Migrate from System.Data.SQLite to Microsoft.Data.Sqlite 8.0.0 by Felixmil · Pull Request #2699 · Open-Systems-Pharmacology/OSPSuite.Core

Felixmil · 2025-11-04T08:46:27Z

Closes #2701

Sister PRs:

PKSim: Microsoft.data.sqlite PK-Sim#3323
MoBi: Microsoft.data.sqlite MoBi#2163

Summary

Migrated from System.Data.SQLite to Microsoft.Data.Sqlite 8.0.0 across the codebase.

Key Changes:

Replaced System.Data.SQLite package references with Microsoft.Data.Sqlite 8.0.0
Updated SessionFactoryProvider to use Microsoft.Data.Sqlite with NHibernate
Updated ConnectionProvider and SQLiteProjectCommandExecuter to use SqliteConnection
Updated test projects to reference Microsoft.Data.Sqlite

Type of change

Please mark relevant options with an x in the brackets.

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires documentation changes (link at least one user or developer documentation issue):
Algorithm update - updates algorithm documentation/questions/answers etc.
Other (please describe): Dependency migration - replaced System.Data.SQLite with Microsoft.Data.Sqlite 8.0.0

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

Integration tests
Unit tests
Manual tests
No tests required

Reviewer checklist

Mark everything that needs to be checked before merging the PR.

Check if the code is well documented
Check if the behavior is what is expected
Check if the code is well tested
Check if the code is readable and well formatted
Additional checks (document below if any)
Check if documentation update issue(s) are created if the option This change requires a documentation update above is selected

Screenshots (if appropriate):

Questions (if appropriate):

- Replace System.Data.SQLite package references with Microsoft.Data.Sqlite 8.0.0 - Update SessionFactoryProvider to use Microsoft.Data.Sqlite with NHibernate - Update ConnectionProvider and SQLiteProjectCommandExecuter to use SqliteConnection - Add SQLite native library configuration (PropertyGroups + PostBuild targets) to test and executable projects to ensure SQLite.Interop.dll is copied on Windows - Update test projects to reference Microsoft.Data.Sqlite

…brary support Microsoft.Data.Sqlite uses SQLitePCLRaw which provides e_sqlite3.dll automatically via SQLitePCLRaw.bundle_e_sqlite3. The previous SQLite.Interop.dll from System.Data.SQLite is no longer needed.

Copilot

Pull Request Overview

This PR migrates the SQLite database integration from System.Data.SQLite.Core to Microsoft.Data.Sqlite. The change modernizes the database provider and removes legacy build configurations.

Replaced System.Data.SQLite.Core package with Microsoft.Data.Sqlite and SQLitePCLRaw.bundle_e_sqlite3
Updated all SQLite connection instantiations from SQLiteConnection to SqliteConnection
Added new SessionFactoryProvider implementation for NHibernate configuration

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
OSPSuite.Starter.csproj	Updated package references and removed PostBuild SQLite.Interop.dll copy target
OSPSuite.R.Performance.csproj	Updated package references and removed PostBuild SQLite.Interop.dll copy target
OSPSuite.Infrastructure.Tests.csproj	Updated package references and removed PostBuild SQLite.Interop.dll copy target
OSPSuite.Infrastructure.Serialization.csproj	Replaced System.Data.SQLite.Core with Microsoft.Data.Sqlite
SessionFactoryProvider.cs	New implementation for NHibernate session factory configuration with Microsoft.Data.Sqlite
SQLiteProjectCommandExecuter.cs	Updated connection type from SQLiteConnection to SqliteConnection
IConnectionProvider.cs	Simplified connection string and updated to SqliteConnection

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src/OSPSuite.Infrastructure.Serialization/Services/SessionFactoryProvider.cs

Copilot · 2025-11-04T11:50:04Z

src/OSPSuite.Infrastructure.Serialization/Journal/IConnectionProvider.cs

      {
-         var connectionString = $"Data Source={databasePath};Version=3;New=True;Compress=True;foreign keys=True";
-         var cn = new SQLiteConnection(connectionString);
+         var connectionString = $"Data Source={databasePath}";


The simplified connection string removes important SQLite configuration parameters that were present in the old implementation: 'Version=3;New=True;Compress=True;foreign keys=True'. Most critically, 'foreign keys=True' enforces referential integrity constraints. Consider adding back essential parameters, particularly foreign key enforcement using: var connectionString = $\"Data Source={databasePath};Foreign Keys=True\";

Suggested change

var connectionString = $"Data Source={databasePath}";

var connectionString = $"Data Source={databasePath};Foreign Keys=True";

@Felixmil Not sure about Version and New arguments, but ForeignKeys and Compress must be set.

