1772 ensure that output mapping are exported (#1775)

* Ensure that WeightedObservedData is also in domain

* Fixes #1772 ensure that output mapping are exported

* Fixes tests

* Fixes tests also that was hard coding number of pk parameters"

src/OSPSuite.Core/Domain/ISimulation.cs

@@ -1,7 +1,6 @@
 using System.Collections.Generic;
 using OSPSuite.Core.Chart;
 using OSPSuite.Core.Domain.Data;
-using OSPSuite.Core.Domain.ParameterIdentifications;
 
 namespace OSPSuite.Core.Domain
 {

src/OSPSuite.Core/Domain/OutputMapping.cs

@@ -1,17 +1,16 @@
 using OSPSuite.Core.Domain.Data;
-using OSPSuite.Core.Domain.ParameterIdentifications;
 using OSPSuite.Core.Domain.UnitSystem;
 
 namespace OSPSuite.Core.Domain
 {
    public class OutputMapping
    {
       public virtual WeightedObservedData WeightedObservedData { get; set; }
-    
+
       public virtual SimulationQuantitySelection OutputSelection { get; set; }
-      
+
       public virtual Scalings Scaling { get; set; }
-      
+
       public float Weight { get; set; } = Constants.DEFAULT_WEIGHT;
 
       /// <summary>
@@ -29,7 +28,7 @@ public class OutputMapping
       /// </summary>
       public virtual IQuantity Output => OutputSelection?.Quantity;
 
-      public virtual ISimulation Simulation => OutputSelection?.Simulation;
+      public virtual IModelCoreSimulation Simulation => OutputSelection?.Simulation;
 
       public IDimension Dimension => OutputSelection?.Quantity?.Dimension;
 

src/OSPSuite.Core/Domain/OutputMappings.cs

@@ -1,12 +1,13 @@
-using System.Collections.Generic;
+using System.Collections;
+using System.Collections.Generic;
 using System.Linq;
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Domain.Services;
 using OSPSuite.Utility.Extensions;
 
 namespace OSPSuite.Core.Domain
 {
-   public class OutputMappings : IUpdatable
+   public class OutputMappings : IUpdatable, IEnumerable<OutputMapping>
    {
       private readonly List<OutputMapping> _allOutputMappings = new List<OutputMapping>();
 
@@ -76,5 +77,12 @@ public bool Contains(OutputMapping outputMapping)
       {
          return _allOutputMappings.Contains(outputMapping);
       }
+
+      public IEnumerator<OutputMapping> GetEnumerator() => _allOutputMappings.GetEnumerator();
+
+      IEnumerator IEnumerable.GetEnumerator()
+      {
+         return GetEnumerator();
+      }
    }
 }

src/OSPSuite.Core/Domain/ParameterSelection.cs

@@ -9,11 +9,11 @@ public ParameterSelection()
       {
       }
 
-      public ParameterSelection(ISimulation simulation, QuantitySelection quantitySelection) : base(simulation, quantitySelection)
+      public ParameterSelection(IModelCoreSimulation simulation, QuantitySelection quantitySelection) : base(simulation, quantitySelection)
       {
       }
 
-      public ParameterSelection(ISimulation simulation, string parameterPath) : this(simulation, new QuantitySelection(parameterPath, QuantityType.Parameter))
+      public ParameterSelection(IModelCoreSimulation simulation, string parameterPath) : this(simulation, new QuantitySelection(parameterPath, QuantityType.Parameter))
       {
       }
 

src/OSPSuite.Core/Domain/Repositories/ObservedDataRepository.cs

@@ -1,8 +1,8 @@
 using System.Collections.Generic;
 using System.Linq;
-using OSPSuite.Utility.Collections;
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Domain.Services;
+using OSPSuite.Utility.Collections;
 
 namespace OSPSuite.Core.Domain.Repositories
 {
@@ -37,7 +37,7 @@ public DataRepository FindFor(UsedObservedData usedObservedData)
 
       public IEnumerable<DataRepository> AllObservedDataUsedBy(IUsesObservedData observedDataUser)
       {
-         return All().Where(observedDataUser.UsesObservedData);
+         return observedDataUser == null ? Enumerable.Empty<DataRepository>() : All().Where(observedDataUser.UsesObservedData);
       }
 
       public IEnumerable<DataRepository> AllObservedDataUsedBy(IEnumerable<IUsesObservedData> observedDataUsers)

src/OSPSuite.Core/Domain/Services/ISetParameterTask.cs

@@ -8,13 +8,13 @@ public interface ISetParameterTask
       /// Sets the <paramref name="value"/> into <paramref name="parameter"/> defined in <paramref name="simulation"/>
       /// </summary>
       /// <returns>The executed command representing the value being set in the parameter</returns>
-      ICommand SetParameterValue(IParameter parameter, double value, ISimulation simulation);
+      ICommand SetParameterValue(IParameter parameter, double value, IModelCoreSimulation simulation);
 
