Fixes #2084 problem with expression profile (#2085)

* Fixes #2084 problem with expression profile * Remove duplicate in file * Also remove merge union in git attrivutes
Open-Systems-Pharmacology · Feb 3, 2022 · c15f087 · c15f087
1 parent 08f512e
commit c15f087
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Showing 27 changed files with 7,600 additions and 54 deletions.
diff --git a/.gitattributes b/.gitattributes
@@ -25,7 +25,7 @@
 *.coffee text
 *.config text
 *.cs text diff=csharp 
-*.csproj text merge=union 
+*.csproj text 
 *.cshtml text
 *.css text
 *.dtd text

diff --git a/PKSim.sln b/PKSim.sln
@@ -1,10 +1,11 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 16
-VisualStudioVersion = 16.0.29025.244
+# Visual Studio Version 17
+VisualStudioVersion = 17.0.31912.275
 MinimumVisualStudioVersion = 10.0.40219.1
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{9B4D05BE-A0E7-41D6-8FCF-1C6005FBE801}"
 	ProjectSection(SolutionItems) = preProject
+		.gitattributes = .gitattributes
 		.gitignore = .gitignore
 		appveyor-coverage.yml = appveyor-coverage.yml
 		appveyor-nightly.yml = appveyor-nightly.yml
@@ -136,8 +137,8 @@ Global
 		HideSolutionNode = FALSE
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
-		SolutionGuid = {13620E23-1993-42C6-A4AB-468E29DD24DE}
 		VisualSVNWorkingCopyRoot = 
+		SolutionGuid = {13620E23-1993-42C6-A4AB-468E29DD24DE}
 	EndGlobalSection
 	GlobalSection(NDepend) = preSolution
 		Project = ".\PKSim.ndproj"

diff --git a/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj b/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Assets" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.82" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Assets/PKSim.Assets.csproj b/src/PKSim.Assets/PKSim.Assets.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Assets" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.82" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.BatchTool/PKSim.BatchTool.csproj b/src/PKSim.BatchTool/PKSim.BatchTool.csproj
@@ -63,7 +63,7 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
     <PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />

diff --git a/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj b/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj
@@ -28,7 +28,7 @@
 
   <ItemGroup>
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.CLI.Core/Services/ExportSimulationRunner.cs b/src/PKSim.CLI.Core/Services/ExportSimulationRunner.cs
@@ -3,6 +3,7 @@
 using System.Linq;
 using System.Threading.Tasks;
 using OSPSuite.Core.Domain;
+using OSPSuite.Core.Domain.Services;
 using OSPSuite.Core.Qualification;
 using OSPSuite.Core.Services;
 using OSPSuite.Utility;
@@ -11,6 +12,7 @@
 using PKSim.Core;
 using PKSim.Core.Model;
 using PKSim.Core.Services;
+using ILazyLoadTask = PKSim.Core.Services.ILazyLoadTask;
 using SimulationRunOptions = PKSim.Core.Services.SimulationRunOptions;
 
 namespace PKSim.CLI.Core.Services

diff --git a/src/PKSim.CLI/PKSim.CLI.csproj b/src/PKSim.CLI/PKSim.CLI.csproj
@@ -61,8 +61,8 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.8.0" />
     <PackageReference Include="Microsoft.Extensions.Logging.Console" Version="3.1.0" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.82" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />

diff --git a/src/PKSim.Core/Model/PKSimProject.cs b/src/PKSim.Core/Model/PKSimProject.cs
@@ -115,9 +115,9 @@ public virtual void AddBuildingBlock(IPKSimBuildingBlock buildingBlockToAdd)
       {
          //that should never happen. Just in case
          var bbWithTheSameName = All(buildingBlockToAdd.BuildingBlockType)
-            .Where(bb => string.Equals(bb.Name, buildingBlockToAdd.Name));
+            .Where(bb => bb.IsNamed(buildingBlockToAdd.Name));
 
-         if (bbWithTheSameName.Count() != 0)
+         if (bbWithTheSameName.Any())
             throw new BuildingBlockAlreadyExistsInProjectException(buildingBlockToAdd);
 