OK, I don't see an option for compress, only the one for foreign keys.
https://learn.microsoft.com/en-us/dotnet/standard/data/sqlite/connection-strings

Regarding compress: needs to be investigated further (maybe it's always true, or can be set later via a property...)
We should create a separate issue for this.

Created #2700

src/OSPSuite.Infrastructure.Serialization/Services/SessionFactoryProvider.cs

rwmcintosh · 2025-11-04T12:34:26Z

Changing the target branch to V13 will impact how the assemblies are delivered from PKSim.R (and since V13 MoBi.R). Not in this PR, but in the downstream ones.

Yuri05 · 2025-11-04T12:39:35Z

Changing the target branch to V13 will impact how the assemblies are delivered from PKSim.R (and since V13 MoBi.R). Not in this PR, but in the downstream ones.

Then so be it.
This is a technology switch and I think it should not be done before V13 (will require additional testing etc.)

rwmcintosh · 2025-11-04T13:18:48Z

Changing the target branch to V13 will impact how the assemblies are delivered from PKSim.R (and since V13 MoBi.R). Not in this PR, but in the downstream ones.

Then so be it. This is a technology switch and I think it should not be done before V13 (will require additional testing etc.)

Yes, I was going to make this comment that we should only consider it for V13, but also wanted to note for @Felixmil that it will require some rework before it's ready to merge all the way

…onnections - Modified ConnectionProvider, SessionFactoryProvider, and SQLiteProjectCommandExecuter to append 'Foreign Keys=True' to the connection strings.

tests/OSPSuite.Infrastructure.Tests/OSPSuite.Infrastructure.Tests.csproj

tests/OSPSuite.Starter/OSPSuite.Starter.csproj

src/OSPSuite.Infrastructure.Serialization/Services/SessionFactoryProvider.cs

tests/OSPSuite.R.Performance/OSPSuite.R.Performance.csproj

tests/OSPSuite.Infrastructure.Tests/OSPSuite.Infrastructure.Tests.csproj

msevestre

SessionFactoryProvider

@rwmcintosh
why is this removeD? this is what Nhibernate used to connect to the DB

Or is this defined in each application

msevestre · 2025-11-05T18:19:28Z

Added new SessionFactoryProvider implementation for NHibernate configuration

oh this was added with this PR lol. Ok maybe not used then

src/OSPSuite.Infrastructure.Serialization/Journal/IConnectionProvider.cs

msevestre

is probabvly not required everywhere since we are not copying anyhting using GeneratePathProperty =true but I am not sure

src/OSPSuite.Infrastructure.Serialization/Services/SQLiteProjectCommandExecuter.cs

tests/OSPSuite.Infrastructure.Tests/OSPSuite.Infrastructure.Tests.csproj

…ojectCommandExecuter

rwmcintosh · 2025-11-07T10:25:52Z

Ok @Yuri05 @msevestre @Felixmil @benjaperez1983 if all the comments are satisfied, I suggest you get familiar with the changes in PK-Sim and MoBi PR's as well. Those won't build until we get a new core build, but it's a good idea to understand the whole scope of the changes in those as well.

All the tests pass on my local builds of PK-Sim and MoBi and I can open projects normally.

@Felixmil has an updated set of dll's that he will test with OSPSuite-R (that's the last app in the line to get these updates)

Copilot

Pull Request Overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated no new comments.

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Felixmil added 4 commits November 4, 2025 09:45

Restore TargetDir/Folder

640d903

Add SQLite native library configuration for Microsoft.Data.Sqlite 8.0.0

99bceef

Add SQLitePCLRaw.bundle_e_sqlite3 for Microsoft.Data.Sqlite native li…

8986b95

…brary support Microsoft.Data.Sqlite uses SQLitePCLRaw which provides e_sqlite3.dll automatically via SQLitePCLRaw.bundle_e_sqlite3. The previous SQLite.Interop.dll from System.Data.SQLite is no longer needed.

