Microsoft.data.sqlite

.github/workflows/build-nightly_12.2.yml

@@ -106,7 +106,16 @@ jobs:
         run: |
           pushd .
           cd src\PKSimRDependencyResolution\bin\Debug\${{env.TARGET_FRAMEWORK}}
-          7z.exe a pk-sim-r-dependencies.zip -x@"excludedFiles.txt" * -xr!runtimes
+          @("win-x64", "linux-x64", "osx-arm64") | ForEach-Object {
+            $nativePath = "runtimes\$_\native"
+            if (Test-Path $nativePath) {
+              Copy-Item "$nativePath\*sqlite*" -Destination "." -Force -ErrorAction SilentlyContinue
+            }
+          }
+          if (Test-Path "runtimes") {
+            Remove-Item -Recurse -Force "runtimes"
+          }
+          7z.exe a pk-sim-r-dependencies.zip -x@"excludedFiles.txt" *
           popd
 
       - name: Sign PKSim setup with CodeSignTool

src/PKSim.BatchTool/PKSim.BatchTool.csproj

@@ -66,7 +66,7 @@
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.73" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.75" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.19" GeneratePathProperty="true" />
-    <PackageReference Include="System.Data.SQLite.Core" Version="1.0.119" GeneratePathProperty="true" />
+    <PackageReference Include="Microsoft.Data.Sqlite" Version="8.0.0" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.CLI.Core/Services/SnapshotRunner.cs

@@ -101,21 +101,37 @@ private async Task startSnapshotRun(IReadOnlyList<FileMap> fileMaps, Func<FileMa
       private async Task createProjectFromSnapshotFile(FileMap file, bool runSimulations)
       {
          _logger.AddInfo($"Starting project export for '{file.SnapshotFile}'");
-         var project = await _snapshotTask.LoadProjectFromSnapshotFileAsync(file.SnapshotFile, runSimulations);
-         if (project == null)
-            return;
-
-         _logger.AddDebug($"Snapshot loaded successfully from '{file.SnapshotFile}'");
-         _workspace.Project = project;
          try
          {
-            _workspacePersistor.SaveSession(_workspace, file.ProjectFile);
+            var project = await _snapshotTask.LoadProjectFromSnapshotFileAsync(file.SnapshotFile, runSimulations);
+            if (project == null)
+            {
+               _logger.AddError($"Failed to load project from snapshot file '{file.SnapshotFile}'. The snapshot may be corrupted or incompatible.");
+               return;
+            }
+
+            _logger.AddDebug($"Snapshot loaded successfully from '{file.SnapshotFile}'");
+            _workspace.Project = project;
+            try
+            {
+               _workspacePersistor.SaveSession(_workspace, file.ProjectFile);
+               _logger.AddInfo($"Project saved to '{file.ProjectFile}'");
+            }
+            catch (Exception ex)
+            {
+               _logger.AddError($"Failed to save project to '{file.ProjectFile}': {ex.Message}");
+               throw;
+            }
+         }
+         catch (Exception ex)
+         {
+            _logger.AddError($"Error processing snapshot file '{file.SnapshotFile}': {ex.Message}");
+            throw;
          }
          finally
          {
             _workspacePersistor.CloseSession();
          }
-         _logger.AddInfo($"Project saved to '{file.ProjectFile};");
       }
 
       private async Task createSnapshotFromProjectFile(FileMap file)

src/PKSim.CLI/PKSim.CLI.csproj

@@ -62,7 +62,7 @@
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.73" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.75" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.19" GeneratePathProperty="true" />
-    <PackageReference Include="System.Data.SQLite.Core" Version="1.0.119" GeneratePathProperty="true" />
+    <PackageReference Include="Microsoft.Data.Sqlite" Version="8.0.0" />
 
