Fixes #820 individual serialization (#849)

* work in progress

* update core

src/MoBi.Assets/AppConstants.cs

@@ -1607,6 +1607,7 @@ public static class Captions
          public static readonly string AddMetabolizingEnzyme = "Add Metagbolizing Enzyme";
          public static readonly string AddTransportProtein = "Add Transport Protein";
          public static readonly string AddSpecificBindingPartner = "Add Binding Partner";
+         public static readonly string Individuals = "Individuals";
 
          public static string SumFormulaDescription(string iterationPattern) => $"Sum formula is defined as R1*…*Rm*∑{iterationPattern}*Q1_#i*…Qn_#i where R1…Rm (m>=0) are the quantities of an independent object (as absolute path or relative path); {iterationPattern} is a control variable (parameter, molecule amount, … defined by certain conditions); and Q1_#i…Qn_#i (n>=0) are the quantities that are obtained from a path relative to {iterationPattern}";
 

src/MoBi.Assets/MoBi.Assets.csproj

@@ -26,9 +26,9 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.77" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.84" />
   </ItemGroup>
 
   <ItemGroup>

src/MoBi.BatchTool/MoBi.BatchTool.csproj

@@ -60,7 +60,7 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.84" />
     <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" />

src/MoBi.Core/Domain/Model/MoBiProject.cs

@@ -22,6 +22,7 @@ public interface IMoBiProject : IProject
       IReadOnlyList<IMoleculeStartValuesBuildingBlock> MoleculeStartValueBlockCollection { get; }
       IReadOnlyList<IParameterStartValuesBuildingBlock> ParametersStartValueBlockCollection { get; }
       IReadOnlyList<ExpressionProfileBuildingBlock> ExpressionProfileCollection { get; }
+      IReadOnlyList<IndividualBuildingBlock> IndividualsCollection { get; }
       IReadOnlyList<ISimulationSettings> SimulationSettingsCollection { get; }
 
       ReactionDimensionMode ReactionDimensionMode { get; set; }
@@ -124,6 +125,8 @@ private IReadOnlyList<T> get<T>()
 
       public IReadOnlyList<ExpressionProfileBuildingBlock> ExpressionProfileCollection => get<ExpressionProfileBuildingBlock>();
 
+      public IReadOnlyList<IndividualBuildingBlock> IndividualsCollection => get<IndividualBuildingBlock>();
+
       public IReadOnlyList<ISimulationSettings> SimulationSettingsCollection => get<ISimulationSettings>();
 
       public IReadOnlyList<IPassiveTransportBuildingBlock> PassiveTransportCollection => get<IPassiveTransportBuildingBlock>();

src/MoBi.Core/MoBi.Core.csproj

@@ -32,13 +32,13 @@
     <PackageReference Include="FluentNHibernate" Version="2.1.2" />
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.84" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

src/MoBi.Engine/MoBi.Engine.csproj

@@ -32,8 +32,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.84" />
   </ItemGroup>
 
   <ItemGroup>

src/MoBi.Presentation/MenusAndBars/ContextMenus/ContextMenuFactoryForBuildBlocks.cs

@@ -65,6 +65,13 @@ public bool IsSatisfiedBy(IViewItem viewItem, IPresenterWithContextMenu<IViewIte
       }
    }
 
+   public class RootContextMenuFactoryForIndividualBuildingBlock : RootNodeContextMenuFactoryFor<IndividualBuildingBlock>
+   {
+      public RootContextMenuFactoryForIndividualBuildingBlock() : base(MoBiRootNodeTypes.IndividualsFolder)
+      {
+      }
+   }
+
    public class RootContextMenuFactoryForExpressionProfileBuildingBlock : RootNodeContextMenuFactoryFor<ExpressionProfileBuildingBlock>
    {
       public RootContextMenuFactoryForExpressionProfileBuildingBlock() : base(MoBiRootNodeTypes.ExpressionProfilesFolder)

src/MoBi.Presentation/MenusAndBars/ContextMenus/RootContextMenuForExpressionProfileBuildingBlock.cs

