omnigraph/docs/runs.md

Runs — REMOVED (MR-771)

The Run state machine and __run__<id> staging branches were removed in MR-771. mutate_as and load now write directly to the target table and call ManifestBatchPublisher::publish once at the end with expected_table_versions (the per-table manifest versions captured before the first write). Cross-table OCC is enforced inside the publisher; the publisher's row-level CAS on __manifest is the single fence.

What this means in practice

• No RunRecord, no _graph_runs.lance, no _graph_run_actors.lance.
• No omnigraph run * CLI subcommands and no /runs/* HTTP endpoints.
• No __run__<id> staging branches. (Legacy on-disk artifacts from pre-MR-771 repos are inert; MR-770 sweeps them in production.)
• Cancelled mutation futures leave no graph-level state — only orphaned Lance fragments, which the existing omnigraph cleanup pipe reclaims.

Read-your-writes within a multi-statement mutation

A .gq query with multiple ops (e.g. insert Person … insert Knows …) must observe earlier ops' writes when validating later ops (referential integrity, edge cardinality). After MR-794 step 2+ this is implemented via an in-memory MutationStaging accumulator in crates/omnigraph/src/exec/staging.rs, shared by both mutate_as and the bulk loader:

• On the first touch of each table, the pre-write manifest version is captured into expected_versions[table_key] (the publisher's CAS fence at end-of-query).
• Each insert/update op pushes a RecordBatch into the per-table pending accumulator. Lance HEAD does not advance during op execution.
• Read sites (validation, predicate matching for update) consume TableStore::scan_with_pending, which scans committed via Lance and applies the same SQL filter to the pending batches via DataFusion MemTable. Same-query writes are visible to subsequent reads.
• At end-of-query, MutationStaging::finalize issues exactly one stage_* + commit_staged per touched table (concatenating accumulated batches; merge-mode dedupes by id, last-write-wins), and the publisher publishes the manifest atomically across all touched sub-tables. Cross-table conflicts surface as ManifestConflictDetails::ExpectedVersionMismatch.
• Deletes still inline-commit. Lance's Dataset::delete is not exposed as a two-phase op in 4.0.0; deletes go through delete_where immediately and record their post-write state in MutationStaging.inline_committed. The parse-time D₂ rule (below) prevents inserts/updates from coexisting with deletes in one query, so the inline path is safe for delete-only mutations.

This upholds docs/invariants.md §VI.23 (atomicity per query) and §VI.25 (read-your-writes within a multi-statement mutation, upheld).

D₂ — parse-time mixed-mode rejection

A single mutation query is either insert/update-only or delete-only. Mixed → rejected at parse time with a clear error directing the user to split the query. Reason: mixing creates ordering hazards (insert→delete on the same row would silently no-op because the staged insert isn't visible to delete; cascading deletes of just-inserted edges break referential integrity). Until Lance exposes a two-phase delete API, the parse-time rejection keeps both paths atomic and correct. Tracked: MR-793, plus a Lance-upstream ticket.

MR-793 status (storage trait two-phase invariant) — partial

MR-793 hoists the staged-write pattern into a TableStorage trait surface with sealed-trait enforcement and opaque SnapshotHandle / StagedHandle types — see crates/omnigraph/src/storage_layer.rs. The trait is the canonical surface for new engine code; existing call sites still use the inherent TableStore methods (mechanical migration deferred to a follow-up cycle — tracked).

Three writers have been migrated onto staged primitives:

• ensure_indices (db/omnigraph/table_ops.rs::build_indices_on_dataset_for_catalog) — scalar indices (BTree, Inverted) now use stage_create_*_index + commit_staged. Vector indices stay inline (residual — Lance build_index_metadata_from_segments is pub(crate) in 4.0.0; companion ticket to lance-format/lance#6658 needed).
• branch_merge::publish_rewritten_merge_table (exec/merge.rs) — merge_insert now uses stage_merge_insert + commit_staged. Deletes stay inline (Lance #6658 residual).
• schema_apply rewritten_tables (db/omnigraph/schema_apply.rs) — non-empty rewrites use stage_overwrite + commit_staged. Empty-batch rewrites stay inline (Lance InsertBuilder::execute_uncommitted rejects empty data; the empty case is rare and bounded by the schema-apply lock branch).

A defense-in-depth integration test (tests/forbidden_apis.rs) walks engine source and fails if non-allow-listed code calls Lance's inline-commit APIs directly. The trait surface itself is the primary enforcement (sealed + only-callable-via-trait once call sites land); the grep test catches type-system bypass attempts.

