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Merge pull request #576 from SiaFoundation/nate/integrity-check
Add SQLite integrity check command
2 parents deb74a2 + ac5e97e commit 9e3e816

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4 files changed

+97
-33
lines changed

4 files changed

+97
-33
lines changed

‎.changeset/added_sqlite_integrity_command.md

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@@ -0,0 +1,5 @@
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---
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default: patch
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---
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# Added "sqlite integrity" command

‎cmd/hostd/main.go

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@@ -225,6 +225,13 @@ Perform various operations on the SQLite3 database.
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Commands:
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backup Create a backup of the SQLite3 database
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integrity Check the integrity of the SQLite3 database
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`
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sqlite3IntegrityUsage = `Usage:
232+
hostd sqlite3 integrity <srcPath>
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Check the integrity of the SQLite3 database at the specified path. This is not safe to run while the host is running.
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`
229236

230237
sqlite3BackupUsage = `Usage:
@@ -256,6 +263,10 @@ func runBackupCommand(srcPath, destPath string) error {
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return nil
257264
}
258265

266+
func runIntegrityCommand(ctx context.Context, srcPath string, log *zap.Logger) error {
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return sqlite.IntegrityCheck(ctx, srcPath, log)
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}
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func runRecalcCommand(srcPath string, log *zap.Logger) error {
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db, err := sqlite.OpenDatabase(srcPath, log)
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if err != nil {
@@ -313,6 +324,7 @@ func main() {
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recalculateCmd := flagg.New("recalculate", recalculateUsage)
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sqlite3Cmd := flagg.New("sqlite3", sqlite3Usage)
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sqlite3BackupCmd := flagg.New("backup", sqlite3BackupUsage)
327+
sqlite3IntegrityCmd := flagg.New("integrity", sqlite3IntegrityUsage)
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cmd := flagg.Parse(flagg.Tree{
318330
Cmd: rootCmd,
@@ -324,6 +336,7 @@ func main() {
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{
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Cmd: sqlite3Cmd,
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Sub: []flagg.Tree{
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{Cmd: sqlite3IntegrityCmd},
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{Cmd: sqlite3BackupCmd},
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},
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},
@@ -368,6 +381,25 @@ func main() {
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checkFatalError("command failed", runRecalcCommand(cmd.Arg(0), log))
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case sqlite3Cmd:
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cmd.Usage()
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case sqlite3IntegrityCmd:
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if len(cmd.Args()) != 1 {
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cmd.Usage()
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return
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}
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log := initStdoutLog(cfg.Log.StdOut.EnableANSI, "info")
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defer log.Sync()
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ctx, cancel := signal.NotifyContext(context.Background(), os.Interrupt, syscall.SIGTERM)
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defer cancel()
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log.Info("running integrity check")
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checkFatalError("integrity check failed", runIntegrityCommand(ctx, cmd.Arg(0), log))
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log.Info("integrity check passed")
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log.Info("running foreign key check")
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checkFatalError("foreign key check failed", sqlite.ForeignKeyCheck(ctx, cmd.Arg(0), log))
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log.Info("foreign key check passed")
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case sqlite3BackupCmd:
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if len(cmd.Args()) != 2 {
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cmd.Usage()

‎persist/sqlite/init.go

Lines changed: 30 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,9 @@
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package sqlite
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33
import (
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"database/sql"
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_ "embed" // for init.sql
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"errors"
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"time"
68

79
"fmt"
@@ -41,7 +43,7 @@ func (s *Store) upgradeDatabase(current, target int64) error {
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return fmt.Errorf("failed to enable foreign key deferral: %w", err)
4244
} else if err := fn(tx, log); err != nil {
4345
return err
44-
} else if err := foreignKeyCheck(tx, log); err != nil {
46+
} else if err := checkFKConsistency(tx, log); err != nil {
4547
return fmt.Errorf("failed foreign key check: %w", err)
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}
4749
return setDBVersion(tx, version)
@@ -75,6 +77,33 @@ func (s *Store) init() error {
7577
return nil
7678
}
7779

80+
func checkFKConsistency(txn *txn, log *zap.Logger) error {
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rows, err := txn.Query("PRAGMA foreign_key_check")
82+
if err != nil {
83+
return fmt.Errorf("failed to run foreign key check: %w", err)
84+
}
85+
defer rows.Close()
86+
var hasErrors bool
87+
for rows.Next() {
88+
var table string
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var rowid sql.NullInt64
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var fkTable string
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var fkRowid sql.NullInt64
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93+
if err := rows.Scan(&table, &rowid, &fkTable, &fkRowid); err != nil {
94+
return fmt.Errorf("failed to scan foreign key check result: %w", err)
95+
}
96+
hasErrors = true
97+
log.Error("foreign key constraint violated", zap.String("table", table), zap.Int64("rowid", rowid.Int64), zap.String("fkTable", fkTable), zap.Int64("fkRowid", fkRowid.Int64))
98+
}
99+
if err := rows.Err(); err != nil {
100+
return fmt.Errorf("failed to iterate foreign key check results: %w", err)
101+
} else if hasErrors {
102+
return errors.New("foreign key constraint violated")
103+
}
104+
return nil
105+
}
106+
78107
func generateHostKey(tx *txn) (err error) {
79108
key := types.NewPrivateKeyFromSeed(frand.Bytes(32))
80109
var dbID int64