          _allBuildingBlocks.Add(buildingBlockToAdd);

diff --git a/src/PKSim.Core/PKSim.Core.csproj b/src/PKSim.Core/PKSim.Core.csproj
@@ -30,10 +30,10 @@
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Assets" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.82" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

diff --git a/src/PKSim.Core/Snapshots/Mappers/ExpressionProfileMapper.cs b/src/PKSim.Core/Snapshots/Mappers/ExpressionProfileMapper.cs
@@ -90,7 +90,7 @@ public override async Task<ModelExpressionProfile> MapToModel(SnapshotExpression
          expressionProfile.Category = snapshot.Category;
 
          var (molecule, individual) = expressionProfile;
-         await _parameterMapper.MapLocalizedParameters(snapshot.Parameters, individual);
+         await _parameterMapper.MapLocalizedParameters(snapshot.Parameters, individual, !isV9Format(snapshot));
 
          updateMoleculePropertiesToMolecule(molecule, snapshot, individual);
 

diff --git a/src/PKSim.Core/Snapshots/Mappers/IndividualMapper.cs b/src/PKSim.Core/Snapshots/Mappers/IndividualMapper.cs
@@ -62,7 +62,7 @@ public override async Task<ModelIndividual> MapToModel(SnapshotIndividual indivi
          await updateIndividualParameters(individualSnapshot, individual);
 
          if (isV10Format(individualSnapshot))
-            await convertMoleculesToExpressionProfiles(individualSnapshot,   project);
+            await convertMoleculesToExpressionProfiles(individualSnapshot, project);
 
          individualSnapshot.ExpressionProfiles?.Each(x =>
          {
@@ -74,7 +74,7 @@ public override async Task<ModelIndividual> MapToModel(SnapshotIndividual indivi
          return individual;
       }
 
-      private async Task convertMoleculesToExpressionProfiles(SnapshotIndividual individualSnapshot,   PKSimProject project)
+      private async Task convertMoleculesToExpressionProfiles(SnapshotIndividual individualSnapshot, PKSimProject project)
       {
          var expressionProfilesSnapshot = individualSnapshot.Molecules;
          expressionProfilesSnapshot.Each(x =>
@@ -84,11 +84,15 @@ private async Task convertMoleculesToExpressionProfiles(SnapshotIndividual indiv
             x.Molecule = x.Name;
          });
 
-         var expressionProfiles = await _expressionProfileMapper.MapToModels(individualSnapshot.Molecules);
+         var expressionProfiles = await _expressionProfileMapper.MapToModels(expressionProfilesSnapshot);
          foreach (var expressionProfile in expressionProfiles)
          {
-            var (molecule, individual) = expressionProfile;
-            project.AddBuildingBlock(expressionProfile);
+            var (_, individual) = expressionProfile;
+            //Expression profile may have been added already to the project when converting a project with population 
+            //and individual. So we only add if not available already
+            if (project.BuildingBlockByName<Model.ExpressionProfile>(expressionProfile.Name) == null)
+               project.AddBuildingBlock(expressionProfile);
+
             //this needs to happen here since molecule parameters were defined in individual in v10
             await updateIndividualParameters(individualSnapshot, individual);
          }
@@ -103,6 +107,5 @@ private Task updateIndividualParameters(SnapshotIndividual snapshot, ModelIndivi
          //We do not show warning for v10 format as we will FOR SURE have missing parameters
          return _parameterMapper.MapLocalizedParameters(snapshot.Parameters, individual, showParameterNotFoundWarning: !isV10Format(snapshot));
       }
-
    }
 }
diff --git a/src/PKSim.Infrastructure/PKSim.Infrastructure.csproj b/src/PKSim.Infrastructure/PKSim.Infrastructure.csproj
@@ -41,14 +41,14 @@
     <PackageReference Include="Microsoft.Extensions.Logging.Abstractions" Version="3.1.0" />
     <PackageReference Include="Newtonsoft.Json.Schema" Version="3.0.13" />
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Infrastructure" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.82" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
   </ItemGroup>
 

diff --git a/src/PKSim.Matlab/PKSim.Matlab.csproj b/src/PKSim.Matlab/PKSim.Matlab.csproj
@@ -27,7 +27,7 @@
 
   <ItemGroup>
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Presentation/PKSim.Presentation.csproj b/src/PKSim.Presentation/PKSim.Presentation.csproj
@@ -29,8 +29,8 @@
   <ItemGroup>
     <PackageReference Include="OSPSuite.TeXReporting" Version="3.0.0.4" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.R/PKSim.R.csproj b/src/PKSim.R/PKSim.R.csproj
@@ -50,7 +50,7 @@
 
