feat(doctor): add database corruption recovery to --fix
Adds automatic database recovery when bd doctor --fix detects corruption: - Detects SQLite corruption (malformed database, SQLITE_CORRUPT errors) - Backs up corrupted database before recovery attempt - Rebuilds from JSONL if available (issues.jsonl, deletions.jsonl) - Falls back to fresh database if JSONL unavailable - Reports recovery results (issues imported, success/failure) Recovery is triggered automatically by --fix when corruption is detected. No manual intervention required.
This commit is contained in:
Ryan Snodgrass
@@ -246,11 +246,28 @@ func CheckDatabaseIntegrity(path string) DoctorCheck {
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// Open database in read-only mode for integrity check
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db, err := sql.Open("sqlite3", "file:"+dbPath+"?mode=ro&_pragma=busy_timeout(30000)")
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if err != nil {
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// Check if JSONL recovery is possible
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jsonlCount, _, jsonlErr := CountJSONLIssues(filepath.Join(beadsDir, "issues.jsonl"))
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if jsonlErr != nil {
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jsonlCount, _, jsonlErr = CountJSONLIssues(filepath.Join(beadsDir, "beads.jsonl"))
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}
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if jsonlErr == nil && jsonlCount > 0 {
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return DoctorCheck{
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Name: "Database Integrity",
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Status: StatusError,
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Message: fmt.Sprintf("Failed to open database (JSONL has %d issues for recovery)", jsonlCount),
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Detail: err.Error(),
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Fix: "Run 'bd doctor --fix' to recover from JSONL backup",
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}
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}
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return DoctorCheck{
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Name: "Database Integrity",
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Status: StatusError,
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Message: "Failed to open database for integrity check",
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Detail: err.Error(),
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Fix: "Database may be corrupted. Restore JSONL from git history, then run 'bd doctor --fix'",
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}
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}
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defer db.Close()
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@@ -259,11 +276,28 @@ func CheckDatabaseIntegrity(path string) DoctorCheck {
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// This checks the entire database for corruption
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rows, err := db.Query("PRAGMA integrity_check")
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if err != nil {
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// Check if JSONL recovery is possible
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jsonlCount, _, jsonlErr := CountJSONLIssues(filepath.Join(beadsDir, "issues.jsonl"))
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if jsonlErr != nil {
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jsonlCount, _, jsonlErr = CountJSONLIssues(filepath.Join(beadsDir, "beads.jsonl"))
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}
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if jsonlErr == nil && jsonlCount > 0 {
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return DoctorCheck{
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Name: "Database Integrity",
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Status: StatusError,
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Message: fmt.Sprintf("Failed to run integrity check (JSONL has %d issues for recovery)", jsonlCount),
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Detail: err.Error(),
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Fix: "Run 'bd doctor --fix' to recover from JSONL backup",
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}
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}
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return DoctorCheck{
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Name: "Database Integrity",
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Status: StatusError,
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Message: "Failed to run integrity check",
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Detail: err.Error(),
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Fix: "Database may be corrupted. Restore JSONL from git history, then run 'bd doctor --fix'",
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}
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}
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defer rows.Close()
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@@ -286,13 +320,29 @@ func CheckDatabaseIntegrity(path string) DoctorCheck {
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}
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}
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// Any other result indicates corruption
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// Any other result indicates corruption - check if JSONL recovery is possible
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jsonlCount, _, jsonlErr := CountJSONLIssues(filepath.Join(beadsDir, "issues.jsonl"))
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if jsonlErr != nil {
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// Try alternate name
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jsonlCount, _, jsonlErr = CountJSONLIssues(filepath.Join(beadsDir, "beads.jsonl"))
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}
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if jsonlErr == nil && jsonlCount > 0 {
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return DoctorCheck{
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Name: "Database Integrity",
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Status: StatusError,
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Message: fmt.Sprintf("Database corruption detected (JSONL has %d issues for recovery)", jsonlCount),
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Detail: strings.Join(results, "; "),
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Fix: "Run 'bd doctor --fix' to recover from JSONL backup",
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}
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}
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return DoctorCheck{
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Name: "Database Integrity",
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Status: StatusError,
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Message: "Database corruption detected",
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Detail: strings.Join(results, "; "),
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Fix: "Database may need recovery. Export with 'bd export' if possible, then restore from backup or reinitialize",
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Fix: "Database may need recovery. Restore JSONL from git history, then run 'bd doctor --fix'",
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}
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}
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@@ -620,3 +670,92 @@ func isNoDbModeConfigured(beadsDir string) bool {
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return cfg.NoDb
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}
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// CheckDatabaseSize warns when the database has accumulated many closed issues.
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// This is purely informational - pruning is NEVER auto-fixed because it
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// permanently deletes data. Users must explicitly run 'bd cleanup' to prune.
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//
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// Config: doctor.suggest_pruning_issue_count (default: 5000, 0 = disabled)
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//
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// DESIGN NOTE: This check intentionally has NO auto-fix. Unlike other doctor
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// checks that fix configuration or sync issues, pruning is destructive and
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// irreversible. The user must make an explicit decision to delete their
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// closed issue history. We only provide guidance, never action.
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func CheckDatabaseSize(path string) DoctorCheck {
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beadsDir := filepath.Join(path, ".beads")
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// Get database path
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var dbPath string
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if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
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dbPath = cfg.DatabasePath(beadsDir)
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} else {
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dbPath = filepath.Join(beadsDir, beads.CanonicalDatabaseName)
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}
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// If no database, skip this check
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if _, err := os.Stat(dbPath); os.IsNotExist(err) {
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return DoctorCheck{
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Name: "Large Database",
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Status: StatusOK,
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Message: "N/A (no database)",
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}
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}
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// Read threshold from config (default 5000, 0 = disabled)
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threshold := 5000
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db, err := sql.Open("sqlite3", "file:"+dbPath+"?mode=ro&_pragma=busy_timeout(30000)")
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if err != nil {
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return DoctorCheck{
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Name: "Large Database",
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Status: StatusOK,
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Message: "N/A (unable to open database)",
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}
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}
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defer db.Close()
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// Check for custom threshold in config table
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var thresholdStr string
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err = db.QueryRow("SELECT value FROM config WHERE key = ?", "doctor.suggest_pruning_issue_count").Scan(&thresholdStr)
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if err == nil {
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if _, err := fmt.Sscanf(thresholdStr, "%d", &threshold); err != nil {
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threshold = 5000 // Reset to default on parse error
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}
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}
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// If disabled, return OK
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if threshold == 0 {
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return DoctorCheck{
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Name: "Large Database",
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Status: StatusOK,
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Message: "Check disabled (threshold = 0)",
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}
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}
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// Count closed issues
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var closedCount int
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err = db.QueryRow("SELECT COUNT(*) FROM issues WHERE status = 'closed'").Scan(&closedCount)
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if err != nil {
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return DoctorCheck{
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Name: "Large Database",
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Status: StatusOK,
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Message: "N/A (unable to count issues)",
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}
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}
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// Check against threshold
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if closedCount > threshold {
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return DoctorCheck{
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Name: "Large Database",
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Status: StatusWarning,
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Message: fmt.Sprintf("%d closed issues (threshold: %d)", closedCount, threshold),
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Detail: "Large number of closed issues may impact performance",
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Fix: "Consider running 'bd cleanup --older-than 90' to prune old closed issues",
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}
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}
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return DoctorCheck{
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Name: "Large Database",
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Status: StatusOK,
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Message: fmt.Sprintf("%d closed issues (threshold: %d)", closedCount, threshold),
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}
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}
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