   </ItemGroup>
 

src/PKSim.Infrastructure/ORM/DAS/DAS.cs

@@ -1,7 +1,7 @@
 using System;
 using System.Data;
 using System.Data.Common;
-using System.Data.SQLite;
+using Microsoft.Data.Sqlite;
 
 namespace PKSim.Infrastructure.ORM.DAS
 {
@@ -19,6 +19,12 @@ public class DAS : IDisposable
 
       public DbConnection Connection { get; private set; }
 
+      public DAS()
+      {
+         // Initialize the provider factory to Microsoft.Data.Sqlite by default
+         _providerFactory = Microsoft.Data.Sqlite.SqliteFactory.Instance;
+      }
+
       //this is just a dummy command to create a parameters collection to store parameters
       private DbCommand _command;
       private DbParameterCollection _parameters;
@@ -89,9 +95,9 @@ public bool Connect(string dataProvider, string connectionString)
 
          if (!IsConnected)
          {
-            if ((dataProvider == "System.Data.SQLite"))
+            if ((dataProvider == "Microsoft.Data.Sqlite"))
             {
-               _providerFactory = new SQLiteFactory();
+               _providerFactory = SqliteFactory.Instance;
             }
             else
             {
@@ -153,8 +159,9 @@ public bool Connect(string dbName, string workgroupDb, string user, string passw
             switch (dataProvider)
             {
                case DataProviders.SQLite:
-                  sProvider = "System.Data.SQLite";
+                  sProvider = "Microsoft.Data.Sqlite";
                   connBuilder.Add("Data Source", dbName);
+                  connBuilder.Add("Foreign Keys", "False");
                   if (!string.IsNullOrEmpty(password))
                   {
                      connBuilder.Add("Password", password);
@@ -508,10 +515,36 @@ public void FillDataTable(DASDataTable dataTable, string sql)
          dataTable.Rows.Clear();
          try
          {
-            using (var adapter = _providerFactory.CreateDataAdapter())
+            // Manual data reading to avoid constraint issues with DataTable.Load()
+            using (var reader = cmd.ExecuteReader())
             {
-               adapter.SelectCommand = cmd;
-               adapter.Fill(dataTable);
+               // Build column schema if table is empty
+               if (dataTable.Columns.Count() == 0)
+               {
+                  var schemaTable = reader.GetSchemaTable();
+                  if (schemaTable != null)
+                  {
+                     foreach (System.Data.DataRow schemaRow in schemaTable.Rows)
+                     {
+                        var columnName = schemaRow["ColumnName"].ToString();
+                        var dataType = (Type)schemaRow["DataType"];
+                        // Use base DataTable's Columns collection
+                        ((DataTable)dataTable).Columns.Add(columnName, dataType);
+                     }
+                  }
+               }
+
+               // Read data row by row to avoid constraint issues
+               while (reader.Read())
+               {
+                  var row = dataTable.NewRow();
+                  for (int fieldIndex = 0; fieldIndex < reader.FieldCount; fieldIndex++)
+                  {
+                     row[fieldIndex] = reader.IsDBNull(fieldIndex) ? DBNull.Value : reader.GetValue(fieldIndex);
+                  }
+                  // Use base DataTable's Rows collection
+                  ((DataTable)dataTable).Rows.Add(row);
+               }
             }
          }
          catch (Exception ex)
@@ -564,7 +597,7 @@ public object GetAutoValue(string autoValueCreator)
       ///    <para>
       ///       Each parameter has an identifying name and an associated value.
       ///       You can automatically bind a parameter to SQL and PL/SQL statements of other objects,
-      ///       by using the parameter�s name as a placeholder (@Name) in the SQL statement.
+      ///       by using the parameter s name as a placeholder (@Name) in the SQL statement.
       ///       Such use of parameters can simplify dynamic queries and increase program performance.
       ///    </para>
       ///    <para>
@@ -676,7 +709,7 @@ public void AddParameter(string paramName, object paramValue, ParameterModes par
       ///    <para>
       ///       Each parameter has an identifying name and an associated value.
       ///       You can automatically bind a parameter to SQL and PL/SQL statements of other objects,
-      ///       by using the parameter�s name as a placeholder (@Name) in the SQL statement.
+      ///       by using the parameter s name as a placeholder (@Name) in the SQL statement.
       ///       Such use of parameters can simplify dynamic queries and increase program performance.
       ///    </para>
       ///    <para>
@@ -764,7 +797,7 @@ public void AddParameter(string paramName, object paramValue, ParameterModes par
       /// <remarks>
       ///    Each parameter has an identifying name and an associated value.
       ///    You can automatically bind a parameter to SQL and PL/SQL statements of other objects,
-      ///    by using the parameter�s name as a placeholder (:Name) in the SQL or PL/SQL statement.
+      ///    by using the parameter s name as a placeholder (:Name) in the SQL or PL/SQL statement.
       ///    Such use of parameters can simplify dynamic queries and increase program performance.
       ///    If you set an incorrect <see cref="ParameterModes"></see>, such as <see cref="ParameterModes.PARM_INOUT"></see>
       ///    for a stored procedure parameter type IN, this can result in errors.