The "finalize → publisher residual" described below applies equally to the migrated writers — Lance has no multi-dataset atomic commit primitive, so the per-table commit_staged → manifest publish gap is the same drift class. Closing it requires either upstream Lance multi-dataset commit OR the omnigraph-side recovery-on-open reconciler described in .context/mr-793-design.md §15 (deferred to MR-795).

Inline-commit method residuals on TableStorage (MR-793 acceptance §1 option b)

MR-793's acceptance criterion §1 ("TableStore public API has no method that performs a manifest commit as a side effect of writing") is met per-method by enumerating every inline-commit method that remains on the trait surface, naming why it cannot yet be removed, and keeping the residual comment at every call site:

Method on TableStore	Inline-commit reason	Closes when
delete_where	DeleteJob is pub(crate) in lance-4.0.0 — no public two-phase delete API	lance-format/lance#6658 lands and stage_delete joins the trait
create_vector_index	Vector indices take Lance's "segment commit path"; the helper build_index_metadata_from_segments is pub(crate)	lance-format/lance#6666 lands and stage_create_vector_index joins the trait
append_batch	Legacy inherent method; some engine call sites haven't migrated to stage_append + commit_staged yet	MR-793 Phase 1b (call-site conversion) + Phase 9 (demote to pub(crate))
merge_insert_batch / merge_insert_batches	Legacy inherent method	Same — Phase 1b + Phase 9
overwrite_batch	Legacy inherent method	Same — Phase 1b + Phase 9
create_btree_index (inherent)	Legacy inherent method (the migrated callers use stage_create_btree_index + commit_staged; the inherent stays for tests / un-migrated paths)	Same — Phase 1b + Phase 9
create_inverted_index (inherent)	Same	Same — Phase 1b + Phase 9 + index-class split (MR-848)
truncate_table (inherent on TableStore)	Used by overwrite_batch internally	Phase 9

After lance#6658 + lance#6666 ship + MR-793 Phase 1b + MR-793 Phase 9 all complete, the trait surface exposes only staged-write primitives + commit_staged. Until then this matrix names every residual explicitly, every call site carries a one-line residual comment, and no engine code outside table_store.rs is permitted to reach the inline-commit Lance APIs (enforced by the tests/forbidden_apis.rs guard).

LoadMode::Overwrite residual

The bulk loader's Append and Merge modes use the staged-write path described above. LoadMode::Overwrite keeps the legacy inline-commit path: truncate-then-append doesn't fit the staged shape cleanly in Lance 4.0.0, and overwrite has no in-flight read-your-writes requirement (the prior data is being wiped). A mid-overwrite failure can leave Lance HEAD on a partially-truncated table; the next overwrite will replace it. Operator-driven (rare in agent workloads); document permanently until Lance exposes Operation::Overwrite { fragments } as a two-phase op.

Open-time recovery sweep

The staged-write rewire eliminates one drift class by construction at the writer layer: an op that fails before pushing to the in-memory accumulator (validation errors, missing endpoints, parse-time D₂ rejection) leaves Lance HEAD untouched on every staged table. This is the case the partial_failure_leaves_target_queryable_and_unblocks_next_mutation test pins.

A second, narrower drift class — the finalize → publisher window — is closed across one open cycle by the open-time recovery sweep:

MutationStaging::finalize runs stage_* + commit_staged per touched table sequentially, then the publisher commits the manifest. Lance has no multi-dataset atomic commit, so the per-table commit_staged calls are independent operations: if commit_staged on table N+1 fails after commit_staged on tables 1..N succeeded, or if the publisher's CAS pre-check rejects after every commit_staged succeeded, tables 1..N are left at Lance HEAD = manifest_pinned + 1.

Recovery protocol (lifecycle of every staged-write writer — MutationStaging::finalize, schema_apply::apply_schema_with_lock, branch_merge_on_current_target, ensure_indices_for_branch):

1. Phase A: writer writes a sidecar JSON to __recovery/{ulid}.json BEFORE its first commit_staged. The sidecar names every (table_key, table_path, expected_version, post_commit_pin) it intends to commit + the writer kind + actor_id.
2. Phase B: writer's per-table commit_staged loop runs.
3. Phase C: publisher commits the manifest.
4. Phase D: writer deletes the sidecar.

