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fix(daemon): check large tables in bounded chunks during integrity sweeps - #2133
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…eeps The incremental integrity checker ran PRAGMA quick_check on each table as one owner job. SQLite cannot interrupt that statement, so on a table too large for the owner deadline the owner stayed busy until the check finished, the client discarded the result as timed out, and the cursor never advanced. Every retry repeated the same whole-table check. A bounded row count now gates the whole-table check. Larger rowid tables are read in rowid chunks, one owner job per chunk, with the position persisted in the checkpoint so each slice resumes where the last one stopped. A read error marks the table failed and the sweep continues. Tables checked this way are counted separately and the published quick-check status says their b-tree structure and indexes were not verified. Assisted-by: Claude-Code:claude-opus-5-5
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Check name Status Explanation Title check The title clearly and concisely describes the main change: checking large tables in bounded chunks during daemon integrity sweeps. Description check The description is complete and relevant. It includes the summary, changes, type, affected package, testing results, AI disclosure, references, and known limitations. Screenshots and migration details… Linked Issues check Check skipped because no linked issues were found for this pull request. Out of Scope Changes check Check skipped because no linked issues were found for this pull request.
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The bounded-scan test asserted on the published quick-check status, which keeps its previous value while another test's global integrity latch is set. In the full suite a leaked latch and a stale timed-out message replaced the coverage note. Both large-table tests now clear the latch first, the corrupt-chunk test clears it on exit instead of publishing a global healthy state, and both loop until the sweep completes under a generous run budget and owner deadline. Assisted-by: Claude-Code:claude-opus-5-5
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Review comments at @platform/daemon/src/incremental-database-integrity.ts:
- Around line 741-757: In the ordinary-table scan flow, catch deadline errors
only around the initial size probe in the `!resuming` branch and set `large` to
true so scanning continues via the existing rowid chunk path. Keep the probe
capped at `largeTableRows + 1`, and continue rethrowing deadlines from chunk
scans and all later operations.
- Around line 775-800: Update the chunk query in the table scan to select,
order, and resume using an unshadowed alias chosen from rowid, _rowid_, and oid.
If all three aliases are declared columns, use the existing full-table check
instead of chunk scanning.
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platform/daemon/src/database-integrity.tsplatform/daemon/src/incremental-database-integrity.test.tsplatform/daemon/src/incremental-database-integrity.tsscripts/event-loop-contract-baseline.jsonweb/docs/src/content/docs/api/health-status.md
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…ed rowids A size probe or whole-table check that hit the owner deadline left no trace in the checkpoint, so the next slice repeated the same work. Each ordinary table is now marked in the checkpoint before its probe. A slice that finds the mark reads the table in rowid chunks instead of probing or checking it whole again, so every table gets at most one whole-table attempt per sweep. The chunked scan also ordered and resumed by `rowid`, which a declared column of that name shadows. The scan now uses the first of rowid, _rowid_, and oid that the table does not declare, and counts a large table that declares all three as skipped instead of checking it whole. Assisted-by: Claude-Code:claude-opus-5-5
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This was referenced Oct 14, 2026
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Summary
The incremental integrity checker never finishes on a database with a very large table, and it stalls the DB owner every time it retries.
Each table is checked with one
PRAGMA quick_check(table)owner job. SQLite can't interrupt that statement, so on a table too large for the 1s owner deadline the owner stays busy until the whole check finishes. The client gives up at the deadline, waits for the owner, throws the result away astimed_out, and leaves the cursor where it was. The next slice, up to 30s later, issues the same whole-table check again. On a live workspace with an 18M-rowentity_dependency_history(grown by the re-index loop fixed in #2129), that meant a stall of roughly 38s on each retry and an integrity status that stayedunavailableindefinitely.Changes
incremental-database-integrity.ts: beforequick_check, the checker counts each ordinary table's rows up to a cap (SELECT count(*) FROM (SELECT 1 FROM t LIMIT 100001)), so the probe itself is bounded. Tables within the cap are checked as before.object_cursor,object_rowid), so each slice resumes where the previous one stopped and the sweep moves forward. Rowids are passed as exact text, so negative rowids and rowids above 2^53 are neither skipped nor read twice.unavailableand retried the same table.WITHOUT ROWIDtable over the cap can't be split by rowid and is counted inskippedObjects.database-integrity.ts: tables checked by the chunked scan are counted in the newincrementalProgress.scannedObjects. A completed sweep that used the scan keepsquickCheck.ok: true, andquickCheck.messagessays how many large tables were read in chunks and that their b-tree structure and indexes were not verified. The scan covers less thanquick_check, and the status says so.health-status.mddocuments the large-table behavior and the new field.Measured locally on a 1M-row table built like
entity_dependency_history, with three indexes: a whole-tablequick_checktook 361ms, and the cost grows with the table. The chunked sweep finished in 7 slices; the slowest slice took 199ms of wall time and 68ms of owner execution, about 8ms per chunk whatever the table size.Tests
runningwith objects remaining in between. No owner statement runsquick_checkorintegrity_checkon the table. Resume points strictly increase, including across a rowid above 2^53. The final status reports one scanned table and the coverage note. Against main this fails, because main runs the whole-table check.corrupt. Against main the run endsunavailable.9007199254740992nreceived for9007199254740993n).incremental-database-integrity,database-integrity,migration-integrity-verify,startup-recovery,daemon-production-wiring: 70/70.Not in this PR:
remainingObjects: 0, which P1: v0.237.10 post-OOM recovery remains degraded for hours as integrity checks repeatedly time out #2126 points out is misleading. That needs its own decision about an "unknown" count.Type
feat— new user-facing feature (bumps minor)fix— bug fixrefactor— restructure without behavior changechore— build, deps, config, docsperf— performance improvementtest— test coveragePackages affected
@signet/daemonRefs #2126
AI assistance: Claude Code (claude-opus-5-5), disclosed per AI_POLICY.md.
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