fix(store): make cleanupOrphanedVectors atomic across both vector tables - #766
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cleanupOrphanedVectors ran its two DELETEs (vectors_vec, then content_vectors) as separate implicit transactions. An interruption between them (process crash, SQLITE_BUSY under a concurrent writer) desyncs the two tables: the embedding rows are gone from vectors_vec while content_vectors still reports the chunks as embedded, so the index silently loses vector-search coverage with no way to notice or repair short of re-embedding. Wrap the orphan count and both DELETEs in a single db.transaction(). The count shares the transaction so the returned number always matches what the DELETEs actually removed, even when another connection mutates documents concurrently. Nested callers are safe: both better-sqlite3 and bun:sqlite implement nested transaction functions via savepoints. Tests: happy path, fault injection between the DELETEs proving the first one rolls back and the connection stays usable, and savepoint participation in an outer transaction.
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Dear tobi/qmd,
We would like to acknowledge that we have received your request and a ticket has been created.
A support representative will be reviewing your request and will send you a personal response.(usually within 24-48 hours).
Thank you for your patience.
…On Mon, Jul 13 2026, at 07:41 PM, tobi/qmd ***@***.***> wrote:
Summary cleanupOrphanedVectors() runs its two DELETEs ( vectors_vec, then content_vectors) as separate implicit transactions. An interruption between them — process crash, or SQLITE_BUSY from a concurrent writer hitting the second statement — desyncs the two tables: the embedding rows are already gone from vectors_vec while content_vectors still reports the chunks as embedded.
Since these rows are orphaned (no active document) and vector search post-filters on documents.active = 1, live search is unaffected right away. The failure is latent: qmd is content-addressable, so if the same content later returns and that hash is reactivated, the stale content_vectors rows make getHashesNeedingEmbedding treat it as already embedded — qmd embed skips it, and the document is silently unsearchable by vector with no orphan left for a future cleanup to catch.
What changed
* The orphan count and both DELETEs now run inside a single db.transaction(), executed as BEGIN IMMEDIATE: the count reads before the DELETEs write, and upgrading a deferred read snapshot under a concurrent WAL writer fails with SQLITE_BUSY_SNAPSHOT instead of honoring the busy timeout. The shared Database interface type now reflects the .immediate variant both drivers already expose.
* The count shares the transaction so the returned number always matches what the DELETEs actually removed, even when another connection mutates documents concurrently.
* Nested callers stay safe: both better-sqlite3 and bun:sqlite implement nested transaction functions via savepoints (an immediate transaction invoked inside an outer transaction becomes a savepoint).
* Changelog entry under [Unreleased].
Verification
* New tests in test/store.test.ts ( cleanupOrphanedVectors atomicity):
* happy path: orphaned chunks removed from both tables, survivors intact, count correct
* fault injection between the two DELETEs: the vectors_vec DELETE rolls back (this test fails against the previous code) and the connection stays usable for a plain retry
* outer-transaction rollback also restores the cleanup's deletions
* inner-savepoint isolation: a cleanup failure caught inside an outer transaction rolls back alone while the outer transaction's own write commits bun run test:types clean, bun run build passes
* Suites green under both runtimes (vitest via Node and bun test) You can view, comment on, or merge this pull request online at: #766 (#766) Commit Summary c7c18b8 fix(store): make cleanupOrphanedVectors atomic across both vector tables (c7c18b8) File Changes
( 4 files) (https://github.com/tobi/qmd/pull/766/files) M CHANGELOG.md
(10) (https://github.com/tobi/qmd/pull/766/files#diff-06572a96a58dc510037d5efa622f9bec8519bc1beab13c9f251e97e657a9d4ed) M src/db.ts
(4) (https://github.com/tobi/qmd/pull/766/files#diff-1d214e57ddda9095d296e5700ebce701333bfefcf417e234c584d14091b2f50d) M src/store.ts
(69) (https://github.com/tobi/qmd/pull/766/files#diff-2717c7fb31c2070dd96f07394997809bc9be7f3fff03ab638db696cc480f39b6) M test/store.test.ts
(133) (https://github.com/tobi/qmd/pull/766/files#diff-ecc9e7b9a74de1ebac3cd3038ffc91cd42684ca2890738d3b93139c723c36407) Patch Links: https://github.com/tobi/qmd/pull/766.patch (https://github.com/tobi/qmd/pull/766.patch) https://github.com/tobi/qmd/pull/766.diff (https://github.com/tobi/qmd/pull/766.diff)
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Dear tobi/qmd,
We would like to acknowledge that we have received your request and a ticket has been created.
A support representative will be reviewing your request and will send you a personal response.(usually within 24-48 hours).
Thank you for your patience.
…On Thu, Aug 13 2026, at 02:15 AM, tobi/qmd ***@***.***> wrote:
tobi left a comment (tobi/qmd#766) (#766 (comment))
Superseded by #856 — same atomic cleanup, rebased onto current main after (#856) #851 extracted countOrphanedVectors (CHANGELOG + that refactor were the conflicts here). (#851)
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Closed in favor of #856, which lands this fix on current main. |
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Dear tobi/qmd,
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A support representative will be reviewing your request and will send you a personal response.(usually within 24-48 hours).
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…On Thu, Aug 13 2026, at 02:19 AM, tobi/qmd ***@***.***> wrote:
Closed #766. (#766)
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…On Thu, Aug 13 2026, at 02:19 AM, tobi/qmd ***@***.***> wrote:
tobi left a comment (tobi/qmd#766) (#766 (comment))
Closed in favor of #856, which lands this fix on current main. (#856)
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Summary
cleanupOrphanedVectors()runs its two DELETEs (vectors_vec, thencontent_vectors) as separate implicit transactions. An interruption between them — process crash, orSQLITE_BUSYfrom a concurrent writer hitting the second statement — desyncs the two tables: the embedding rows are already gone fromvectors_vecwhilecontent_vectorsstill reports the chunks as embedded.Since these rows are orphaned (no active document) and vector search post-filters on
documents.active = 1, live search is unaffected right away. The failure is latent: qmd is content-addressable, so if the same content later returns and that hash is reactivated, the stalecontent_vectorsrows makegetHashesNeedingEmbeddingtreat it as already embedded —qmd embedskips it, and the document is silently unsearchable by vector with no orphan left for a futurecleanupto catch.What changed
db.transaction(), executed asBEGIN IMMEDIATE: the count reads before the DELETEs write, and upgrading a deferred read snapshot under a concurrent WAL writer fails withSQLITE_BUSY_SNAPSHOTinstead of honoring the busy timeout. The sharedDatabaseinterface type now reflects the.immediatevariant both drivers already expose.documentsconcurrently.bun:sqliteimplement nested transaction functions via savepoints (an immediate transaction invoked inside an outer transaction becomes a savepoint).[Unreleased].Verification
test/store.test.ts(cleanupOrphanedVectors atomicity):vectors_vecDELETE rolls back (this test fails against the previous code) and the connection stays usable for a plain retrybun run test:typesclean,bun run buildpassesbun test)