 
       /// <summary>
       /// Updates the parameter value origin in the <paramref name="parameter"/> defined in <paramref name="simulation"/>
       /// </summary>
       /// <returns>The executed command representing the <see cref="ValueOrigin"/> being set in the parameter</returns>
-      ICommand UpdateParameterValueOrigin(IParameter parameter, ValueOrigin valueOrigin, ISimulation simulation);
+      ICommand UpdateParameterValueOrigin(IParameter parameter, ValueOrigin valueOrigin, IModelCoreSimulation simulation);
    }
 }

src/OSPSuite.Core/Domain/Services/ParameterIdentifications/JacobianMatrixCalculator.cs

@@ -1,21 +1,20 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
-using OSPSuite.Utility.Collections;
-using OSPSuite.Utility.Extensions;
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Domain.ParameterIdentifications;
+using OSPSuite.Utility.Extensions;
 
 namespace OSPSuite.Core.Domain.Services.ParameterIdentifications
 {
    public interface IJacobianMatrixCalculator
    {
-      JacobianMatrix CalculateFor(ParameterIdentification parameterIdentification, OptimizationRunResult runResult, IDictionary<ISimulation, ISimModelBatch> simModelBatches);
+      JacobianMatrix CalculateFor(ParameterIdentification parameterIdentification, OptimizationRunResult runResult, IDictionary<IModelCoreSimulation, ISimModelBatch> simModelBatches);
    }
 
    public class JacobianMatrixCalculator : IJacobianMatrixCalculator
    {
-      public JacobianMatrix CalculateFor(ParameterIdentification parameterIdentification, OptimizationRunResult runResult, IDictionary<ISimulation, ISimModelBatch> simModelBatches)
+      public JacobianMatrix CalculateFor(ParameterIdentification parameterIdentification, OptimizationRunResult runResult, IDictionary<IModelCoreSimulation, ISimModelBatch> simModelBatches)
       {
          var allVariableIdentificationParameters = parameterIdentification.AllVariableIdentificationParameters.ToList();
          var matrix = new JacobianMatrix(allVariableIdentificationParameters.AllNames());
@@ -76,6 +75,7 @@ private static double retrievePartialDerivativeFor(IdentificationParameter ident
 
             sensitivityValue += sensitivityForParameter;
          }
+
          return sensitivityValue;
       }
 

src/OSPSuite.Core/Domain/Services/ParameterIdentifications/ParameterIdentificationRun.cs

@@ -45,7 +45,7 @@ public class ParameterIdentificationRun : IParameterIdentificationRun
       private readonly IOutputSelectionUpdater _outputSelectionUpdater;
       private readonly ICoreUserSettings _coreUserSettings;
       private readonly IJacobianMatrixCalculator _jacobianMatrixCalculator;
-      private readonly ConcurrentDictionary<ISimulation, ISimModelBatch> _allSimModelBatches = new ConcurrentDictionary<ISimulation, ISimModelBatch>();
+      private readonly ConcurrentDictionary<IModelCoreSimulation, ISimModelBatch> _allSimModelBatches = new ConcurrentDictionary<IModelCoreSimulation, ISimModelBatch>();
       private readonly List<float> _totalErrorHistory = new List<float>();
 
       private readonly Cache<string, IdentificationParameterHistory> _parametersHistory =

src/OSPSuite.Core/Domain/Services/ParameterIdentifications/TransferOptimizedParametersToSimulationsTask.cs

@@ -77,7 +77,7 @@ private IEnumerable<ICommand> updateParameterValue(IdentificationParameter ident
          return new[] {setValueCommand, updateValueOriginCommand(identificationParameter, parameter, linkedParameter.Simulation).AsHidden()};
       }
 
-      private ICommand updateValueOriginCommand(IdentificationParameter identificationParameter, IParameter parameter, ISimulation simulation)
+      private ICommand updateValueOriginCommand(IdentificationParameter identificationParameter, IParameter parameter, IModelCoreSimulation simulation)
       {
          var isoDate = SystemTime.Now().ToIsoFormat();
          var valueOrigin = new ValueOrigin

src/OSPSuite.Core/Domain/SimulationQuantitySelection.cs

@@ -9,18 +9,19 @@ public class SimulationQuantitySelection
    {
       private IQuantity _quantity;
       private string _fullQuantityPath;
-      public virtual ISimulation Simulation { get; private set; }
-
-      public virtual string SimulationId { get; set; }
+
+      public virtual IModelCoreSimulation Simulation { get; private set; }
+
       public virtual QuantitySelection QuantitySelection { get; }
+
       public virtual IDimension Dimension => Quantity?.Dimension;
 
