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omnigraph/docs/user/maintenance.md
Ragnor Comerford 595c6516f2
docs: pre-stage write precondition tolerates benign drift, defers sidecar-covered 
- writes.md: new subsection specifying the tolerant precondition (OCC fence =
  fresh manifest pin; benign drift proceeds, sidecar-covered defers, stale
  handle still 409s), the load-bearing content-preserving invariant, and the
  Hyrum's-law observable change (409 -> success on benign drift).
- invariants.md: Truth Matrix row for the precondition + deny-list entry
  forbidding non-content-preserving uncovered HEAD advances without a sidecar.
- testing.md: list the five new tolerance tests under the writes.rs /
  schema_apply.rs rows.
- maintenance.md + AGENTS.md: correct the now-stale claim that optimize's
  publish is required for strict writes / schema apply to pass their
  precondition — they tolerate benign drift; the publish is for reader
  visibility and bounded drift.
2026-06-08 11:54:52 +02:00

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Maintenance: Optimize & Cleanup

db/omnigraph/optimize.rs.

optimize_all_tables(db) — non-destructive

  • Lance compact_files() on every node + edge table on main, then publishes the compacted version to the __manifest so the manifest's table_version tracks the compacted Lance HEAD. Reads pin the manifest version, so without this publish compaction would be invisible to readers until the next write. The publish advances the graph version (a system-attributed commit) only for tables that actually compacted. (Even if a graph is left with uncompacted HEAD > manifest drift — e.g. an old-binary optimize that never published, or an external compact_files — strict writes and schema apply now tolerate that benign drift and reconcile it on the next write; see the pre-stage write precondition in docs/dev/writes.md. The publish is still done so reads observe compaction immediately and system-produced drift stays bounded.)
  • Rewrites small fragments into fewer large ones; old fragments remain reachable via older manifests until cleanup runs.
  • Each table's compact→publish runs under its per-(table, main) write queue (serializing with concurrent mutations — compaction is a Lance Rewrite op that retryable-conflicts with a concurrent merge/update/delete on overlapping fragments). The Lance-HEAD-before-manifest-publish gap is covered by a SidecarKind::Optimize recovery sidecar (loose-match): a crash in that window rolls the compacted version forward on the next Omnigraph::open (compaction is content-preserving, so roll-forward is always safe).
  • Requires a recovered graph. optimize refuses (errors) when an unresolved recovery sidecar is present under __recovery — operating on an unrecovered graph could publish a partial write the open-time recovery sweep would roll back. Reopen the graph to run the recovery sweep, then re-run optimize. (Recovery roll-back now publishes its restored version, so a recovered graph always satisfies manifest == Lance HEAD going in; there is no leftover drift for optimize to interpret.)
  • Bounded by OMNIGRAPH_MAINTENANCE_CONCURRENCY (default 8).
  • Returns [TableOptimizeStats { table_key, fragments_removed, fragments_added, committed, skipped }].
  • Blob tables are skipped. A table that declares any Blob property is not compacted: it is reported with skipped: Some(BlobColumnsUnsupportedByLance) (and logged via tracing::warn) instead of compacted, and the rest of the sweep proceeds normally. The current Lance compact_files mis-decodes blob-v2 columns under its forced BlobHandling::AllBinary read; reads and writes are unaffected — only compaction is. This is gated by LANCE_SUPPORTS_BLOB_COMPACTION (db/omnigraph/optimize.rs) and removed when the upstream Lance fix lands (see docs/dev/lance.md). Consequence: fragment count and deleted-row space on blob tables are not reclaimed until then; query results are never affected.

cleanup_all_tables(db, options) — destructive

  • Lance cleanup_old_versions() per table.
  • Removes manifests (and their unique fragments) older than the retention policy.
  • CleanupPolicyOptions { keep_versions: Option<u32>, older_than: Option<Duration> } — at least one is required.
  • Returns [TableCleanupStats { table_key, bytes_removed, old_versions_removed, error }].
  • Fault-isolated per table. A single table's transient failure (version GC or orphan reclaim) is recorded on that table's stats row (error: Some(..), logged via tracing) and never aborts the healthy tables — cleanup is the convergence backstop, so it does as much as it can and converges on re-run. The CLI reports any failed tables; rerun cleanup to retry them.
  • CLI guards with --confirm; without it, prints a preview line.
  • Recovery floor: --keep < 3 may garbage-collect Lance versions that the open-time recovery sweep needs as a rollback target (the sweep restores to the branch's manifest-pinned table version, which is HEAD-1 in the typical Phase B → Phase C drift case). Default --keep 10 is safe.
  • Orphaned-branch reconciliation: before the version GC, cleanup runs reconcile_orphaned_branches, which force_delete_branches any per-table or commit-graph Lance branch absent from the manifest branch list. These orphans arise when a branch_delete flips the manifest authority but a downstream best-effort reclaim does not complete (see branches-commits.md). The reconciler is authority-derived and idempotent (it no-ops once nothing is orphaned), runs regardless of the keep_versions / older_than values (those gate version GC only), and never reclaims main or system-branch forks. Reclaimed forks are logged via tracing::info.

Tombstones

Logical sub-table delete markers in __manifest; tombstone_object_id(table_key, version) excludes a sub-table version from snapshot reconstruction.

Internal schema migrations (db/manifest/migrations.rs)

Version evolutions of the on-disk __manifest shape are reconciled automatically on the first write under a new binary. INTERNAL_MANIFEST_SCHEMA_VERSION declares the shape the binary expects; the on-disk stamp omnigraph:internal_schema_version (Lance schema-level metadata) records the on-disk shape. The publisher's open-for-write path calls migrate_internal_schema before reading state; reads are side-effect-free. No operator action is required for in-place upgrades. See storage.md → Internal schema versioning for the full mechanism.

A binary opening a manifest stamped at a version higher than it knows about refuses to publish with a clear "upgrade omnigraph first" error — old binaries cannot clobber a newer schema.