fix: use BEGIN IMMEDIATE to prevent SQLite deadlocks

crates/goose/src/session/session_manager.rs

@@ -665,7 +665,7 @@ impl SessionStorage {
     }
 
     async fn import_legacy_session(pool: &Pool<Sqlite>, session: &Session) -> Result<()> {
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
 
         let recipe_json = match &session.recipe {
             Some(recipe) => Some(serde_json::to_string(recipe)?),
@@ -724,7 +724,7 @@ impl SessionStorage {
     }
 
     async fn run_migrations(pool: &Pool<Sqlite>) -> Result<()> {
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
 
         let current_version = Self::get_schema_version(&mut tx).await?;
 
@@ -899,7 +899,7 @@ impl SessionStorage {
         session_type: SessionType,
     ) -> Result<Session> {
         let pool = self.pool().await?;
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
 
         let today = chrono::Utc::now().format("%Y%m%d").to_string();
         let session = sqlx::query_as(
@@ -1071,7 +1071,7 @@ impl SessionStorage {
         }
 
         let pool = self.pool().await?;
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
         q = q.bind(&builder.session_id);
         q.execute(&mut *tx).await?;
 
@@ -1116,7 +1116,7 @@ impl SessionStorage {
 
     async fn add_message(&self, session_id: &str, message: &Message) -> Result<()> {
         let pool = self.pool().await?;
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
 
         let metadata_json = serde_json::to_string(&message.metadata)?;
 
@@ -1154,7 +1154,7 @@ impl SessionStorage {
         session_id: &str,
         conversation: &Conversation,
     ) -> Result<()> {
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
 
         sqlx::query("DELETE FROM messages WHERE session_id = ?")
             .bind(session_id)
@@ -1237,7 +1237,7 @@ impl SessionStorage {
 
     async fn delete_session(&self, session_id: &str) -> Result<()> {
         let pool = self.pool().await?;
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
 
         let exists =
             sqlx::query_scalar::<_, bool>("SELECT EXISTS(SELECT 1 FROM sessions WHERE id = ?)")
@@ -1416,7 +1416,7 @@ impl SessionStorage {
         ) -> crate::conversation::message::MessageMetadata,
     {
         let pool = self.pool().await?;
-        let mut tx = pool.begin().await?;
+        let mut tx = pool.begin_with("BEGIN IMMEDIATE").await?;
 
         let current_metadata_json = sqlx::query_scalar::<_, String>(
             "SELECT metadata_json FROM messages WHERE message_id = ? AND session_id = ?",
@@ -1455,6 +1455,97 @@ mod tests {
 
     const NUM_CONCURRENT_SESSIONS: i32 = 10;
 
+    async fn run_lock_upgrade_attempt(
+        pool: Pool<Sqlite>,
+        session_id: String,
+        begin_statement: &'static str,
+        worker_id: i32,
+        barrier: Option<Arc<tokio::sync::Barrier>>,
+    ) -> anyhow::Result<()> {
+        let mut tx = pool.begin_with(begin_statement).await?;
+
+        sqlx::query_scalar::<_, i64>("SELECT COUNT(*) FROM sessions WHERE id = ?")
+            .bind(&session_id)
+            .fetch_one(&mut *tx)
+            .await?;
+
+        if let Some(barrier) = barrier {
+            barrier.wait().await;
+        }
+
+        sqlx::query("UPDATE sessions SET total_tokens = ? WHERE id = ?")
+            .bind(worker_id)
+            .bind(&session_id)
+            .execute(&mut *tx)
+            .await?;
+
+        tx.commit().await?;
+        Ok(())
+    }
+
+    async fn run_lock_upgrade_race(
+        pool: Pool<Sqlite>,
+        session_id: String,
+        begin_statement: &'static str,
+        use_barrier: bool,
+    ) -> Vec<anyhow::Result<()>> {
+        let barrier = if use_barrier {
+            Some(Arc::new(tokio::sync::Barrier::new(2)))
+        } else {
+            None
+        };
+        let mut handles = Vec::new();
+
+        for worker_id in 0..2 {
+            let pool = pool.clone();
+            let session_id = session_id.clone();
+            let barrier = barrier.clone();
+            handles.push(tokio::spawn(async move {
+                run_lock_upgrade_attempt(pool, session_id, begin_statement, worker_id, barrier)
+                    .await
+            }));
+        }
+
+        let mut results = Vec::new();
+        for handle in handles {
+            results.push(handle.await.expect("lock-upgrade task panicked"));
+        }
+        results
+    }
+
+    #[tokio::test]
+    async fn test_begin_immediate_prevents_lock_upgrade_deadlock() {
+        let temp_dir = TempDir::new().unwrap();
+        let session_manager = SessionManager::new(temp_dir.path().to_path_buf());
+
+        let session = session_manager
+            .create_session(
+                PathBuf::from("/tmp/lock-upgrade-test"),
+                "Lock Upgrade Session".to_string(),
+                SessionType::User,
+            )
+            .await
+            .unwrap();
+
+        let pool = session_manager.storage().pool.clone();
+
+        let results = run_lock_upgrade_race(pool.clone(), session.id.clone(), "BEGIN", true).await;
+        assert!(
+            results.iter().any(Result::is_err),
+            "BEGIN (DEFERRED) should cause SQLITE_BUSY when two tasks try to upgrade SHARED → RESERVED"
+        );
+
+        let results = run_lock_upgrade_race(pool, session.id, "BEGIN IMMEDIATE", false).await;
+        assert!(
+            results.iter().all(Result::is_ok),
+            "BEGIN IMMEDIATE should serialize contention without SQLITE_BUSY: {:?}",
+            results
+                .iter()
+                .filter_map(|r| r.as_ref().err().map(ToString::to_string))
+                .collect::<Vec<_>>()
+        );
+    }
+
     #[tokio::test]
     async fn test_concurrent_session_creation() {
         let temp_dir = TempDir::new().unwrap();