Fixes #2638 cannot export HI to snapshot (#2639)

* Fixes #2638 cannot export HI to snapshot

* Update DiseaseState.cs

make sure we use old way of namespacing

* Update DiseaseStateMapper.cs

* Update DiseaseStateMapper.cs

* Fixes #2638. Use file scoped namespace

* Fixes #2638 by reverting to namespace

appveyor-coverage.yml

@@ -1,8 +1,5 @@
 configuration: Debug
-image: Visual Studio 2019
-
-environment:
-  MIK_TEX_INSTALL_DIR: 'C:\MikTex\'
+image: Visual Studio 2022
 
 version: '{build}'
 
@@ -27,11 +24,6 @@ install:
 
       Start-Process msiexec.exe -ArgumentList /i, C:\msxml.msi, /quiet, /qn, /norestart -Wait
 
-  - ps: >-
-      (new-object net.webclient).DownloadFile('https://github.com/Open-Systems-Pharmacology/MiKTeX/releases/download/v2.9.3/MikTex.2.9.3.msi', 'C:\\MikTex.msi')
-
-      Start-Process msiexec.exe -ArgumentList /i, C:\MikTex.msi, /quiet, /qn, /norestart, INSTALLDIR=$env:MIK_TEX_INSTALL_DIR -Wait
-
 before_build:
   - nuget sources add -name bddhelper -source https://ci.appveyor.com/nuget/ospsuite-bddhelper
   - nuget sources add -name utility -source https://ci.appveyor.com/nuget/ospsuite-utility

appveyor-nightly.yml

@@ -1,5 +1,5 @@
 configuration: Debug
-image: Visual Studio 2019
+image: Visual Studio 2022
 
 version: '{build}'
 

appveyor.yml

@@ -1,5 +1,5 @@
 configuration: Debug
-image: Visual Studio 2019
+image: Visual Studio 2022
 
 version: '{build}'
 

src/PKSim.Core/Snapshots/DiseaseState.cs

@@ -0,0 +1,17 @@
+using OSPSuite.Core.Domain;
+
+namespace PKSim.Core.Snapshots
+{
+   public class DiseaseState : IWithName
+   {
+      /// <summary>
+      ///    Name of disease state associated with OriginData
+      /// </summary>
+      public string Name { get; set; }
+
+      /// <summary>
+      ///    List of disease state parameters associated with the selected disease state
+      /// </summary>
+      public Parameter[] Parameters { get; set; }
+   }
+}

src/PKSim.Core/Snapshots/ExpressionProfile.cs

@@ -35,6 +35,9 @@ public class ExpressionProfile : SnapshotBase, IBuildingBlockSnapshot
       public ExpressionContainer[] Expression { get; set; }
       public Ontogeny Ontogeny { get; set; }
 
-      public PKSimBuildingBlockType BuildingBlockType { get; } =PKSimBuildingBlockType.ExpressionProfile;
+      public PKSimBuildingBlockType BuildingBlockType { get; } = PKSimBuildingBlockType.ExpressionProfile;
+
+      //Null if no disease state defined
+      public DiseaseState Disease { get; set; }
    }
 }