src/PKSim.Infrastructure/PKSim.Infrastructure.csproj

@@ -45,6 +45,7 @@
     <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="12.2.17" />
     <PackageReference Include="OSPSuite.Presentation.Serialization" Version="12.2.17" />
     <PackageReference Include="OSPSuite.Utility" Version="4.1.1.1" />
+    <PackageReference Include="Microsoft.Data.Sqlite" Version="8.0.0" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.Infrastructure/Serialization/DatabaseSchemaMigrator.cs

@@ -1,6 +1,6 @@
 using System;
 using System.Data;
-using System.Data.SQLite;
+using Microsoft.Data.Sqlite;
 using OSPSuite.Core.Extensions;
 
 namespace PKSim.Infrastructure.Serialization
@@ -19,7 +19,7 @@ public class DatabaseSchemaMigrator : IDatabaseSchemaMigrator
       public void MigrateSchema(string fileFullPath)
       {
          var path = fileFullPath.ToUNCPath();
-         using (var sqlLite = new SQLiteConnection($"Data Source={path}"))
+         using (var sqlLite = new SqliteConnection($"Data Source={path}"))
          {
             sqlLite.Open();
             migrateTo5_3(sqlLite);
@@ -28,7 +28,7 @@ public void MigrateSchema(string fileFullPath)
       }
 
       //change from 5.2 to 5.3
-      private void migrateTo5_3(SQLiteConnection sqlite)
+      private void migrateTo5_3(SqliteConnection sqlite)
       {
          if (!needsConversionTo5_3(sqlite)) return;
 
@@ -53,27 +53,27 @@ PRIMARY KEY (Id),
       }
 
       //change from 6.1 to 6.2
-      private void migrateTo6_2(SQLiteConnection sqlite)
+      private void migrateTo6_2(SqliteConnection sqlite)
       {
          if (!needsConversionTo6_2(sqlite)) return;
 
          //rename table SUMMARY_CHART to SIMULATION_COMPARISONS
          sqlite.ExecuteNonQuery("ALTER TABLE OBSERVED_DATA RENAME TO USED_OBSERVED_DATA");
       }
 
-      private bool needsConversionTo6_2(SQLiteConnection sqlite)
+      private bool needsConversionTo6_2(SqliteConnection sqlite)
       {
          //USED_OBSERVED_DATA table was added in 6.2
          return !hasTable(sqlite, "USED_OBSERVED_DATA");
       }
 
-      private bool needsConversionTo5_3(SQLiteConnection sqlLite)
+      private bool needsConversionTo5_3(SqliteConnection sqlLite)
       {
          //SIMULATION_COMPARISONS table was added in 5.3
          return !hasTable(sqlLite, "SIMULATION_COMPARISONS");
       }
 
