fix(datastore): auto-recover malformed peewee SQLite on startup by TimeToBuildBob · Pull Request #154 · ActivityWatch/aw-core

TimeToBuildBob · 2026-09-01T19:07:40Z

Problem

aw-server (Peewee/SQLite) can enter a restart loop when the on-disk
peewee-sqlite.v2.db is SQLITE_CORRUPT (database disk image is malformed).
PRAGMA quick_check fails, the process exits, and the bundled restart action
hits the same file again. The database is often still partially readable, and
SQLite's recovery tools can salvage events.

Change

On PeeweeStorage init, if the file fails PRAGMA quick_check:

Copy it aside as <path>.corrupt-<UTC> (plus -wal/-shm if present).
Try sqlite3 .recover when sqlite_dbpage is available (typical on macOS).
Otherwise use sqlite3 .bail off .dump and rewrite ROLLBACK → COMMIT.
Debian/Ubuntu sqlite3 is commonly built without SQLITE_ENABLE_DBPAGE_VTAB,
so .recover fails there with no such table: sqlite_dbpage.
Reconstruct any eventmodel.bucket_id rows missing from bucketmodel as
recovered-<key> so the datastore can open after a dump that salvaged events
but not bucket metadata.
Replace the live file only after the recovered copy itself passes
PRAGMA quick_check. WAL/SHM on the live path are removed first so the old
log cannot be applied to the new file.

Disable with AW_SQLITE_AUTO_RECOVER=0. If recovery cannot run (no sqlite3
CLI, or both strategies fail), the original file is left in place and the error
includes the manual commands.

Tests

tests/test_sqlite_recover.py:

xor-corrupt a real Peewee DB after WAL checkpoint; startup recovers 30/30 events
healthy DB is a no-op (no sidecar)
AW_SQLITE_AUTO_RECOVER=0 raises without copying
dump sanitizer rewrites ROLLBACK and drops corruption markers

Full suite: 201 passed, 2 skipped.

Notes

This does not change the on-disk schema of a healthy database. Recovered bucket
rows may be named recovered-<key> when the bucket page was the corrupt one;
events are kept.

Preserve a corrupt peewee-sqlite.v2.db as <path>.corrupt-<UTC> and replace it with a recovered copy so aw-server can start instead of restart-looping. Uses sqlite3 .recover when sqlite_dbpage is available; otherwise a sanitized .bail-off .dump (Debian/Ubuntu sqlite3 is built without dbpage). Reconstructs any eventmodel.bucket_id rows missing from bucketmodel. Disable with AW_SQLITE_AUTO_RECOVER=0. Git-Session-Id: 08b7

greptile-apps · 2026-09-01T19:11:20Z

Greptile Summary

This PR adds automatic startup recovery for malformed Peewee SQLite databases while preserving the original file and validating recovered state before replacement.

Detects malformed databases with PRAGMA quick_check and supports CLI and Python recovery strategies.
Reconstructs missing bucket metadata so salvaged events remain accessible.
Secures the recovery inode before writing and preserves the original database permissions.
Adds coverage for recovery, disabled recovery, partial schemas, and permission handling.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failure remains; the previously reported schema-reachability and temporary-file permission issues are fixed in the current code.

Important Files Changed

Filename	Overview
aw_datastore/storages/peewee.py	Invokes malformed-database recovery before initializing the Peewee connection.
aw_datastore/storages/sqlite_recover.py	Implements guarded recovery, bucket reconstruction, integrity validation, secured temporary-file handling, and atomic replacement.
tests/test_sqlite_recover.py	Covers healthy and corrupt startup paths, fallback recovery, partial schemas, opt-out behavior, and POSIX permission preservation.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[PeeweeStorage startup] --> B{Database healthy?}
    B -->|Yes| C[Open normally]
    B -->|No| D{Auto-recovery enabled?}
    D -->|No| E[Raise recovery instructions]
    D -->|Yes| F[Copy original and sidecars]
    F --> G[Create secured temporary inode]
    G --> H[Try sqlite3 recover]
    H -->|Unavailable or failed| I[Try dump recovery]
    I -->|Failed| J[Try Python row copy]
    H -->|Recovered| K[Reconstruct missing buckets]
    I -->|Recovered| K
    J -->|Recovered| K
    K --> L[Validate integrity and schema]
    L -->|Valid| M[Remove stale journals and replace live DB]
    L -->|Invalid| N[Delete temporary file and preserve original]

_{Reviews (4): Last reviewed commit: "fix(datastore): typecheck fchmod on Wind..." | Re-trigger Greptile}

greptile-apps · 2026-09-01T19:11:23Z

+        if not is_sqlite_healthy(tmp_dest):
+            raise SqliteRecoverError("recovered file still fails PRAGMA quick_check")
+        _replace_live_db(path, tmp_dest)


Incomplete schemas pass recovery

When a corrupt dump retains eventmodel but omits bucketmodel, _reconstruct_missing_buckets returns without repair and quick_check still permits replacement. Peewee then recreates an empty bucket table, leaving the salvaged events unreachable while startup reports a usable datastore.

