Fix nested read migration transactions

changelog.d/unreleased/2607.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 2607
+affected:
+  - src/CodeIndex/Database/DbContext.cs
+  - tests/CodeIndex.Tests/DatabaseTests.cs
+---
+
+## English
+
+- **Schema read migrations now respect existing SQLite transactions (#2607)** — `TryMigrateForRead` no longer starts a nested transaction when it is invoked inside an already-active SQLite transaction, avoiding intermittent `cannot start a transaction within a transaction` failures in concurrent freshness snapshot reads.
+
+## 日本語
+
+- **読み取り用 schema migration が既存の SQLite transaction を尊重するようになりました (#2607)** — `TryMigrateForRead` は既存の SQLite transaction 内で呼ばれた場合に nested transaction を開始しなくなり、concurrent freshness snapshot 読み取りで断続的に発生していた `cannot start a transaction within a transaction` 失敗を回避します。

src/CodeIndex/Database/DbContext.cs

@@ -1686,11 +1686,23 @@ public void TryMigrateForRead()
         try
         {
             EnsureForeignKeysEnabled();
-            SqliteTransaction transaction;
+            SqliteTransaction? transaction;
             try
             {
                 transaction = _connection.BeginTransaction(deferred: false);
             }
+            catch (SqliteException ex) when (IsNestedTransactionError(ex))
+            {
+                if (RunReadMigrationSteps())
+                    EnsureForeignKeysEnabled();
+                return;
+            }
+            catch (InvalidOperationException ex) when (IsNestedTransactionError(ex))
+            {
+                if (RunReadMigrationSteps())
+                    EnsureForeignKeysEnabled();
+                return;
+            }
             catch (SqliteException ex) when (IsReadOnlyOpenError(ex))
             {
                 RecordMigrationFailure("BEGIN IMMEDIATE schema migration", ex);
@@ -1699,43 +1711,13 @@ public void TryMigrateForRead()
 
             using (transaction)
             {
-            _activeMigrationTransaction = transaction;
-
-            try
-            {
-                foreach (var (description, action) in BuildReadMigrationSteps())
-                {
-                    try
-                    {
-                        action();
-                    }
-                    catch (SqliteException ex)
-                    {
-                        RecordMigrationFailure(description, ex);
-
-                        // Read-only DB / filesystem / sandbox — stop further steps and degrade.
-                        // Catches SQLITE_READONLY (8), SQLITE_IOERR (10), and SQLITE_CANTOPEN (14):
-                        // some restricted environments report CANTOPEN when SQLite tries to create
-                        // -journal side files for the DDL. DbReader.LoadColumns() / table-detection
-                        // will drive the degraded read path; later read queries that hit a still-
-                        // missing column will now have a single clear preceding diagnostic to refer to.
-                        // 読み取り専用 DB・FS・サンドボックスでの DDL 失敗は縮退扱いで打ち切る。
-                        if (IsReadOnlyOpenError(ex)) return;
-
-                        // Other SQLite errors (e.g. corruption, full disk) are not opportunistic-
-                        // migration concerns — preserve the existing surface-the-exception behavior.
-                        // それ以外の SQLite エラーは従来通り上位に伝播させる。
-                        throw;
-                    }
-                }
-
+                _activeMigrationTransaction = transaction;
+                if (!RunReadMigrationSteps())
+                    return;
                 transaction.Commit();
             }
-            finally
-            {
-                _activeMigrationTransaction = null;
-            }
-            }
+
+            _activeMigrationTransaction = null;
 
             EnsureForeignKeysEnabled();
         }
@@ -1748,6 +1730,51 @@ public void TryMigrateForRead()
         }
     }
 