@@ -9,6 +9,18 @@
 
 namespace MoBi.Presentation.MenusAndBars.ContextMenus
 {
+   public class RootContextMenuForIndividualBuildingBlock : RootContextMenuFor<IMoBiProject, IndividualBuildingBlock>
+   {
+      public RootContextMenuForIndividualBuildingBlock(IObjectTypeResolver objectTypeResolver, IMoBiContext context) : base(objectTypeResolver, context)
+      {
+      }
+
+      protected override void CreateAddItems(IMoBiProject parent)
+      {
+         _allMenuItems.Add(CreateAddExistingItemFor(parent));
+      }
+   }
+
    public class RootContextMenuForExpressionProfileBuildingBlock : RootContextMenuFor<IMoBiProject, ExpressionProfileBuildingBlock>
    {
       public RootContextMenuForExpressionProfileBuildingBlock(IObjectTypeResolver objectTypeResolver, IMoBiContext context) : base(objectTypeResolver, context)

src/MoBi.Presentation/MoBi.Presentation.csproj

@@ -28,9 +28,9 @@
     <PackageReference Include="Northwoods.GoWin" Version="5.2.0" />
     <PackageReference Include="OSPSuite.TeXReporting" Version="3.0.0.4" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Presentation" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="12.0.77" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.77" />  
+    <PackageReference Include="OSPSuite.Presentation" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="12.0.84" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.84" />  
    </ItemGroup>
   <ItemGroup>
     <None Include="..\..\LICENSE">

src/MoBi.Presentation/Nodes/MoleculeTreeNode.cs

@@ -1,6 +1,6 @@
-using System.ComponentModel;
+using MoBi.Presentation.DTO;
 using OSPSuite.Presentation.Nodes;
-using MoBi.Presentation.DTO;
+using System.ComponentModel;
 
 namespace MoBi.Presentation.Nodes
 {

src/MoBi.Presentation/Nodes/RootNodeType.cs

@@ -15,6 +15,7 @@ public class MoBiRootNodeTypes
       public static readonly RootNodeType MoleculeStartValuesFolder = new RootNodeType(AppConstants.Captions.MoleculeStartValues, ApplicationIcons.MoleculeStartValuesFolder);
       public static readonly RootNodeType ParameterStartValuesFolder = new RootNodeType(AppConstants.Captions.ParameterStartValues, ApplicationIcons.ParameterStartValuesFolder);
       public static readonly RootNodeType ExpressionProfilesFolder = new RootNodeType(AppConstants.Captions.ExpressionProfiles, ApplicationIcons.ExpressionProfileFolder);
+      public static readonly RootNodeType IndividualsFolder = new RootNodeType(AppConstants.Captions.Individuals, ApplicationIcons.IndividualFolder);
       public static readonly RootNodeType SimulationSettingsFolder = new RootNodeType(AppConstants.Captions.SimulationSettings, ApplicationIcons.SimulationSettingsFolder);
    }
 }

src/MoBi.Presentation/Presenter/Main/BuildingBlockExplorerPresenter.cs

@@ -63,6 +63,7 @@ protected override void AddProjectToTree(IMoBiProject project)
             _view.AddNode(_treeNodeFactory.CreateFor(MoBiRootNodeTypes.MoleculeStartValuesFolder));
             _view.AddNode(_treeNodeFactory.CreateFor(MoBiRootNodeTypes.ParameterStartValuesFolder));
             _view.AddNode(_treeNodeFactory.CreateFor(MoBiRootNodeTypes.ExpressionProfilesFolder));
+            _view.AddNode(_treeNodeFactory.CreateFor(MoBiRootNodeTypes.IndividualsFolder));
             _view.AddNode(_treeNodeFactory.CreateFor(RootNodeTypes.ObservedDataFolder));
 
             project.MoleculeBlockCollection.Each(bb => addBuildingBlockToTree(bb, MoBiRootNodeTypes.MoleculeFolder));
@@ -74,6 +75,7 @@ protected override void AddProjectToTree(IMoBiProject project)
             project.MoleculeStartValueBlockCollection.Each(bb => addBuildingBlockToTree(bb, MoBiRootNodeTypes.MoleculeStartValuesFolder));
             project.ParametersStartValueBlockCollection.Each(bb => addBuildingBlockToTree(bb, MoBiRootNodeTypes.ParameterStartValuesFolder));
             project.ExpressionProfileCollection.Each(bb => addBuildingBlockToTree(bb, MoBiRootNodeTypes.ExpressionProfilesFolder));
+            project.IndividualsCollection.Each(bb => addBuildingBlockToTree(bb, MoBiRootNodeTypes.IndividualsFolder));
 
             project.SimulationSettingsCollection.Each(bb => addBuildingBlockToTree(bb, MoBiRootNodeTypes.SimulationSettingsFolder));
 
