fix(sqlite): add retry logic to transaction entry points (GH#1272)
Update withTx to use BEGIN IMMEDIATE with exponential backoff retry on SQLITE_BUSY errors. This prevents "database is locked" failures during concurrent operations (daemon + CLI, multi-agent workflows). Changes: - withTx now uses beginImmediateWithRetry (same pattern as RunInTransaction) - Add dbExecutor interface for helper functions that work with both *sql.Tx and *sql.Conn - Update all withTx callers to use *sql.Conn - Refactor DeleteIssue to use withTx (fixes the specific error in auto-import) - Update markIssuesDirtyTx to accept dbExecutor interface Affected paths: - MarkIssuesDirty, ClearDirtyIssuesByID (dirty.go) - AddDependency, RemoveDependency (dependencies.go) - executeLabelOperation (labels.go) - AddComment (events.go) - ApplyCompaction (compact.go) - DeleteIssue (queries.go) Note: Some direct BeginTx calls in queries.go (CloseIssue, UpdateIssue, ReopenIssue, DeleteIssues) still use the old pattern and could be refactored in a follow-up. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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ruby
@@ -1407,82 +1407,73 @@ func (s *SQLiteStorage) CreateTombstone(ctx context.Context, id string, actor st
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// DeleteIssue permanently removes an issue from the database
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func (s *SQLiteStorage) DeleteIssue(ctx context.Context, id string) error {
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tx, err := s.db.BeginTx(ctx, nil)
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if err != nil {
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return fmt.Errorf("failed to begin transaction: %w", err)
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}
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defer func() { _ = tx.Rollback() }()
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// Mark issues that depend on this one as dirty so they get re-exported
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// without the stale dependency reference (fixes orphan deps in JSONL)
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rows, err := tx.QueryContext(ctx, `SELECT issue_id FROM dependencies WHERE depends_on_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to query dependent issues: %w", err)
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}
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var dependentIDs []string
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for rows.Next() {
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var depID string
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if err := rows.Scan(&depID); err != nil {
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_ = rows.Close()
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return fmt.Errorf("failed to scan dependent issue ID: %w", err)
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return s.withTx(ctx, func(conn *sql.Conn) error {
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// Mark issues that depend on this one as dirty so they get re-exported
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// without the stale dependency reference (fixes orphan deps in JSONL)
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rows, err := conn.QueryContext(ctx, `SELECT issue_id FROM dependencies WHERE depends_on_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to query dependent issues: %w", err)
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}
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dependentIDs = append(dependentIDs, depID)
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}
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_ = rows.Close()
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if err := rows.Err(); err != nil {
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return fmt.Errorf("failed to iterate dependent issues: %w", err)
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}
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if len(dependentIDs) > 0 {
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if err := markIssuesDirtyTx(ctx, tx, dependentIDs); err != nil {
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return fmt.Errorf("failed to mark dependent issues dirty: %w", err)
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var dependentIDs []string
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for rows.Next() {
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var depID string
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if err := rows.Scan(&depID); err != nil {
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_ = rows.Close()
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return fmt.Errorf("failed to scan dependent issue ID: %w", err)
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}
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dependentIDs = append(dependentIDs, depID)
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}
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_ = rows.Close()
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if err := rows.Err(); err != nil {
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return fmt.Errorf("failed to iterate dependent issues: %w", err)
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}
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}
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// Delete dependencies (both directions)
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_, err = tx.ExecContext(ctx, `DELETE FROM dependencies WHERE issue_id = ? OR depends_on_id = ?`, id, id)
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if err != nil {
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return fmt.Errorf("failed to delete dependencies: %w", err)
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}
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if len(dependentIDs) > 0 {
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if err := markIssuesDirtyTx(ctx, conn, dependentIDs); err != nil {
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return fmt.Errorf("failed to mark dependent issues dirty: %w", err)
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}
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}
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// Delete events
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_, err = tx.ExecContext(ctx, `DELETE FROM events WHERE issue_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete events: %w", err)
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}
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// Delete dependencies (both directions)
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_, err = conn.ExecContext(ctx, `DELETE FROM dependencies WHERE issue_id = ? OR depends_on_id = ?`, id, id)
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if err != nil {
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return fmt.Errorf("failed to delete dependencies: %w", err)
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}
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// Delete comments (no FK cascade on this table)
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_, err = tx.ExecContext(ctx, `DELETE FROM comments WHERE issue_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete comments: %w", err)
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}
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// Delete events
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_, err = conn.ExecContext(ctx, `DELETE FROM events WHERE issue_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete events: %w", err)
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}
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// Delete from dirty_issues
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_, err = tx.ExecContext(ctx, `DELETE FROM dirty_issues WHERE issue_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete dirty marker: %w", err)
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}
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// Delete comments (no FK cascade on this table)
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_, err = conn.ExecContext(ctx, `DELETE FROM comments WHERE issue_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete comments: %w", err)
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}
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// Delete the issue itself
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result, err := tx.ExecContext(ctx, `DELETE FROM issues WHERE id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete issue: %w", err)
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}
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// Delete from dirty_issues
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_, err = conn.ExecContext(ctx, `DELETE FROM dirty_issues WHERE issue_id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete dirty marker: %w", err)
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}
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rowsAffected, err := result.RowsAffected()
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if err != nil {
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return fmt.Errorf("failed to check rows affected: %w", err)
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}
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if rowsAffected == 0 {
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return fmt.Errorf("issue not found: %s", id)
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}
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// Delete the issue itself
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result, err := conn.ExecContext(ctx, `DELETE FROM issues WHERE id = ?`, id)
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if err != nil {
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return fmt.Errorf("failed to delete issue: %w", err)
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}
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if err := tx.Commit(); err != nil {
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return wrapDBError("commit delete transaction", err)
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}
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rowsAffected, err := result.RowsAffected()
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if err != nil {
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return fmt.Errorf("failed to check rows affected: %w", err)
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}
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if rowsAffected == 0 {
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return fmt.Errorf("issue not found: %s", id)
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}
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// REMOVED: Counter sync after deletion - no longer needed with hash IDs
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return nil
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return nil
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})
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}
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// DeleteIssuesResult contains statistics about a batch deletion operation
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