‎persist/sqlite/store.go

Lines changed: 30 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -234,14 +234,28 @@ func Backup(ctx context.Context, srcPath, destPath string) (err error) {
234234
return backupDB(ctx, src, destPath)
235235
}
236236

237-
func integrityCheck(db *sql.DB, log *zap.Logger) error {
238-
rows, err := db.Query("PRAGMA integrity_check")
237+
// IntegrityCheck runs a PRAGMA integrity_check on the database and logs any
238+
// integrity errors. If any errors are found, an error is returned.
239+
func IntegrityCheck(ctx context.Context, fp string, log *zap.Logger) error {
240+
db, err := sql.Open("sqlite3", sqliteFilepath(fp))
241+
if err != nil {
242+
return fmt.Errorf("failed to open database: %w", err)
243+
}
244+
defer db.Close()
245+
246+
rows, err := db.QueryContext(ctx, "PRAGMA integrity_check")
239247
if err != nil {
240248
return fmt.Errorf("failed to run integrity check: %w", err)
241249
}
242250
defer rows.Close()
243251
var hasErrors bool
244252
for rows.Next() {
253+
select {
254+
case <-ctx.Done():
255+
return ctx.Err()
256+
default:
257+
}
258+
245259
var result string
246260
if err := rows.Scan(&result); err != nil {
247261
return fmt.Errorf("failed to scan integrity check result: %w", err)
@@ -258,41 +272,29 @@ func integrityCheck(db *sql.DB, log *zap.Logger) error {
258272
return nil
259273
}
260274

261-
func dbForeignKeyCheck(db *sql.DB, log *zap.Logger) error {
262-
rows, err := db.Query("PRAGMA foreign_key_check")
275+
// ForeignKeyCheck runs a PRAGMA foreign_key_check on the database and logs any
276+
// foreign key constraint violations. If any violations are found, an error is
277+
// returned.
278+
func ForeignKeyCheck(ctx context.Context, fp string, log *zap.Logger) error {
279+
db, err := sql.Open("sqlite3", sqliteFilepath(fp))
263280
if err != nil {
264-
return fmt.Errorf("failed to run foreign key check: %w", err)
281+
return fmt.Errorf("failed to open database: %w", err)
265282
}
266-
defer rows.Close()
267-
var hasErrors bool
268-
for rows.Next() {
269-
var table string
270-
var rowid sql.NullInt64
271-
var fkTable string
272-
var fkRowid sql.NullInt64
283+
defer db.Close()
273284

274-
if err := rows.Scan(&table, &rowid, &fkTable, &fkRowid); err != nil {
275-
return fmt.Errorf("failed to scan foreign key check result: %w", err)
276-
}
277-
hasErrors = true
278-
log.Error("foreign key constraint violated", zap.String("table", table), zap.Int64("rowid", rowid.Int64), zap.String("fkTable", fkTable), zap.Int64("fkRowid", fkRowid.Int64))
279-
}
280-
if err := rows.Err(); err != nil {
281-
return fmt.Errorf("failed to iterate foreign key check results: %w", err)
282-
} else if hasErrors {
283-
return errors.New("foreign key constraint violated")
284-
}
285-
return nil
286-
}
287-
288-
func foreignKeyCheck(txn *txn, log *zap.Logger) error {
289-
rows, err := txn.Query("PRAGMA foreign_key_check")
285+
rows, err := db.QueryContext(ctx, "PRAGMA foreign_key_check")
290286
if err != nil {
291287
return fmt.Errorf("failed to run foreign key check: %w", err)
292288
}
293289
defer rows.Close()
294290
var hasErrors bool
295291
for rows.Next() {
292+
select {
293+
case <-ctx.Done():
294+
return ctx.Err()
295+
default:
296+
}
297+
296298
var table string
297299
var rowid sql.NullInt64
298300
var fkTable string
@@ -325,10 +327,6 @@ func OpenDatabase(fp string, log *zap.Logger) (*Store, error) {
325327
}
326328
if err := store.init(); err != nil {
327329
return nil, err
328-
} else if err := dbForeignKeyCheck(db, log.Named("foreignkeys")); err != nil {
329-
return nil, fmt.Errorf("foreign key check failed: %w", err)
330-
} else if err := integrityCheck(db, log.Named("integrity")); err != nil {
331-
return nil, fmt.Errorf("integrity check failed: %w", err)
332330
}
333331
sqliteVersion, _, _ := sqlite3.Version()
334332
log.Debug("database initialized", zap.String("sqliteVersion", sqliteVersion), zap.Int("schemaVersion", len(migrations)+1), zap.String("path", fp))

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