Fixes #2623 Export inputs as the project is created from snapshot (#2624)

* Fixes #2623 Export inputs as the project is created from snapshot

* add extensions for base64 encode/decode

* use extensions

* clean up using

Author: rwmcintosh

src/OSPSuite.Assets/Extensions/StringExtensions.cs

@@ -1,6 +1,8 @@
-using System.Collections.Generic;
+using OSPSuite.Utility.Extensions;
+using System;
+using System.Collections.Generic;
 using System.Linq;
-using OSPSuite.Utility.Extensions;
+using System.Text;
 
 namespace OSPSuite.Assets.Extensions
 {
@@ -67,5 +69,9 @@ public static string PluralizeIf(this string stringToPluralize, bool pluralize)
       {
          return pluralize ? stringToPluralize.Pluralize() : stringToPluralize;
       }
+
+      public static string FromBase64String(this string encodedElement) => Encoding.UTF8.GetString(Convert.FromBase64String(encodedElement));
+
+      public static string ToBase64String(this string serializeAsString) => Convert.ToBase64String(Encoding.UTF8.GetBytes(serializeAsString));
    }
 }

src/OSPSuite.CLI.Core/CLIRegister.cs

@@ -1,8 +1,9 @@
 using OSPSuite.CLI.Core.MinimalImplementations;
+using OSPSuite.CLI.Core.Services;
 using OSPSuite.Core;
 using OSPSuite.Core.Commands;
-using OSPSuite.Core.Diagram;
 using OSPSuite.Core.Domain;
+using OSPSuite.Infrastructure.Import.Services;
 using OSPSuite.Utility.Container;
 using IContainer = OSPSuite.Utility.Container.IContainer;
 
@@ -19,14 +20,16 @@ public override void RegisterInContainer(IContainer container)
             //Register Minimal implementations
             scan.IncludeNamespaceContainingType<DisplayUnitRetriever>();
 
-            // This will be registered as singleton
+            // These will be registered as singleton
             scan.ExcludeType<GroupRepository>();
             scan.WithConvention<OSPSuiteRegistrationConvention>();
+            scan.ExcludeType<CsvSeparatorSelector>();
          });
 
          //Singletons
          container.Register<IGroupRepository, GroupRepository>(LifeStyle.Singleton);
          container.Register<IOSPSuiteExecutionContext, ExecutionContext>(LifeStyle.Singleton);
+         container.Register<ICsvDynamicSeparatorSelector, ICsvSeparatorSelector, CsvSeparatorSelector>(LifeStyle.Singleton);
       }
    }
 }

…Suite.R/Services/CsvSeparatorSelector.cs …LI.Core/Services/CsvSeparatorSelector.cssrc/OSPSuite.R/Services/CsvSeparatorSelector.cs renamed to src/OSPSuite.CLI.Core/Services/CsvSeparatorSelector.cs src/OSPSuite.R/Services/CsvSeparatorSelector.cs renamed to src/OSPSuite.CLI.Core/Services/CsvSeparatorSelector.cs

@@ -1,14 +1,14 @@
 using OSPSuite.Infrastructure.Import.Services;
 
-namespace OSPSuite.R.Services
+namespace OSPSuite.CLI.Core.Services
 {
    public interface ICsvDynamicSeparatorSelector : ICsvSeparatorSelector
    {
       CSVSeparators CsvSeparators { set; }
    }
 
    /// <summary>
-   ///    This class is used by the CsvDataSourceFile ro correctly parse csv files
+   ///    This class is used by the CsvDataSourceFile to correctly parse csv files
    /// </summary>
    public class CsvSeparatorSelector : ICsvDynamicSeparatorSelector
    {

src/OSPSuite.CLI.Core/Services/QualificationRunner.cs

@@ -68,41 +68,6 @@ private string createProjectOutputFolder(string outputPath, string projectName)
          return projectOutputFolder;
       }
 
