborhoodBuilder()
       {
-         return _objectBaseFactory.Create<INeighborhoodBuilder>();
+         return _objectBaseFactory.Create<NeighborhoodBuilder>();
       }
 
       protected IContainer CreateMoleculeProperties()
@@ -67,12 +68,12 @@ protected IContainer CreateMoleculeProperties()
       /// <param name="firstNeighbor">The first neighbor.</param>
       /// <param name="secondNeighbor">The second neighbor.</param>
       ///<returns> the new  <see cref="NeighborhoodBuilder"/></returns>
-      public INeighborhoodBuilder CreateBetween(IContainer firstNeighbor, IContainer secondNeighbor)
+      public NeighborhoodBuilder CreateBetween(IContainer firstNeighbor, IContainer secondNeighbor)
       {
-         var neighborhoohBuilder = Create();
-         neighborhoohBuilder.FirstNeighbor = firstNeighbor;
-         neighborhoohBuilder.SecondNeighbor = secondNeighbor;
-         return neighborhoohBuilder;
+         var neighborhoodBuilder = Create();
+         neighborhoodBuilder.FirstNeighborPath = _objectPathFactory.CreateAbsoluteObjectPath(firstNeighbor);
+         neighborhoodBuilder.SecondNeighborPath = _objectPathFactory.CreateAbsoluteObjectPath(secondNeighbor);
+         return neighborhoodBuilder;
       }
    }
 }