sqlite-fts5-corruption-rebuild

Testing & Quality

Fix SQLite "database disk image is malformed" errors caused by corrupted FTS5 indexes. Use when: (1) UPDATE/INSERT fails with "stepping, database disk image is malformed" but PRAGMA integrity_check returns "ok", (2) Only specific records fail to update while others succeed, (3) Records contain dirty text with tabs, newlines, or unusual characters that were inserted into FTS5-indexed columns. The misleading error message suggests disk corruption, but the actual issue is FTS5 index corruption from malformed text content.

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SQLite FTS5 Index Corruption from Dirty Data

Problem

SQLite returns "database disk image is malformed" (error code 11) when trying to UPDATE or INSERT records, even though PRAGMA integrity_check reports the database as "ok". The error only affects specific records, not all writes.

Context / Trigger Conditions

Error message: Error: stepping, database disk image is malformed (11)
PRAGMA integrity_check returns ok (misleading!)
SELECT queries on the same records work fine
Only certain records fail to update; other records in the same table update successfully
The affected records contain text with embedded tabs (\t), newlines (\n), or other control characters in columns that are indexed by FTS5
A concurrent process (like a Node.js server) may have the database open

Solution

Identify FTS5 tables linked to the affected table:

SELECT name FROM sqlite_master WHERE type='table' AND name LIKE '%fts%';

Stop any processes holding the database open (the rebuild requires exclusive access):
```
kill $(lsof -ti :PORT)  # Kill the server process
```
Rebuild the FTS5 index:
```
INSERT INTO table_fts(table_fts) VALUES('rebuild');
```
Replace table_fts with your actual FTS5 table name (e.g., people_fts).
Retry the failed operation - it should now succeed.
Restart your application server.

Verification

The previously failing UPDATE/INSERT statement now succeeds
Full-text search queries still return correct results
No more "malformed" errors on subsequent writes

Example

# Error occurs:
sqlite3 data/tracker.db "UPDATE people SET name = 'More' WHERE id = 11;"
# Error: stepping, database disk image is malformed (11)

# But integrity check passes:
sqlite3 data/tracker.db "PRAGMA integrity_check;"
# ok

# And SELECT works fine:
sqlite3 data/tracker.db "SELECT id, name FROM people WHERE id = 11;"
# 11|More Masajes\t\n\t\tEscort 23 años...

# Fix: Stop server, rebuild FTS5 index
kill $(lsof -ti :3001)
sqlite3 data/tracker.db "INSERT INTO people_fts(people_fts) VALUES('rebuild');"

# Now the update works:
sqlite3 data/tracker.db "UPDATE people SET name = 'More' WHERE id = 11;"
# Success!

Prevention

Sanitize text before inserting into FTS5-indexed columns:

const cleanName = rawName.replace(/[\t\n\r]+/g, ' ').trim();

Strip control characters from scraped data before database insertion
Consider using content= (external content) FTS5 tables that can be rebuilt independently without affecting the main table

Notes

The error code 11 (SQLITE_CORRUPT) is the same as actual disk corruption, making this hard to diagnose
The corruption is in the FTS5 shadow tables (_data, _idx, _docsize), not the main table, which is why integrity_check passes
If rebuild fails with "database is locked", ensure no other process has the database open (check with lsof or fuser)
This can also happen when records are deleted or updated externally (e.g., via sqlite3 CLI) while a WAL-mode connection is active