@@ -184,6 +186,9 @@ private ITreeNode addBuildingBlock(IBuildingBlock buildingBlock)
 
          if (buildingBlock.IsAnImplementationOf<ExpressionProfileBuildingBlock>())
             return addBuildingBlockToTree(buildingBlock, MoBiRootNodeTypes.ExpressionProfilesFolder);
+
+         if (buildingBlock.IsAnImplementationOf<IndividualBuildingBlock>())
+            return addBuildingBlockToTree(buildingBlock, MoBiRootNodeTypes.IndividualsFolder);
 
          throw new ArgumentOutOfRangeException();
       }

src/MoBi.Presentation/Tasks/Interaction/AbstractStartValuesTask.cs

@@ -168,11 +168,6 @@ protected bool HasEquivalentFormula(IStartValue startValue, IFormula targetFormu
          return _startValuePathTask.HasEquivalentFormula(startValue, targetFormula);
       }
 
-      public override IMoBiCommand ChangeValueFormulaCommand(TBuildingBlock startValues, TStartValue startValue, IFormula formula)
-      {
-         return new ChangeValueFormulaCommand<TStartValue>(startValues, startValue, formula, startValue.Formula).Run(Context);
-      }
-
       protected static bool HasEquivalentStartValue(IStartValue startValue, IParameter parameter)
       {
          var (value, _) = parameter.TryGetValue();
@@ -279,13 +274,6 @@ public ICommand SetValueOrigin(TBuildingBlock buildingBlock, ValueOrigin valueOr
          return new UpdateValueOriginInStartValueCommand<TStartValue>(startValue, valueOrigin, buildingBlock).Run(Context);
       }
 
-      public override IMoBiCommand SetFormula(TBuildingBlock buildingBlock, TStartValue startValue, IFormula formula)
-      {
-         var shouldClearValue = startValue.Value.HasValue;
-
-         return SetFormula(buildingBlock, startValue, formula, shouldClearValue);
-      }
-
       public abstract bool CanResolve(TBuildingBlock buildingBlock, TStartValue startValue);
 
       protected static bool ShouldFormulaBeOverridden(ImportedQuantityDTO quantityDTO, TStartValue startValue)
@@ -327,10 +315,5 @@ public IMoBiCommand EditStartValueContainerPath(TBuildingBlock buildingBlock, TS
       {
          return _startValuePathTask.UpdateStartValueContainerPath(buildingBlock, startValue, indexToUpdate, newValue);
       }
-
-      protected override IMoBiCommand SetValueWithUnit(TStartValue startValue, double? newBaseValue, Unit unit, TBuildingBlock startValues)
-      {
-         return new PathAndValueEntityValueOrUnitChangedCommand<TStartValue, TBuildingBlock>(startValue, newBaseValue, unit, startValues).Run(Context);
-      }
    }
 }

src/MoBi.Presentation/Tasks/Interaction/InteractionTaskForPathAndValueEntity.cs

@@ -52,7 +52,7 @@ public interface IInteractionTaskForPathAndValueEntity<in TBuildingBlock, in TBu
 
    public abstract class InteractionTaskForPathAndValueEntity<TBuildingBlock, TBuilder> : InteractionTasksForEnumerableBuildingBlock<TBuildingBlock, TBuilder>, IInteractionTaskForPathAndValueEntity<TBuildingBlock, TBuilder>
       where TBuildingBlock : class, IBuildingBlock, IBuildingBlock<TBuilder> 
-      where TBuilder : class, IUsingFormula, IWithDisplayUnit
+      where TBuilder : PathAndValueEntity, IUsingFormula, IWithDisplayUnit
    {
       protected readonly IMoBiFormulaTask _moBiFormulaTask;
 