src/PKSim.Core/Snapshots/Mappers/DiseaseStateMapper.cs

@@ -0,0 +1,112 @@
+using System.Linq;
+using System.Threading.Tasks;
+using OSPSuite.Core.Domain;
+using OSPSuite.Core.Domain.UnitSystem;
+using OSPSuite.Utility.Extensions;
+using PKSim.Assets;
+using PKSim.Core.Model;
+using PKSim.Core.Repositories;
+using SnapshotDiseaseState = PKSim.Core.Snapshots.DiseaseState;
+using ModelOriginData = PKSim.Core.Model.OriginData;
+
+namespace PKSim.Core.Snapshots.Mappers
+{
+   public class DiseaseStateContext : SnapshotContext
+   {
+      public ModelOriginData OriginData { get; }
+
+      public DiseaseStateContext(ModelOriginData originData, SnapshotContext baseContext) : base(baseContext)
+      {
+         OriginData = originData;
+      }
+   }
+
+   public class DiseaseStateMapper : SnapshotMapperBase<ModelOriginData, SnapshotDiseaseState, DiseaseStateContext>
+   {
+      private readonly IDiseaseStateRepository _diseaseStateRepository;
+      private readonly ParameterMapper _parameterMapper;
+      private readonly IDimensionRepository _dimensionRepository;
+
+      public DiseaseStateMapper(
+         IDiseaseStateRepository diseaseStateRepository,
+         ParameterMapper parameterMapper,
+         IDimensionRepository dimensionRepository
+      )
+      {
+         _diseaseStateRepository = diseaseStateRepository;
+         _parameterMapper = parameterMapper;
+         _dimensionRepository = dimensionRepository;
+      }
+
+      public override Task<SnapshotDiseaseState> MapToSnapshot(ModelOriginData originData)
+      {
+         var diseaseState = originData?.DiseaseState;
+         if (diseaseState == null || diseaseState.IsHealthy)
+            return Task.FromResult<SnapshotDiseaseState>(null);
+
+         var snapshot = new SnapshotDiseaseState
+         {
+            Name = diseaseState.Name,
+         };
+
+         if (originData.DiseaseStateParameters.Any())
+            snapshot.Parameters = originData.DiseaseStateParameters.Select(namedParameterFrom).ToArray();
+
+         return Task.FromResult(snapshot);
+      }
+
+      public override Task<ModelOriginData> MapToModel(SnapshotDiseaseState diseaseStateSnapshot, DiseaseStateContext diseaseStateContext)
+      {
+         var originData = diseaseStateContext.OriginData;
+
+         if (diseaseStateSnapshot == null)
+            return Task.FromResult(originData);
+
+         var diseaseState = _diseaseStateRepository.AllFor(originData.Population).FindByName(diseaseStateSnapshot.Name);
+         if (diseaseState == null)
+            throw new PKSimException(PKSimConstants.Error.CannotFindDiseaseState(diseaseStateSnapshot.Name, originData.Population.DisplayName));
+
+         originData.DiseaseState = diseaseState;
+         diseaseState.Parameters.Each(x =>
+         {
+            var diseaseStateParameter = new OriginDataParameter {Name = x.Name, Value = x.Value, Unit = x.DisplayUnitName()};
+            var snapshotParameter = diseaseStateSnapshot.Parameters.FindByName(x.Name);
+            if (snapshotParameter != null)
+            {
+               diseaseStateParameter.Value = baseParameterValueFrom(snapshotParameter, x.Value);
+               diseaseStateParameter.Unit = snapshotParameter.Unit;
+            }
+
+            originData.AddDiseaseStateParameter(diseaseStateParameter);
+         });
+
+
+         return Task.FromResult(originData);
+      }
+
+      private Parameter namedParameterFrom(OriginDataParameter parameter)
+      {
+         return parameterFrom(parameter, _dimensionRepository.DimensionForUnit(parameter.Unit)).WithName(parameter.Name);
+      }
+
+      private Parameter parameterFrom(OriginDataParameter parameter, IDimension dimension)
+      {
+         if (parameter == null)
+            return null;
+
+         return _parameterMapper.ParameterFrom(parameter.Value, parameter.Unit, dimension);
+      }
+
+      private double baseParameterValueFrom(Parameter snapshot, double defaultValueInBaseUnit) =>
+         baseParameterValueFrom(snapshot, _dimensionRepository.DimensionForUnit(snapshot.Unit), defaultValueInBaseUnit);
+
+      private double baseParameterValueFrom(Parameter snapshot, IDimension dimension, double defaultValueInBaseUnit)
+      {
+         if (snapshot?.Value == null)
+            return defaultValueInBaseUnit;
+
+         var unit = dimension.Unit(ModelValueFor(snapshot.Unit));
+         return dimension.UnitValueToBaseUnitValue(unit, snapshot.Value.Value);
+      }
+   }
+}

src/PKSim.Core/Snapshots/Mappers/ExpressionProfileMapper.cs

@@ -2,6 +2,7 @@
 using OSPSuite.Core.Domain;
 using PKSim.Core.Commands;
 using PKSim.Core.Model;
+using PKSim.Core.Repositories;
 using PKSim.Core.Services;
 using PKSim.Core.Snapshots.Services;
 using ModelIndividual = PKSim.Core.Model.Individual;
@@ -19,15 +20,17 @@ public class ExpressionProfileMapper : ObjectBaseSnapshotMapperBase<ModelExpress
       private readonly IExpressionProfileFactory _expressionProfileFactory;
       private readonly IMoleculeParameterTask _moleculeParameterTask;
       private readonly OntogenyMapper _ontogenyMapper;
+      private readonly DiseaseStateMapper _diseaseStateMapper;
 