-      private static bool hasTable(SQLiteConnection sqlLite, string tableName)
+      private static bool hasTable(SqliteConnection sqlLite, string tableName)
       {
          try
          {

src/PKSim.Infrastructure/Services/SessionFactoryProvider.cs

@@ -52,7 +52,7 @@ private Configuration createSqlLiteConfigurationFor(string dataSource)
          configuration.SetProperty("dialect", "NHibernate.Dialect.SQLiteDialect");
          configuration.SetProperty("query.substitutions", "true=1;false=0");
          configuration.SetProperty("show_sql", "false");
-         configuration.SetProperty("connection.connection_string", $"Data Source={path};Version=3;New=False;Compress=True;");
+         configuration.SetProperty("connection.connection_string", $"Data Source={path};Cache=Shared");
 
          return Fluently.Configure(configuration)
             .Mappings(cfg =>

src/PKSim.R/PKSim.R.csproj

@@ -47,7 +47,7 @@
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.73" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.75" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.19" GeneratePathProperty="true" />
-    <PackageReference Include="System.Data.SQLite.Core" Version="1.0.119" GeneratePathProperty="true" />
+    <PackageReference Include="Microsoft.Data.Sqlite" Version="8.0.0" />
 
   </ItemGroup>
 
@@ -69,10 +69,6 @@
   </ItemGroup>
 
   <PropertyGroup>
-    <ContentSQLiteInteropFiles>true</ContentSQLiteInteropFiles>
-    <CopySQLiteInteropFiles>false</CopySQLiteInteropFiles>
-    <CleanSQLiteInteropFiles>false</CleanSQLiteInteropFiles>
-    <CollectSQLiteInteropFiles>false</CollectSQLiteInteropFiles>
     <PlatformTarget>AnyCPU</PlatformTarget>
   </PropertyGroup>
 </Project>

src/PKSim/PKSim.csproj

@@ -78,7 +78,7 @@
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.73" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.75" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.19" GeneratePathProperty="true" />
-    <PackageReference Include="System.Data.SQLite.Core" Version="1.0.119" GeneratePathProperty="true" />
+    <PackageReference Include="Microsoft.Data.Sqlite" Version="8.0.0" />
     <PackageReference Include="OSPSuite.Presentation" Version="12.2.17" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.TeXReporting" Version="3.0.1.1" GeneratePathProperty="true" />
   </ItemGroup>
@@ -99,19 +99,4 @@
     <Exec Command="copy $(ProjectDir)..\PKSim.R\$(OutDir)PKSim.R.* $(TargetDir)&#xD;&#xA;copy $(ProjectDir)..\PKSim.Matlab\$(OutDir)PKSim.Matlab.* $(TargetDir)&#xD;&#xA;copy $(ProjectDir)..\PKSim.BatchTool\$(OutDir)PKSim.BatchTool.* $(TargetDir)&#xD;&#xA;copy $(ProjectDir)..\PKSim.CLI\$(OutDir)PKSim.CLI.* $(TargetDir)&#xD;&#xA;copy $(ProjectDir)..\PKSim.CLI\$(OutDir)CommandLine.* $(TargetDir)&#xD;&#xA;copy $(ProjectDir)..\PKSim.CLI\$(OutDir)Microsoft.Extensions.* $(TargetDir)&#xD;&#xA;" />
   </Target>
 
-  <!-- Content comes from Stub.system.data.sqlite.core. Basically, implements the same task as if you 
-  added this binary as content and copy to output folder -->
-  <PropertyGroup>
-    <ContentSQLiteInteropFiles>true</ContentSQLiteInteropFiles>
-    <CopySQLiteInteropFiles>false</CopySQLiteInteropFiles>
-    <CleanSQLiteInteropFiles>false</CleanSQLiteInteropFiles>
-    <CollectSQLiteInteropFiles>false</CollectSQLiteInteropFiles>
-  </PropertyGroup>
-
-  <Target Name="PostBuild" AfterTargets="PostBuildEvent">
-    <ItemGroup>
-	    <WindowsFiles Include="$(TargetDir)x64/SQLite.Interop.dll" />
-    </ItemGroup>
-    <Copy SourceFiles="@(WindowsFiles);" DestinationFolder="$(TargetFolder)" DestinationFiles="@(WindowsFiles-&gt;Replace('x64/SQLite.Interop.dll', 'SQLite.Interop.dll'))" />
-  </Target>
 </Project>