This was referenced Nov 4, 2025

Microsoft.data.sqlite Open-Systems-Pharmacology/PK-Sim#3323

Merged

Microsoft.data.sqlite Open-Systems-Pharmacology/MoBi#2163

Merged

Yuri05 requested review from Yuri05, benjaperez1983, msevestre and rwmcintosh November 4, 2025 11:31

Yuri05 changed the base branch from develop to V13 November 4, 2025 11:38

Yuri05 requested a review from Copilot November 4, 2025 11:43

Copilot AI reviewed Nov 4, 2025

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Merge remote-tracking branch 'upstream/V13' into Microsoft.Data.Sqlite

627b35d

Felixmil mentioned this pull request Nov 4, 2025

Is Compress argument supported by Microsoft.Data.Sqlite ? #2700

Open

Update connection strings to include 'Foreign Keys=True' for SQLite c…

4458f84

…onnections - Modified ConnectionProvider, SessionFactoryProvider, and SQLiteProjectCommandExecuter to append 'Foreign Keys=True' to the connection strings.

Yuri05 reviewed Nov 4, 2025

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tests/OSPSuite.Infrastructure.Tests/OSPSuite.Infrastructure.Tests.csproj Outdated Show resolved Hide resolved

Fix spelling: InitalizeSessionFactoryFor -> InitializeSessionFactoryFor

3512952

Yuri05 reviewed Nov 4, 2025

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tests/OSPSuite.Starter/OSPSuite.Starter.csproj Outdated Show resolved Hide resolved

Remove leftovers

89c26ce

Felixmil requested a review from Yuri05 November 5, 2025 10:26

rwmcintosh reviewed Nov 5, 2025

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src/OSPSuite.Infrastructure.Serialization/Services/SessionFactoryProvider.cs Outdated Show resolved Hide resolved

rwmcintosh reviewed Nov 5, 2025

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tests/OSPSuite.R.Performance/OSPSuite.R.Performance.csproj Outdated Show resolved Hide resolved

Yuri05 reviewed Nov 5, 2025

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Felixmil and others added 3 commits November 5, 2025 17:34

Remove unnecessary reference to SQLitePCLRaw.bundle_e_sqlite3

392671c

Merge branch 'V13' into Microsoft.Data.Sqlite

4f0d93a

remove unused code

5d39464

msevestre requested changes Nov 5, 2025

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msevestre reviewed Nov 6, 2025

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msevestre reviewed Nov 6, 2025

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src/OSPSuite.Infrastructure.Serialization/Journal/IConnectionProvider.cs Outdated Show resolved Hide resolved

msevestre reviewed Nov 6, 2025

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Felixmil added 3 commits November 6, 2025 09:31

Remove comments on SQLite connection string compression

20cbd64

Remove 'Foreign Keys=True' from SQLite connection strings in SQLitePr…

f68c4e5

…ojectCommandExecuter

Remove reference to Microsoft.Data.Sqlite from test project

815c115

rwmcintosh marked this pull request as ready for review November 8, 2025 09:16

rwmcintosh requested review from Yuri05 and msevestre November 8, 2025 09:16

rwmcintosh approved these changes Nov 8, 2025

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Yuri05 requested a review from Copilot November 8, 2025 19:46

Copilot AI reviewed Nov 8, 2025

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Yuri05 approved these changes Nov 8, 2025

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msevestre merged commit c8fbbd0 into Open-Systems-Pharmacology:V13 Nov 10, 2025
7 checks passed

rwmcintosh linked an issue Nov 10, 2025 that may be closed by this pull request

Migrate from System.Data.SQLite to Microsoft.Data.Sqlite #2701

Closed

rwmcintosh added this to v13 Nov 10, 2025

rwmcintosh moved this to Done in v13 Nov 10, 2025

Yuri05 moved this from Done to Verified in v13 Mar 10, 2026

	var connectionString = $"Data Source={databasePath}";
	var connectionString = $"Data Source={databasePath};Foreign Keys=True";

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Felixmil commented Nov 4, 2025 •

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