A failure between Phase A and Phase D leaves the sidecar on disk. The next Omnigraph::open (gated on OpenMode::ReadWrite) runs the recovery sweep in crates/omnigraph/src/db/manifest/recovery.rs:

• For each sidecar in __recovery/, compare every named table's Lance HEAD to the manifest pin. Classify per the all-or-nothing decision tree (RolledPastExpected / NoMovement / UnexpectedAtP1 / UnexpectedMultistep / InvariantViolation).
• If any table is InvariantViolation (Lance HEAD < manifest pinned — should be impossible), abort with a loud error and leave the sidecar on disk for operator review.
• Otherwise, if every table is RolledPastExpected, roll forward: a single ManifestBatchPublisher::publish call extends every pin atomically.
• Otherwise roll back: per-table Dataset::restore to the expected_version (with a fragment-set short-circuit so repeated mid-sweep crashes don't pile up versions).
• After a successful roll-forward or roll-back, an audit row is recorded — _graph_commits.lance carries a commit tagged actor_id = "omnigraph:recovery", and a sibling _graph_commit_recoveries.lance row carries recovery_kind, recovery_for_actor (the original sidecar's actor), operation_id, per-table outcomes. Operators run omnigraph commit list --filter actor=omnigraph:recovery to find recoveries.
• Sidecar deleted as the final step.

Triggers for the residual: transient Lance write errors during finalize (object-store retry budget exhaustion, disk full); persistent publisher contention exceeding PUBLISHER_RETRY_BUDGET = 5 retries.

Long-running servers: Omnigraph::refresh runs roll-forward-only recovery in-process — the common Phase B → Phase C residual closes without a restart. The next mutation on the same handle (after refresh) no longer surfaces ExpectedVersionMismatch for the failed table. Sidecars that would require a Dataset::restore (mixed / unexpected state) are deferred to the next OpenMode::ReadWrite open: restore is unsafe under concurrency because Lance's check_restore_txn accepts the restore against in-flight Append/Update/Delete commits and silently orphans them (pinned by tests/staged_writes.rs::lance_restore_loses_to_concurrent_append_via_orphaning). Continuous in-process recovery for the rollback path is the goal of a future background reconciler with per-(table, branch) writer-queue acquisition.

The publisher-CAS contract is unchanged: a concurrent writer that advances any of our touched tables between snapshot capture and publisher commit produces exactly one winner. The residual above is about our abandoned commits in the failure path, not about concurrency races.

Conflict shape

Concurrent writers to the same (table, branch) produce exactly one success and one failure. The losing writer's error is OmniError::Manifest with kind Conflict and details ManifestConflictDetails::ExpectedVersionMismatch { table_key, expected, actual }. The HTTP server maps this to 409 Conflict with body {"error": "...", "code": "conflict", "manifest_conflict": { "table_key": "...", "expected": N, "actual": M }} — see docs/server.md.

Audit

actor_id lands in _graph_commits.lance via record_graph_commit (no intermediate run record). Audit history is queried via omnigraph commit list.

Migration code

db/manifest/migrations.rs does not change. Active deletion of _graph_runs.lance belongs in MR-770 (the production sweep) — this PR stops creating run state but does not destroy legacy bytes on disk.

Mid-query partial failure: closed by MR-794

The pre-MR-794 design had a known limitation: a multi-statement .gq mutation where op-N inline-committed a Lance fragment and op-N+1 then failed left the touched table at Lance HEAD = manifest_version + 1, blocking the next mutation with ExpectedVersionMismatch.

MR-794 (step 1 + step 2+) closed this for inserts/updates by construction at the writer layer: insert and update batches accumulate in memory; no Lance HEAD advance happens during op execution; one stage_* + commit_staged per touched table runs at end-of-query, and only after every op succeeded. A failed op leaves Lance HEAD untouched on the staged tables, so the next mutation proceeds normally with no drift to reconcile.

The cancellation case (future drop mid-mutation) inherits the same guarantee — the in-memory accumulator evaporates with the dropped task and no Lance write was ever issued.

For delete-touching mutations the legacy inline-commit shape is preserved (Lance has no public two-phase delete in 4.0.0) — the same narrow window remains. The parse-time D₂ rule prevents inserts/updates from coexisting with deletes in one query, so a pure-delete failure cannot drift any staged-table state. If a delete-only multi-table mutation fails mid-cascade, the same workaround as before applies (retry; rely on omnigraph cleanup once a later successful commit moves HEAD past the orphan version). Closing this requires Lance to expose DeleteJob::execute_uncommitted; tracked in MR-793 and a Lance-upstream ticket.