-      private InputMapping exportInput(TModelProject project, QualificationConfiguration configuration, Input input)
-      {
-         var buildingBlock = BuildingBlockBy(project, input);
-
-         var inputsFolder = configuration.InputsFolder;
-         var projectName = FileHelper.RemoveIllegalCharactersFrom(project.Name);
-         var buildingBlockName = FileHelper.RemoveIllegalCharactersFrom(input.Name);
-         var targetFolder = Path.Combine(inputsFolder, projectName, input.Type.ToString());
-         DirectoryHelper.CreateDirectory(targetFolder);
-
-         var fileFullPath = Path.Combine(targetFolder, $"{buildingBlockName}{Constants.Filter.MARKDOWN_EXTENSION}");
-
-         ExportToMarkdown(buildingBlock, fileFullPath, input.SectionLevel).Wait();
-         _logger.AddDebug($"Input data for {input.Type} '{input.Name}' exported to '{fileFullPath}'", project.Name);
-
-         return new InputMapping
-         {
-            SectionId = input.SectionId,
-            SectionReference = input.SectionReference,
-            Path = relativePath(fileFullPath, configuration.OutputFolder)
-         };
-      }
-
-      private InputMapping[] exportInputs(TModelProject project, QualificationConfiguration configuration)
-      {
-         if (configuration.Inputs == null)
-            return Array.Empty<InputMapping>();
-         //            return Task.FromResult(Array.Empty<InputMapping>());
-
-         //TODO Enable parallel runs once https://github.com/Open-Systems-Pharmacology/OSPSuite.Utility/issues/26 is fixed
-         //  return Task.WhenAll(configuration.Inputs.Select(x => exportInput(project, configuration, x)));
-
-         return configuration.Inputs.Select(x => exportInput(project, configuration, x)).ToArray();
-      }
-
       private string relativePath(string path, string relativeTo) => FileHelper.CreateRelativePath(path, relativeTo, useUnixPathSeparator: true);
 
       public async Task RunBatchAsync(QualificationRunOptions runOptions)
@@ -126,7 +91,7 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
          }
 
          var begin = DateTime.UtcNow;
-         var project = await loadProject(runOptions, snapshot);
+         var (project, inputMappings) = await LoadProjectAndExportInputs(runOptions, snapshot, config);
          LoadProjectContext(project);
 
          var projectOutputFolder = createProjectOutputFolder(config.OutputFolder, project.Name);
@@ -151,8 +116,6 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
 
          var observedDataMappings = await exportAllObservedData(project, config);
 
-         var inputMappings = exportInputs(project, config);
-
          var mapping = new QualificationMapping
          {
             SimulationMappings = simulationMappings,
@@ -264,12 +227,10 @@ private PlotMapping[] retrievePlotDefinitionsFrom(TSnapshotProject snapshotProje
          throw new QualificationRunException(SimulationUsedInPlotsAreNotExported(unmappedSimulations, snapshotProject.Name));
       }
 
-      private Task<TModelProject> loadProject(QualificationRunOptions runOptions, TSnapshotProject snapshot) => _snapshotTask.LoadProjectFromSnapshotAsync(snapshot, runOptions.Run);
+      protected abstract Task<(TModelProject, InputMapping[])> LoadProjectAndExportInputs(QualificationRunOptions runOptions, TSnapshotProject snapshot, QualificationConfiguration config);
 
       protected abstract SimulationExportMode ExportMode(QualificationRunOptions runOptions);
 