@@ -82,9 +82,10 @@ protected IMoBiCommand AddFormulaToFormulaCacheAndSetOnBuilder<TFormula>(TBuildi
          return macroCommand;
       }
 
-      protected abstract double? ValueFromBuilder(TBuilder builder);
-
-      public abstract IMoBiCommand ChangeValueFormulaCommand(TBuildingBlock buildingBlock, TBuilder builder, IFormula formula);
+      public IMoBiCommand SetFormula(TBuildingBlock buildingBlock, TBuilder builder, IFormula formula)
+      {
+         return SetFormula(buildingBlock, builder, formula, shouldClearValue: builder.Value.HasValue);
+      }
 
       protected IMoBiCommand setFormula(TBuildingBlock buildingBlock, TBuilder builder, IFormula formula)
       {
@@ -113,14 +114,12 @@ public IMoBiCommand SetDisplayValueWithUnit(TBuilder builder, double? newDisplay
          return SetValueWithUnit(builder, unit.UnitValueToBaseUnitValue(newDisplayValue.GetValueOrDefault(double.NaN)), unit, buildingBlock);
       }
 
-      protected abstract IMoBiCommand SetValueWithUnit(TBuilder builder, double? unitValueToBaseUnitValue, Unit unit, TBuildingBlock buildingBlock);
-
       protected IMoBiCommand setValue(TBuilder builder, double? newDisplayValue, Unit unit, TBuildingBlock buildingBlock)
       {
          return SetDisplayValueWithUnit(builder, newDisplayValue, unit, buildingBlock);
       }
 
-      public abstract IMoBiCommand SetFormula(TBuildingBlock buildingBlock, TBuilder builder, IFormula formula);
+
 
       public IMoBiCommand SetValue(TBuildingBlock buildingBlock, double? valueInDisplayUnit, TBuilder builder)
       {
@@ -155,5 +154,32 @@ public virtual ICommand<IMoBiContext> AddNewFormulaAtBuildingBlock(TBuildingBloc
 
          return macroCommand;
       }
+
+      protected virtual double? ValueFromBuilder(TBuilder builder)
+      {
+         return builder.Value;
+      }
+
+      public  IMoBiCommand ChangeValueFormulaCommand(TBuildingBlock buildingBlock, TBuilder builder, IFormula formula)
+      {
+         return new ChangeValueFormulaCommand<TBuilder>(buildingBlock, builder, formula, builder.Formula).Run(Context);
+      }
+
+      protected IMoBiCommand SetValueWithUnit(TBuilder builder, double? unitValueToBaseUnitValue, Unit unit, TBuildingBlock buildingBlock)
+      {
+         return new PathAndValueEntityValueOrUnitChangedCommand<TBuilder, TBuildingBlock>(builder, unitValueToBaseUnitValue, unit, buildingBlock).Run(Context);
+      }
+
+      public override IMoBiCommand Merge(TBuildingBlock buildingBlockToMerge, TBuildingBlock targetBuildingBlock)
+      {
+         // TODO
+         return new MoBiEmptyCommand();
+      }
+
+      protected override IMoBiMacroCommand GenerateAddCommandAndUpdateFormulaReferences(TBuilder builder, TBuildingBlock targetBuildingBlock, string originalBuilderName = null)
+      {
+         // You cannot add Individual Parameters to the buildingBlock
+         return new MoBiMacroCommand();
+      }
    }
 }

src/MoBi.Presentation/Tasks/Interaction/InteractionTasksForExpressionProfileBuildingBlock.cs

@@ -1,55 +1,35 @@
-using MoBi.Core.Commands;
-using MoBi.Core.Domain.Services;
+using MoBi.Core.Domain.Services;
 using MoBi.Presentation.Tasks.Edit;
-using OSPSuite.Core.Commands.Core;
 using OSPSuite.Core.Domain.Builder;
-using OSPSuite.Core.Domain.Formulas;
-using OSPSuite.Core.Domain.UnitSystem;
 
 namespace MoBi.Presentation.Tasks.Interaction
 {
-   public interface IInteractionTasksForExpressionProfileBuildingBlock : IInteractionTasksForBuildingBlock<ExpressionProfileBuildingBlock>, IInteractionTaskForPathAndValueEntity<ExpressionProfileBuildingBlock, ExpressionParameter>
+   public interface IInteractionTaskForIndividualBuildingBlock: IInteractionTasksForBuildingBlock<IndividualBuildingBlock>, IInteractionTaskForPathAndValueEntity<IndividualBuildingBlock, IndividualParameter>
    {
-      
+
    }
 
