Fixes #2081 PKSim CLI filter simulation (#2082)

* Fixes #2081 PKSim CLI filter simulation * Better comments * Fixes build * Fixes build
Open-Systems-Pharmacology · Feb 1, 2022 · 2821500 · 2821500
1 parent ea7383d
commit 2821500
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Showing 23 changed files with 115 additions and 90 deletions.
diff --git a/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj b/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj
@@ -26,10 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Assets" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.72" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Assets/PKSim.Assets.csproj b/src/PKSim.Assets/PKSim.Assets.csproj
@@ -26,10 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Assets" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.72" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Assets/PKSimConstants.cs b/src/PKSim.Assets/PKSimConstants.cs
@@ -906,6 +906,9 @@ public static string MapToSnapshotNotSupportedWithoutContext(string snapshotType
 
          public static string CannotFindSimulationInSnapshot(string simulationName, string project) => CannotFindBuildingBlockInSnapshot(ObjectTypes.Simulation, simulationName, project);
 
+         public static string SimulationUsedInPlotsAreNotExported(IReadOnlyList<string> simulationNames, string project)
+            => $"{ObjectTypes.Simulation.PluralizeIf(simulationNames)} {simulationNames.ToString(", ", "'")} used in plots {"is".PluralizeIf(simulationNames)} not found in the list of exported simulations for {ObjectTypes.Project} {project}";
+
          public static string CannotFindSimulationParameterInSnapshot(string parameterPath, string simulationName, string project) => 
             $"Could not find {ObjectTypes.Parameter} with path '{parameterPath}' in {ObjectTypes.Simulation} '{simulationName}' defined in snapshot {project}.";
 

diff --git a/src/PKSim.BatchTool/PKSim.BatchTool.csproj b/src/PKSim.BatchTool/PKSim.BatchTool.csproj
@@ -63,8 +63,7 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
     <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
@@ -28,8 +28,7 @@
 
   <ItemGroup>
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.CLI.Core/RunOptions/QualificationRunOptions.cs b/src/PKSim.CLI.Core/RunOptions/QualificationRunOptions.cs
@@ -16,5 +16,10 @@ public class QualificationRunOptions
       ///    Should simulation be performed as part of the run?
       /// </summary>
       public bool Run { get; set; }
+
+      /// <summary>
+      /// Specifies if project files (snapshot and PK-Sim project file should be exported)
+      /// </summary>
+      public bool ExportProjectFiles { get; set; }
    }
 }
diff --git a/src/PKSim.CLI.Core/Services/QualificationRunner.cs b/src/PKSim.CLI.Core/Services/QualificationRunner.cs
@@ -102,7 +102,9 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
          {
             OutputFolder = projectOutputFolder,
             //We run the output, this is for the old matlab implementation where we need xml. Otherwise, we only need pkml export
-            ExportMode = runOptions.Run ?   SimulationExportMode.Xml | SimulationExportMode.Csv  :  SimulationExportMode.Pkml
+            ExportMode = runOptions.Run ? SimulationExportMode.Xml | SimulationExportMode.Csv : SimulationExportMode.Pkml,
+
+            Simulations = config.Simulations
          };
 
          //Using absolute path for simulation folder. We need them to be relative
@@ -124,13 +126,16 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
          await _jsonSerializer.Serialize(mapping, config.MappingFile);
          _logger.AddDebug($"Project mapping for '{project.Name}' exported to '{config.MappingFile}'", project.Name);
 
-         var projectFile = Path.Combine(config.TempFolder, $"{project.Name}{CoreConstants.Filter.PROJECT_EXTENSION}");
-         _workspacePersistor.SaveSession(_workspace, projectFile);
-         _logger.AddDebug($"Project saved to '{projectFile}'", project.Name);
+         if (runOptions.ExportProjectFiles)
+         {
+            var projectFile = Path.Combine(config.TempFolder, $"{project.Name}{CoreConstants.Filter.PROJECT_EXTENSION}");
+            _workspacePersistor.SaveSession(_workspace, projectFile);
+            _logger.AddDebug($"Project saved to '{projectFile}'", project.Name);
 
-         var snapshotFile = Path.Combine(config.TempFolder, $"{project.Name}{Constants.Filter.JSON_EXTENSION}");
-         await _snapshotTask.ExportModelToSnapshotAsync(project, snapshotFile);
-         _logger.AddDebug($"Project snapshot saved to '{snapshotFile}'", project.Name);
+            var snapshotFile = Path.Combine(config.TempFolder, $"{project.Name}{Constants.Filter.JSON_EXTENSION}");
+            await _snapshotTask.ExportModelToSnapshotAsync(project, snapshotFile);
+            _logger.AddDebug($"Project snapshot saved to '{snapshotFile}'", project.Name);
+         }
 