       public ExpressionProfileMapper(
          ParameterMapper parameterMapper,
          ExpressionContainerMapper expressionContainerMapper,
          OntogenyMapper ontogenyMapper,
+         DiseaseStateMapper diseaseStateMapper,
          IOntogenyTask ontogenyTask,
          IMoleculeExpressionTask<ModelIndividual> moleculeExpressionTask,
          IExpressionProfileFactory expressionProfileFactory,
-         IMoleculeParameterTask moleculeParameterTask 
+         IMoleculeParameterTask moleculeParameterTask
       )
       {
          _parameterMapper = parameterMapper;
@@ -36,13 +39,15 @@ IMoleculeParameterTask moleculeParameterTask
          _moleculeExpressionTask = moleculeExpressionTask;
          _expressionProfileFactory = expressionProfileFactory;
          _moleculeParameterTask = moleculeParameterTask;
-
          _ontogenyMapper = ontogenyMapper;
+         _diseaseStateMapper = diseaseStateMapper;
       }
 
       public override async Task<SnapshotExpressionProfile> MapToSnapshot(ModelExpressionProfile expressionProfile)
       {
          var (molecule, individual) = expressionProfile;
+         var originData = individual.OriginData;
+
          //We do not use the base method here as we want to save the name differently using the composite part of the name
          var snapshot = new SnapshotExpressionProfile
          {
@@ -53,7 +58,8 @@ public override async Task<SnapshotExpressionProfile> MapToSnapshot(ModelExpress
             Description = SnapshotValueFor(expressionProfile.Description),
             Ontogeny = await _ontogenyMapper.MapToSnapshot(molecule.Ontogeny),
             Expression = await expressionFor(molecule, individual),
-            Parameters = await allParametersChangedByUserFrom(individual)
+            Parameters = await allParametersChangedByUserFrom(individual),
+            Disease = await _diseaseStateMapper.MapToSnapshot(originData)
          };
 
          updateMoleculeSpecificPropertiesToSnapshot(snapshot, molecule);
@@ -92,6 +98,11 @@ public override async Task<ModelExpressionProfile> MapToModel(SnapshotExpression
          expressionProfile.Category = snapshot.Category;
 
          var (molecule, individual) = expressionProfile;
+
+         //update disease sate if any
+         var diseaseStateContext = new DiseaseStateContext(individual.OriginData, snapshotContext);
+         await _diseaseStateMapper.MapToModel(snapshot.Disease, diseaseStateContext);
+
          //Update molecule properties first
          updateMoleculePropertiesToMolecule(molecule, snapshot, individual, snapshotContext);
 
@@ -102,6 +113,7 @@ public override async Task<ModelExpressionProfile> MapToModel(SnapshotExpression
          var ontogeny = await _ontogenyMapper.MapToModel(snapshot.Ontogeny, snapshotWithSubjectContext);
          _ontogenyTask.SetOntogenyForMolecule(molecule, ontogeny, individual);
 
+
          var context = new ExpressionContainerMapperContext(snapshotContext)
          {
             Molecule = molecule,
@@ -158,6 +170,5 @@ private Localization retrieveLocalizationFrom(SnapshotExpressionProfile snapshot
 
          return LocalizationConverter.ConvertToLocalization(tissueLocation, membraneLocation, intracellularVascularEndoLocation);
       }
-
    }
 }

src/PKSim.Core/Snapshots/Mappers/ExtendedPropertyMapper.cs

@@ -55,7 +55,11 @@ private ExtendedPropertyType mapExtendedPropertyType(Type type)
 
       public override Task<ModelExtendedProperty> MapToModel(SnapshotExtendedProperty snapshot, SnapshotContext snapshotContext)
       {
+         if (snapshot?.Value == null)
+            return Task.FromResult<ModelExtendedProperty>(null);
+
          var snapshotType = snapshot.Type;
+
          var valueAsString = snapshot.Value.ToString();
 
          if (snapshotType.HasValue)
@@ -64,7 +68,7 @@ public override Task<ModelExtendedProperty> MapToModel(SnapshotExtendedProperty
          return mapExtendedPropertyBasedOnValue(snapshot, valueAsString);
       }
 
-      private Task<ModelExtendedProperty> mapExtendedPropertyBasedOnType(ExtendedProperty snapshot, ExtendedPropertyType snapshotType, string valueAsString)
+      private Task<ModelExtendedProperty> mapExtendedPropertyBasedOnType(SnapshotExtendedProperty snapshot, ExtendedPropertyType snapshotType, string valueAsString)
       {
          switch (snapshotType)
          {
@@ -80,7 +84,7 @@ private Task<ModelExtendedProperty> mapExtendedPropertyBasedOnType(ExtendedPrope
          }
       }
 
-      private Task<ModelExtendedProperty> mapExtendedPropertyBasedOnValue(ExtendedProperty snapshot, string valueAsString)
+      private Task<ModelExtendedProperty> mapExtendedPropertyBasedOnValue(SnapshotExtendedProperty snapshot, string valueAsString)
       {
          if (double.TryParse(valueAsString, out var doubleResult))
             return mapExtendedProperty(snapshot, double.Parse, doubleResult);