       [Obsolete("For serialization")]
       public SimulationQuantitySelection()
       {
       }
 
-      public SimulationQuantitySelection(ISimulation simulation, QuantitySelection quantitySelection)
+      public SimulationQuantitySelection(IModelCoreSimulation simulation, QuantitySelection quantitySelection)
       {
          Simulation = simulation;
          QuantitySelection = quantitySelection;

src/OSPSuite.Core/Domain/ParameterIdentifications/WeightedObservedData.cs → src/OSPSuite.Core/Domain/WeightedObservedData.cs

@@ -2,7 +2,7 @@
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Extensions;
 
-namespace OSPSuite.Core.Domain.ParameterIdentifications
+namespace OSPSuite.Core.Domain
 {
    public class WeightedObservedData
    {

src/OSPSuite.Core/Serialization/Exchange/SimulationTransfer.cs

@@ -7,20 +7,15 @@ namespace OSPSuite.Core.Serialization.Exchange
 {
    public class SimulationTransfer : IWithId
    {
+      public string Id { get; set; } = ShortGuid.NewGuid();
+
       public IModelCoreSimulation Simulation { get; set; }
-      public IList<DataRepository> AllObservedData { get; set; }
-      public int PkmlVersion { get; set; }
-      public string Id { get; set; }
-      public Favorites Favorites { get; set; }
-      public string JournalPath { get; set; }
+      public OutputMappings OutputMappings { get; set; } = new OutputMappings();
+      public IList<DataRepository> AllObservedData { get; set; } = new List<DataRepository>();
 
-      public SimulationTransfer()
-      {
-         AllObservedData = new List<DataRepository>();
-         PkmlVersion = Constants.PKML_VERSION;
-         Id = ShortGuid.NewGuid();
-         Favorites = new Favorites();
-         JournalPath = string.Empty;
-      }
+      //MetaData about the export
+      public int PkmlVersion { get; set; } = Constants.PKML_VERSION;
+      public Favorites Favorites { get; set; } = new Favorites();
+      public string JournalPath { get; set; } = string.Empty;
    }
 }

src/OSPSuite.Core/Serialization/Exchange/SimulationTransferXmlSerializer.cs

@@ -12,8 +12,12 @@ public override void PerformMapping()
          Map(x => x.Simulation);
          Map(x => x.JournalPath);
          Map(x => x.Favorites);
-         MapEnumerable(x => x.AllObservedData, x => x.AllObservedData.Add);
          Map(x => x.PkmlVersion).WithMappingName(Constants.Serialization.Attribute.VERSION);
+
+         MapEnumerable(x => x.AllObservedData, x => x.AllObservedData.Add);
+         //This needs to be done after observed data serialization to ensure that the observed data were deserialized
+         Map(x => x.OutputMappings);
+
       }
    }
 }

src/OSPSuite.Core/Serialization/ParameterIdentificationExport/Serializer/WeightedObservedDataSerializer.cs

@@ -1,5 +1,6 @@
 using System.Globalization;
 using System.Xml.Linq;
+using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Serializer.Xml.Extensions;
 using OSPSuite.Core.Domain.ParameterIdentifications;

src/OSPSuite.Core/Serialization/Xml/DataRepositoryXmlSerializer.cs

@@ -1,4 +1,5 @@
 using System;
+using System.Xml.Linq;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Data;
 
@@ -25,5 +26,11 @@ private Action<IExtendedProperty> addFunction(DataRepository dataRepository)
       {
          return dataRepository.ExtendedProperties.Add;
       }
+
+      protected override void TypedDeserialize(DataRepository dataRepository, XElement outputToDeserialize, SerializationContext serializationContext)
+      {
+         base.TypedDeserialize(dataRepository, outputToDeserialize, serializationContext);
+         serializationContext.Register(dataRepository);
+      }
    }
 }

src/OSPSuite.Core/Serialization/Xml/WeightedObservedDataXmlSerializer.cs

@@ -1,4 +1,4 @@
-using OSPSuite.Core.Domain.ParameterIdentifications;
+using OSPSuite.Core.Domain;
 
 namespace OSPSuite.Core.Serialization.Xml
 {

src/OSPSuite.Presentation/DTO/SimulationQuantitySelectionDTO.cs

@@ -5,10 +5,10 @@ namespace OSPSuite.Presentation.DTO
    public class SimulationQuantitySelectionDTO : ValidatableDTO, IPathRepresentableDTO
    {
       public virtual QuantitySelectionDTO QuantitySelectionDTO { get; }
-      public virtual ISimulation Simulation { get; }
+      public virtual IModelCoreSimulation Simulation { get; }
       public virtual string DisplayString { get; }
 