          var end = DateTime.UtcNow;
          var timeSpent = end - begin;
@@ -140,7 +145,15 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
       private PlotMapping[] retrievePlotDefinitionsFrom(Project snapshotProject, QualifcationConfiguration configuration)
       {
          var plotMappings = configuration.SimulationPlots?.SelectMany(x => retrievePlotDefinitionsForSimulation(x, snapshotProject));
-         return plotMappings?.ToArray() ?? Array.Empty<PlotMapping>();
+         var plotMappingsArray = plotMappings?.ToArray() ?? Array.Empty<PlotMapping>();
+         var exportedSimulations = configuration.Simulations?.ToArray() ?? Array.Empty<string>();
+         var unmappedSimulations = plotMappingsArray.Select(x => x.Simulation).Distinct().Where(x => !exportedSimulations.Contains(x)).ToList();
+
+         //All simulations referenced in the the plot mapping are also exported. We are good
+         if (!unmappedSimulations.Any())
+            return plotMappingsArray;
+
+         throw new QualificationRunException(SimulationUsedInPlotsAreNotExported(unmappedSimulations, snapshotProject.Name));
       }
 
       private void validateInputs(Project snapshotProject, QualifcationConfiguration configuration)

diff --git a/src/PKSim.CLI/Commands/QualificationRunCommand.cs b/src/PKSim.CLI/Commands/QualificationRunCommand.cs
@@ -19,13 +19,17 @@ public class QualificationRunCommand : CLICommand<QualificationRunOptions>
       [Option('r', "run", Required = false, HelpText = "Should the qualification runner also run the simulation or simply export the qualification report for further processing. Default is false")]
       public bool Run { get; set; } = false;
 
+      [Option('e', "exp", Required = false, HelpText = "Should the qualification runner also export the project files (snapshot and PK-Sim project file). Default is false")]
+      public bool ExportProjectFiles { get; set; } = false;
+
       public override QualificationRunOptions ToRunOptions()
       {
          return new QualificationRunOptions
          {
             ConfigurationFile = ConfigurationFile,
             Validate = Validate,
-            Run = Run
+            Run = Run,
+            ExportProjectFiles = ExportProjectFiles
          };
       }
 
@@ -35,7 +39,8 @@ public override string ToString()
          LogDefaultOptions(sb);
          sb.AppendLine($"Validate: {Validate}");
          sb.AppendLine($"Configuration file: {ConfigurationFile}");
-         sb.AppendLine($"Run Simulations: {Run}");
+         sb.AppendLine($"Run simulations: {Run}");
+         sb.AppendLine($"Export project files: {ExportProjectFiles}");
          return sb.ToString();
       }
    }

diff --git a/src/PKSim.CLI/PKSim.CLI.csproj b/src/PKSim.CLI/PKSim.CLI.csproj
@@ -61,10 +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="11.0.62" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.72" />
     <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/PKSim.Core.csproj b/src/PKSim.Core/PKSim.Core.csproj
@@ -30,14 +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="11.0.62" />
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Assets" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Assets" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.72" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

diff --git a/src/PKSim.Infrastructure/PKSim.Infrastructure.csproj b/src/PKSim.Infrastructure/PKSim.Infrastructure.csproj
@@ -41,22 +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="11.0.62" />
-    <PackageReference Include="OSPSuite.Infrastructure" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Infrastructure" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Infrastructure" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.72" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
   </ItemGroup>
 

diff --git a/src/PKSim.Infrastructure/Services/ImportObservedDataTask.cs b/src/PKSim.Infrastructure/Services/ImportObservedDataTask.cs
@@ -306,13 +306,13 @@ public IEnumerable<string> PredefinedValuesFor(string name)
          return Enumerable.Empty<string>();
       }
 
-      public IReadOnlyList<string> DefaultMetaDataCategories => CoreConstants.ObservedData.DefaultProperties;
+      public IReadOnlyList<string> DefaultMetaDataCategories { get; } = CoreConstants.ObservedData.DefaultProperties;
 
-      public IReadOnlyList<string> ReadOnlyMetaDataCategories => new List<string> { };
+      public IReadOnlyList<string> ReadOnlyMetaDataCategories { get; } = new List<string> { };
+
+      public bool MolWeightAlwaysEditable { get; } = false;
 
-      public bool MolWeightEditable => false;
-
-      public bool MolWeightVisible => true;
+      public bool MolWeightVisible { get; }=  true;
 
       private IEnumerable<string> predefinedGenders => predefinedValuesFor(addPredefinedGenderValues);
 

diff --git a/src/PKSim.Matlab/PKSim.Matlab.csproj b/src/PKSim.Matlab/PKSim.Matlab.csproj
@@ -27,8 +27,7 @@
 
   <ItemGroup>
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Presentation/PKSim.Presentation.csproj b/src/PKSim.Presentation/PKSim.Presentation.csproj
@@ -29,10 +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="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.R/PKSim.R.csproj b/src/PKSim.R/PKSim.R.csproj
@@ -50,8 +50,7 @@
 
   <ItemGroup>
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
     <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
@@ -51,12 +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="11.0.62" />
-    <PackageReference Include="OSPSuite.UI" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.UI" Version="11.0.60" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.UI" Version="11.0.72" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim/PKSim.csproj b/src/PKSim/PKSim.csproj
@@ -76,15 +76,13 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
     <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="11.0.62" GeneratePathProperty="true" />
-    <PackageReference Include="OSPSuite.Presentation" Version="11.0.60" GeneratePathProperty="true" />
+    <PackageReference Include="OSPSuite.Presentation" Version="11.0.72" 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
@@ -23,8 +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="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
     <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
@@ -23,8 +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="11.0.62" />
-    <PackageReference Include="OSPSuite.Core" Version="11.0.60" />
+    <PackageReference Include="OSPSuite.Core" Version="11.0.72" />
     <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" />