-      protected abstract Task ExportToMarkdown(object buildingBlock, string fileFullPath, int? inputSectionLevel);
-
       protected abstract Task<SimulationMapping[]> ExportSimulationsIn(TModelProject project, ExportRunOptions exportRunOptions);
 
       protected abstract object BuildingBlockBy(TModelProject project, Input input);

src/OSPSuite.Core/Domain/Project.cs

@@ -1,4 +1,3 @@
-using System;
 using System.Collections.Generic;
 using System.Linq;
 using OSPSuite.Utility.Collections;

src/OSPSuite.Infrastructure.Export/OSPSuite.Infrastructure.Export.csproj

@@ -24,7 +24,7 @@
 
   <ItemGroup>
     <PackageReference Include="Microsoft.Extensions.Logging.Abstractions" Version="9.0.2" />
-    <PackageReference Include="NPOI" Version="2.7.2" />
+    <PackageReference Include="NPOI" Version="2.7.4" />
     <PackageReference Include="OSPSuite.Utility" Version="4.1.1.3" />
   </ItemGroup>
 

src/OSPSuite.Infrastructure.Import/OSPSuite.Infrastructure.Import.csproj

@@ -25,7 +25,7 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="NPOI" Version="2.7.2" />
+    <PackageReference Include="NPOI" Version="2.7.4" />
     <PackageReference Include="OSPSuite.Utility" Version="4.1.1.3" />
     <PackageReference Include="LumenWorksCsvReader" Version="4.0.0" />
   </ItemGroup>

src/OSPSuite.Infrastructure.Serialization/Json/JsonSerializer.cs

@@ -9,8 +9,8 @@
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
-using System.Text;
 using System.Threading.Tasks;
+using OSPSuite.Assets.Extensions;
 
 namespace OSPSuite.Infrastructure.Serialization.Json
 {
@@ -33,7 +33,7 @@ public async Task Serialize(object objectToSerialize, string fileName)
 
       public string Serialize(object objectToSerialize) => JsonConvert.SerializeObject(objectToSerialize, Formatting.Indented, _settings);
 
-      public string SerializeToBase64String(object objectToSerialize) => Convert.ToBase64String(Encoding.UTF8.GetBytes(Serialize(objectToSerialize)));
+      public string SerializeToBase64String(object objectToSerialize) => Serialize(objectToSerialize).ToBase64String();
 
       public async Task<object[]> DeserializeAsArray(string fileName, Type objectType)
       {
@@ -94,7 +94,7 @@ public async Task<T> DeserializeFromString<T>(string jsonString) where T : class
 
       public async Task<T> DeserializeFromBase64String<T>(string base64String) where T : class
       {
-         var jsonString = Encoding.UTF8.GetString(Convert.FromBase64String(base64String));
+         var jsonString = base64String.FromBase64String();
          var deserializedObject = await DeserializeFromString(jsonString, typeof(T));
          return deserializedObject as T;
       }

src/OSPSuite.R/RRegister.cs

@@ -1,6 +1,5 @@
 using OSPSuite.Core;
 using OSPSuite.Core.Services;
-using OSPSuite.Infrastructure.Import.Services;
 using OSPSuite.R.Domain;
 using OSPSuite.R.Mapper;
 using OSPSuite.R.Services;
@@ -24,7 +23,6 @@ public override void RegisterInContainer(IContainer container)
             //Register Mappers
             scan.IncludeNamespaceContainingType<ISensitivityAnalysisToCoreSensitivityAnalysisMapper>();
 
-            scan.ExcludeType<CsvSeparatorSelector>();
             scan.WithConvention<OSPSuiteRegistrationConvention>();
          });
 
@@ -34,7 +32,6 @@ public override void RegisterInContainer(IContainer container)
 
          container.Register<IOSPSuiteLogger, RLogger, RLogger>(LifeStyle.Singleton);
          container.Register<IEventPublisher, EventPublisher>(LifeStyle.Singleton);
-         container.Register<ICsvDynamicSeparatorSelector, ICsvSeparatorSelector, CsvSeparatorSelector>(LifeStyle.Singleton);
       }
    }
 }

src/OSPSuite.R/Services/DataImporterTask.cs

@@ -1,5 +1,6 @@
 using System.Collections.Generic;
 using System.Linq;
+using OSPSuite.CLI.Core.Services;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Domain.UnitSystem;