-   public class InteractionTasksForExpressionProfileBuildingBlock : InteractionTaskForPathAndValueEntity<ExpressionProfileBuildingBlock, ExpressionParameter>, IInteractionTasksForExpressionProfileBuildingBlock
+   public class InteractionTaskForIndividualBuildingBlock : InteractionTaskForPathAndValueEntity<IndividualBuildingBlock, IndividualParameter>
    {
-      public InteractionTasksForExpressionProfileBuildingBlock(IInteractionTaskContext interactionTaskContext, IEditTasksForBuildingBlock<ExpressionProfileBuildingBlock> editTask, IMoBiFormulaTask formulaTask) : 
-         base(interactionTaskContext, editTask, formulaTask)
+      public InteractionTaskForIndividualBuildingBlock(IInteractionTaskContext interactionTaskContext, IEditTasksForBuildingBlock<IndividualBuildingBlock> editTask, IMoBiFormulaTask moBiFormulaTask) : base(interactionTaskContext, editTask, moBiFormulaTask)
       {
       }
 
-      public override IMoBiCommand Merge(ExpressionProfileBuildingBlock buildingBlockToMerge, ExpressionProfileBuildingBlock targetBuildingBlock)
-      {
-         // TODO
-         return new MoBiEmptyCommand();
-      }
 
-      public override IMoBiCommand SetFormula(ExpressionProfileBuildingBlock buildingBlock, ExpressionParameter builder, IFormula formula)
-      {
-         return SetFormula(buildingBlock, builder, formula, shouldClearValue:builder.Value.HasValue);
-      }
+   }
 
-      protected override IMoBiMacroCommand GenerateAddCommandAndUpdateFormulaReferences(ExpressionParameter builder, ExpressionProfileBuildingBlock targetBuildingBlock, string originalBuilderName = null)
-      {
-         // You cannot add ExpressionParameters to the buildingBlock
-         return new MoBiMacroCommand();
-      }
+   public interface IInteractionTasksForExpressionProfileBuildingBlock : IInteractionTasksForBuildingBlock<ExpressionProfileBuildingBlock>, IInteractionTaskForPathAndValueEntity<ExpressionProfileBuildingBlock, ExpressionParameter>
+   {
+
+   }
 
-      protected override double? ValueFromBuilder(ExpressionParameter builder)
+   public class InteractionTasksForExpressionProfileBuildingBlock : InteractionTaskForPathAndValueEntity<ExpressionProfileBuildingBlock, ExpressionParameter>, IInteractionTasksForExpressionProfileBuildingBlock
+   {
+      public InteractionTasksForExpressionProfileBuildingBlock(IInteractionTaskContext interactionTaskContext, IEditTasksForBuildingBlock<ExpressionProfileBuildingBlock> editTask, IMoBiFormulaTask formulaTask) : 
+         base(interactionTaskContext, editTask, formulaTask)
       {
-         return builder.Value;
       }
 
-      public override IMoBiCommand ChangeValueFormulaCommand(ExpressionProfileBuildingBlock buildingBlock, ExpressionParameter builder, IFormula formula)
-      {
-         return new ChangeValueFormulaCommand<ExpressionParameter>(buildingBlock, builder, formula, builder.Formula).Run(Context);
-      }
 
-      protected override IMoBiCommand SetValueWithUnit(ExpressionParameter builder, double? unitValueToBaseUnitValue, Unit unit, ExpressionProfileBuildingBlock startValues)
-      {
-         return new PathAndValueEntityValueOrUnitChangedCommand<ExpressionParameter, ExpressionProfileBuildingBlock>(builder, unitValueToBaseUnitValue, unit, startValues).Run(Context);
-      }
    }
 }