+    private bool RunReadMigrationSteps()
+    {
+        try
+        {
+            foreach (var (description, action) in BuildReadMigrationSteps())
+            {
+                try
+                {
+                    action();
+                }
+                catch (SqliteException ex)
+                {
+                    RecordMigrationFailure(description, ex);
+
+                    // Read-only DB / filesystem / sandbox — stop further steps and degrade.
+                    // Catches SQLITE_READONLY (8), SQLITE_IOERR (10), and SQLITE_CANTOPEN (14):
+                    // some restricted environments report CANTOPEN when SQLite tries to create
+                    // -journal side files for the DDL. DbReader.LoadColumns() / table-detection
+                    // will drive the degraded read path; later read queries that hit a still-
+                    // missing column will now have a single clear preceding diagnostic to refer to.
+                    // 読み取り専用 DB・FS・サンドボックスでの DDL 失敗は縮退扱いで打ち切る。
+                    if (IsReadOnlyOpenError(ex)) return false;
+
+                    // Other SQLite errors (e.g. corruption, full disk) are not opportunistic-
+                    // migration concerns — preserve the existing surface-the-exception behavior.
+                    // それ以外の SQLite エラーは従来通り上位に伝播させる。
+                    throw;
+                }
+            }
+
+            return true;
+        }
+        finally
+        {
+            _activeMigrationTransaction = null;
+        }
+    }
+
+    private static bool IsNestedTransactionError(SqliteException exception) =>
+        exception.SqliteErrorCode == 1 &&
+        exception.Message.Contains("cannot start a transaction within a transaction", StringComparison.OrdinalIgnoreCase);
+
+    private static bool IsNestedTransactionError(InvalidOperationException exception) =>
+        exception.Message.Contains("does not support nested transactions", StringComparison.OrdinalIgnoreCase);
+
     private void RecordMigrationFailure(string description, SqliteException exception)
     {
         var failure = new DbMigrationFailure(

tests/CodeIndex.Tests/DatabaseTests.cs

@@ -486,6 +486,78 @@ public void Constructor_WritableOpenRejectsNewerUserVersion()
         }
     }
 
+    [Fact]
+    public void TryMigrateForRead_InsideExistingTransaction_DoesNotStartNestedTransaction()
+    {
+        var dbPath = Path.Combine(Path.GetTempPath(), $"codeindex_nested_migration_test_{Guid.NewGuid():N}.db");
+        try
+        {
+            using (var connection = new SqliteConnection(new SqliteConnectionStringBuilder { DataSource = dbPath }.ConnectionString))
+            {
+                connection.Open();
+                using var cmd = connection.CreateCommand();
+                cmd.CommandText = """
+                    CREATE TABLE files (
+                        id INTEGER PRIMARY KEY AUTOINCREMENT,
+                        path TEXT NOT NULL UNIQUE
+                    );
+                    CREATE TABLE symbols (
+                        id INTEGER PRIMARY KEY AUTOINCREMENT,
+                        file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+                        kind TEXT,
+                        name TEXT,
+                        line INTEGER
+                    );
+                    CREATE TABLE symbol_references (
+                        id INTEGER PRIMARY KEY AUTOINCREMENT,
+                        file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+                        symbol_name TEXT,
+                        reference_kind TEXT,
+                        line INTEGER,
+                        column_number INTEGER,
+                        context TEXT,
+                        container_kind TEXT,
+                        container_name TEXT
+                    );
+                    """;
+                cmd.ExecuteNonQuery();
+            }
+
+            using var db = new DbContext(dbPath);
+            using var transaction = db.Connection.BeginTransaction(deferred: true);
+
+            db.TryMigrateForRead();
+
+            using var check = db.Connection.CreateCommand();
+            check.Transaction = transaction;
+            check.CommandText = "SELECT COUNT(*) FROM pragma_table_info('symbols') WHERE name = 'signature'";
+            Assert.Equal(1L, (long)check.ExecuteScalar()!);
+
+            transaction.Rollback();
+        }
+        finally
+        {
+            SqliteConnection.ClearAllPools();
+            if (File.Exists(dbPath))
+            {
+                try
+                {
+                    File.Delete(dbPath);
+                }
+                catch (IOException) when (OperatingSystem.IsWindows())
+                {
+                    SqliteConnection.ClearAllPools();
+                    File.Delete(dbPath);
+                }
+                catch (UnauthorizedAccessException) when (OperatingSystem.IsWindows())
+                {
+                    SqliteConnection.ClearAllPools();
+                    File.Delete(dbPath);
+                }
+            }
+        }
+    }
+
     [Fact]
     public void TryMigrateForRead_EnforcesForeignKeysAfterAddingReferenceLineColumn()
     {