Fixed in e93b303. _reconstruct_missing_buckets now creates bucketmodel (and the unique id index) when a dump salvaged eventmodel but omitted the catalog, then inserts recovered-<key> rows. _assert_recovered_schema refuses replacement if any salvaged events would still be unreachable after that.

greptile-apps · 2026-09-01T19:11:23Z

+    # Drop WAL/SHM first so SQLite cannot apply the old log to the new file.
+    for suffix in ("-wal", "-shm", "-journal"):
+        _remove_if_exists(path + suffix)
+    os.replace(recovered, path)


Replacement drops database permissions

If the original database has stricter permissions than the process's current umask, os.replace installs the newly created recovery file without preserving those restrictions, broadening local read access to activity records. How this was verified: The recovery file is created as a new inode and the replacement path contains no mode-restoration step.

Fixed in e93b303. _replace_live_db copies the original mode onto the recovered file with os.chmod before os.replace, so a restrictive 0600 database does not become world-readable under a permissive umask.

Windows CI has no sqlite3.exe, so CLI .recover/.dump never ran and the xor-corrupt fixture failed. Copy schema plus surviving rows through the stdlib sqlite3 module, reopening poisoned connections after DatabaseError. Git-Session-Id: 08b7

Git-Session-Id: 08b7

Create bucketmodel when a corrupt dump salvages eventmodel but omits the bucket catalog, then refuse replacement if events would still be unreachable. Preserve the original file mode on os.replace so recovery does not widen local read access under a permissive umask.

TimeToBuildBob · 2026-09-01T19:24:13Z

@greptileai review

Windows leaves non-empty -wal/-shm next to the .corrupt-<UTC> copy, so glob(path + '.corrupt-*') matched three files and tripped assert len==1. Git-Session-Id: 08b7

greptile-apps · 2026-09-01T19:28:50Z

+    _preserve_mode(path, recovered)
+    os.replace(recovered, path)


Recovered file permissions remain exposed

If the original database is restrictive but the process umask is permissive, recovery populates .recovered-tmp before applying the original mode, exposing activity data to other local accounts during recovery. If os.chmod fails, _preserve_mode suppresses the error and os.replace installs the permissive inode permanently.

How this was verified: The recovery path writes the temporary database before line 538, and lines 525-539 suppress chmod failures before unconditionally replacing the live database.

Fixed in ed07f01. Recovery now creates the temporary inode with the live database's mode and applies that exact mode with fchmod before any recovery strategy writes data. Permission setup errors propagate before data is written or replacement begins. Fallbacks truncate the same pre-secured inode instead of deleting and recreating it. Added tests for pre-write mode and fail-closed fchmod failure.

ActivityWatch peewee SQLite auto-recover: restart loops on SQLITE_CORRUPT while events are still readable. Portable fallback when sqlite_dbpage is missing, dump ROLLBACK trap, open PR ActivityWatch/aw-core#154. Git-Session-Id: e09f

Git-Session-Id: 5f4c1144-c5d9-5e51-a701-52c1c2fa45a9

TimeToBuildBob · 2026-09-01T20:01:31Z

@greptileai review

Git-Session-Id: 5f4c1144-c5d9-5e51-a701-52c1c2fa45a9

TimeToBuildBob · 2026-09-01T20:11:48Z

@greptileai review

TimeToBuildBob · 2026-09-01T20:25:28Z

CI-green and mergeable (Greptile 5/5) — waiting only on a maintainer click.

This PR is ready to merge, but the bot has pull-only access to this repo and can't self-merge — surfacing it here so it isn't lost. The monitoring loop will stop re-flagging it now that this note is posted.

greptile-apps Bot reviewed Sep 1, 2026

View reviewed changes

TimeToBuildBob added 3 commits September 1, 2026 19:12

fix(datastore): satisfy mypy on python recover src_con close

bbc6cbd

Git-Session-Id: 08b7

test(datastore): sidecar glob should ignore WAL/SHM copies

a053ccc

Windows leaves non-empty -wal/-shm next to the .corrupt-<UTC> copy, so glob(path + '.corrupt-*') matched three files and tripped assert len==1. Git-Session-Id: 08b7

greptile-apps Bot reviewed Sep 1, 2026

View reviewed changes

fix(datastore): secure recovery file before writing

ed07f01

Git-Session-Id: 5f4c1144-c5d9-5e51-a701-52c1c2fa45a9

TimeToBuildBob added 2 commits September 1, 2026 20:04

fix(datastore): support recovery file setup on Windows

6c6209b

Git-Session-Id: 5f4c1144-c5d9-5e51-a701-52c1c2fa45a9

fix(datastore): typecheck fchmod on Windows

c544da7

Git-Session-Id: 5f4c1144-c5d9-5e51-a701-52c1c2fa45a9

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fix(datastore): auto-recover malformed peewee SQLite on startup - #154

fix(datastore): auto-recover malformed peewee SQLite on startup#154
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TimeToBuildBob:fix/sqlite-corrupt-recover

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Greptile Summary

Confidence Score: 5/5

Important Files Changed

Flowchart

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