   <ItemGroup>
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />

diff --git a/src/PKSim.UI/PKSim.UI.csproj b/src/PKSim.UI/PKSim.UI.csproj
@@ -51,9 +51,9 @@
     <PackageReference Include="OSPSuite.DataBinding.DevExpress" Version="6.0.0.2" />
     <PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.UI" Version="11.0.77" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.UI" Version="11.0.82" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.UI/Views/ExpressionProfiles/ExpressionProfileMoleculesView.Designer.cs b/src/PKSim.UI/Views/ExpressionProfiles/ExpressionProfileMoleculesView.Designer.cs
diff --git a/src/PKSim/PKSim.csproj b/src/PKSim/PKSim.csproj
@@ -76,13 +76,13 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
     <PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
     <PackageReference Include="System.Data.SQLite.Core" Version="1.0.112" GeneratePathProperty="true" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.77" GeneratePathProperty="true" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.82" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.TeXReporting" Version="3.0.0.4" GeneratePathProperty="true" />
   </ItemGroup>
 

diff --git a/tests/PKSim.Matlab.Tests/PKSim.Matlab.Tests.csproj b/tests/PKSim.Matlab.Tests/PKSim.Matlab.Tests.csproj
@@ -23,7 +23,7 @@
     </PackageReference>
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
     <PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />

diff --git a/tests/PKSim.R.Tests/PKSim.R.Tests.csproj b/tests/PKSim.R.Tests/PKSim.R.Tests.csproj
@@ -23,7 +23,7 @@
     </PackageReference>
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
     <PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.77" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.82" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />

diff --git a/tests/PKSim.Tests/CLI/ExportSimulationRunnerSpecs.cs b/tests/PKSim.Tests/CLI/ExportSimulationRunnerSpecs.cs
@@ -7,6 +7,7 @@
 using OSPSuite.BDDHelper.Extensions;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Builder;
+using OSPSuite.Core.Domain.Services;
 using OSPSuite.Core.Qualification;
 using OSPSuite.Utility;
 using OSPSuite.Utility.Exceptions;
@@ -17,17 +18,19 @@
 using PKSim.Core.Model;
 using PKSim.Core.Services;
 using OSPSuite.Core.Services;
+using ILazyLoadTask = PKSim.Core.Services.ILazyLoadTask;
 using SimulationRunOptions = PKSim.Core.Services.SimulationRunOptions;
 
 namespace PKSim.CLI
 {
    public abstract class concern_for_ExportSimulationRunner : ContextSpecificationAsync<ExportSimulationRunner>
    {
       protected IOSPSuiteLogger _logger;
-      protected IWorkspacePersistor _workspacePersitor;
+      protected IWorkspacePersistor _workspacePersistor;
       protected ICoreWorkspace _workspace;
       protected ISimulationExporter _simulationExporter;
       protected ILazyLoadTask _lazyLoadTask;
+
       protected ExportRunOptions _exportRunOptions = new ExportRunOptions {ExportMode = SimulationExportMode.Json | SimulationExportMode.Xml};
 
       private Func<string, bool> _oldFileExists;
@@ -74,17 +77,17 @@ public override async Task GlobalContext()
       protected override Task Context()
       {
          _logger = A.Fake<IOSPSuiteLogger>();
-         _workspacePersitor = A.Fake<IWorkspacePersistor>();
+         _workspacePersistor = A.Fake<IWorkspacePersistor>();
          _workspace = A.Fake<ICoreWorkspace>();
          _simulationExporter = A.Fake<ISimulationExporter>();
          _lazyLoadTask = A.Fake<ILazyLoadTask>();
-         sut = new ExportSimulationRunner(_logger, _workspacePersitor, _workspace, _simulationExporter, _lazyLoadTask);
+         sut = new ExportSimulationRunner(_logger, _workspacePersistor, _workspace, _simulationExporter, _lazyLoadTask);
 
          _project = new PKSimProject {Name = _projectName};
          _simulation1 = createSimulationWithResults(_simulation1Name);
          _simulation2 = createSimulationWithResults(_simulation2Name);
 
-         A.CallTo(() => _workspacePersitor.LoadSession(_workspace, _projectFileName)).Invokes(x => { _workspace.Project = _project; });
+         A.CallTo(() => _workspacePersistor.LoadSession(_workspace, _projectFileName)).Invokes(x => { _workspace.Project = _project; });
 
 
          return _completed;