-      public SimulationQuantitySelectionDTO(ISimulation simulation, QuantitySelectionDTO quantitySelectionDTO, string displayString)
+      public SimulationQuantitySelectionDTO(IModelCoreSimulation simulation, QuantitySelectionDTO quantitySelectionDTO, string displayString)
       {
          DisplayString = displayString;
          QuantitySelectionDTO = quantitySelectionDTO;
@@ -25,7 +25,7 @@ public override string ToString()
 
       public PathElements PathElements
       {
-         get { return QuantitySelectionDTO?.PathElements; }
+         get => QuantitySelectionDTO?.PathElements;
          set
          {
             if (QuantitySelectionDTO != null)

src/OSPSuite.Presentation/Mappers/ParameterIdentifications/WeightedDataRepositoryToDataTableMapper.cs

@@ -1,6 +1,7 @@
 using System.Data;
 using System.Linq;
 using OSPSuite.Assets;
+using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Domain.ParameterIdentifications;
 using OSPSuite.Core.Domain.Services;

src/OSPSuite.Presentation/Mappers/QuantityToSimulationQuantitySelectionDTOMapper.cs

@@ -6,7 +6,7 @@ namespace OSPSuite.Presentation.Mappers
 {
    public interface IQuantityToSimulationQuantitySelectionDTOMapper
    {
-      SimulationQuantitySelectionDTO MapFrom(ISimulation simulation, IQuantity quantity);
+      SimulationQuantitySelectionDTO MapFrom(IModelCoreSimulation simulation, IQuantity quantity);
    }
 
    public class QuantityToSimulationQuantitySelectionDTOMapper : AbstractQuantityToSimulationQuantitySelectionDTOMapper, IQuantityToSimulationQuantitySelectionDTOMapper
@@ -21,7 +21,7 @@ public QuantityToSimulationQuantitySelectionDTOMapper(IQuantityToQuantitySelecti
          _quantityDisplayPathMapper = quantityDisplayPathMapper;
       }
 
-      public SimulationQuantitySelectionDTO MapFrom(ISimulation simulation, IQuantity quantity)
+      public SimulationQuantitySelectionDTO MapFrom(IModelCoreSimulation simulation, IQuantity quantity)
       {
          var quantitySelectionDTO = _quantitySelectionDTOMapper.MapFrom(quantity);
          if (quantitySelectionDTO == null)

src/OSPSuite.Presentation/Presenters/ParameterIdentifications/ParameterIdentificationOutputMappingPresenter.cs

@@ -157,7 +157,8 @@ private IEnumerable<DataRepository> allPossibleObservedDataForOutput(SimulationQ
          if (outputSelectionDTO == null)
             return Enumerable.Empty<DataRepository>();
 
-         return _observedDataRepository.AllObservedDataUsedBy(outputSelectionDTO.Simulation)
+         var usesObservedData = outputSelectionDTO.Simulation as IUsesObservedData;
+         return _observedDataRepository.AllObservedDataUsedBy(usesObservedData)
             .Distinct()
             .OrderBy(x => x.Name);
       }
@@ -184,7 +185,7 @@ public void ObservedDataSelectionChanged(OutputMappingDTO dto, DataRepository ne
          raiseObservedDataMappedFor(dto.WeightedObservedData);
       }
 
-      public int? nextUniqueIdFor(List<OutputMappingDTO> outputMappings)
+      private int? nextUniqueIdFor(List<OutputMappingDTO> outputMappings)
       {
          if (!outputMappings.Any())
             return null;

src/OSPSuite.Presentation/Presenters/ParameterIdentifications/ParameterIdentificationWeightedObservedDataCollectorPresenter.cs

@@ -1,5 +1,6 @@
 using System.Collections.Generic;
 using System.Linq;
+using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.ParameterIdentifications;
 using OSPSuite.Presentation.Core;
 using OSPSuite.Presentation.Views;

src/OSPSuite.Presentation/Presenters/ParameterIdentifications/ParameterIdentificationWeightedObservedDataPresenter.cs

@@ -1,4 +1,5 @@
-using OSPSuite.Core.Domain.Data;
+using OSPSuite.Core.Domain;
+using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Domain.ParameterIdentifications;
 using OSPSuite.Core.Events;
 using OSPSuite.Presentation.Presenters.Charts;