src/PKSimRDependencyResolution/PKSimRDependencyResolution.csproj

@@ -7,6 +7,7 @@
     <GenerateAssemblyInfo>false</GenerateAssemblyInfo>
     <Version Condition="'$(Version)' == ''">12.2.0</Version>
     <PlatformTarget>x64</PlatformTarget>
+    <RuntimeIdentifiers>win-x64;linux-x64;osx-x64;osx-arm64</RuntimeIdentifiers>
   </PropertyGroup>
   <ItemGroup>
     <Compile Include="..\..\SolutionInfo.cs" Link="Properties\SolutionInfo.cs" />
@@ -24,6 +25,7 @@
     <PackageReference Include="OSPSuite.SimModel.MacOS.Arm64" Version="4.0.0.75" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES.Ubuntu22" Version="4.1.0.19" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES.MacOSArm64" Version="4.1.0.19" GeneratePathProperty="true" />
+    <PackageReference Include="SQLitePCLRaw.bundle_e_sqlite3" Version="2.1.8" GeneratePathProperty="true" />
   </ItemGroup>
   <ItemGroup>
     <Content Include="$(PkgOSPSuite_FuncParser_Ubuntu22)\OSPSuite.FuncParserNative\bin\native\x64\Release\libOSPSuite.FuncParserNative.so" Link="libOSPSuite.FuncParserNative.so">
@@ -50,20 +52,4 @@
   <ItemGroup>
     <ProjectReference Include="..\PKSim.R\PKSim.R.csproj" />
   </ItemGroup>
-  <PropertyGroup>
-    <ContentSQLiteInteropFiles>true</ContentSQLiteInteropFiles>
-    <CopySQLiteInteropFiles>false</CopySQLiteInteropFiles>
-    <CleanSQLiteInteropFiles>false</CleanSQLiteInteropFiles>
-    <CollectSQLiteInteropFiles>false</CollectSQLiteInteropFiles>
-  </PropertyGroup>
-  <Target Name="PostBuild" AfterTargets="PostBuildEvent">
-    <ItemGroup>
-      <LinuxFiles Include="$(TargetDir)runtimes/linux-x64/native/SQLite.Interop.dll" />
-      <WindowsFiles Include="$(TargetDir)runtimes/win-x64/native/SQLite.Interop.dll" />
-      <MacFiles Include="$(TargetDir)runtimes/osx-x64/native/SQLite.Interop.dll" />
-    </ItemGroup>
-    <Copy SourceFiles="@(WindowsFiles);" DestinationFolder="$(TargetFolder)" DestinationFiles="@(WindowsFiles-&gt;Replace('runtimes/win-x64/native/SQLite.Interop.dll', 'SQLite.Interop.dll'))" />
-    <Copy SourceFiles="@(LinuxFiles);" DestinationFolder="$(TargetFolder)" DestinationFiles="@(LinuxFiles-&gt;Replace('runtimes/linux-x64/native/SQLite.Interop.dll', 'libSQLite.Interop.dll'))" />
-    <Copy SourceFiles="@(MacFiles);" DestinationFolder="$(TargetFolder)" DestinationFiles="@(MacFiles-&gt;Replace('runtimes/osx-x64/native/SQLite.Interop.dll', 'SQLite.Interop.dll.dylib'))" />
-  </Target>
 </Project>

tests/PKSim.Matlab.Tests/PKSim.Matlab.Tests.csproj

@@ -28,7 +28,7 @@
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.59" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.59" 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="Microsoft.Data.Sqlite" Version="8.0.0" />
   </ItemGroup>
 
   <ItemGroup>

tests/PKSim.R.Tests/PKSim.R.Tests.csproj

@@ -23,7 +23,7 @@
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.73" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.75" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.19" GeneratePathProperty="true" />
-    <PackageReference Include="System.Data.SQLite.Core" Version="1.0.119" GeneratePathProperty="true" />
+    <PackageReference Include="Microsoft.Data.Sqlite" Version="8.0.0" />
   </ItemGroup>
 
   <ItemGroup>