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`](../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](invariants.md) (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](https://github.com/lance-format/lance/issues/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](https://github.com/lance-format/lance/issues/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. `SchemaApply` sidecars are eligible only when schema-state
  recovery promoted the matching staging files in the same recovery pass;
  otherwise full open-time recovery rolls them back and refresh-time
  recovery leaves them for the next read-write open.
- Otherwise **roll back**: per-table `Dataset::restore` to the
  manifest-pinned table version for that branch. Rollback records the
  actual restore target in the audit row's `to_version`.
- 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](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.