Bot reviewers (cubic, cursor, chatgpt-codex) caught 4 merge-blocking
bugs + 3 strongly-recommended fixes + 3 doc errors in the initial PR.
Each fix has a paired test demonstrating the bug before the fix.
Merge-blocking fixes:
- BranchMerge moved to loose-match classifier arm. publish_rewritten_
merge_table runs multiple commit_staged calls per table (merge_insert
+ delete_where + index rebuilds). Strict classification rolled back
valid completed Phase B work as UnexpectedMultistep. Three new unit
tests pin the loose-match behavior for BranchMerge.
- branch_merge sidecar uses self.active_branch() (the resolved target
branch) instead of inferring from the first sorted table key. The
previous heuristic could record None (== main) when the merge target
was a non-main branch, causing recovery to publish to the wrong
manifest namespace.
- Best-effort sidecar delete in all 5 writer sites (mutation, loader,
schema_apply, branch_merge, ensure_indices). Previously, a sidecar
cleanup failure after a successful manifest publish would error out
the user's call for a write that already landed. Now: log a warning
and ignore — the next open's recovery sweep tidies the stale sidecar
via NoMovement classification.
- ensure_indices sidecar scoped to tables that need work via new
helpers needs_index_work_node / needs_index_work_edge. Previously
the sidecar pinned every catalog table; if only one needed indexing,
the others classified as NoMovement and the all-or-nothing decision
rolled back legitimate index work.
Strongly-recommended fixes:
- recover_manifest_drift now takes &mut GraphCoordinator and refreshes
between sidecars. Sidecar B's classification needs to see sidecar
A's manifest changes, otherwise B can be classified against stale
pins and incorrectly roll back work that just landed.
- list_sidecars sorts URIs before reading. Sidecar filenames are
ULIDs (chronologically sortable), so this gives deterministic,
time-ordered processing. Filesystem-order was nondeterministic.
- ReadOnly opens skip recover_schema_state_files too (was: only the
MR-847 sweep was gated). Read-only consumers may run with read-only
credentials; silent open-time mutations violate the contract.
Doc cleanups:
- Removed stale "Phase 4 placeholder" comment from
recover_manifest_drift.
- docs/runs.md decision-tree wording now correctly surfaces the
InvariantViolation abort path.
- docs/branches-commits.md clarifies actor_id is in
_graph_commit_actors.lance (joined by graph_commit_id), not on
_graph_commits.lance itself.
Test surface (post-fixes):
- 25 unit tests in db::manifest::recovery (+4 from this commit).
- 10 integration tests in tests/recovery.rs (+3 from this commit).
- ~672 tests across ~25 binaries pass with --features failpoints.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Update the doc surface to reflect MR-847 having shipped end to end —
sidecar protocol, classifier, all-or-nothing decision tree, roll-forward
via ManifestBatchPublisher, roll-back via Dataset::restore with
fragment-set short-circuit, audit trail in
_graph_commit_recoveries.lance, OpenMode::{ReadWrite, ReadOnly}, and
the four migrated writers all carrying sidecars across Phase B → Phase C.
- docs/invariants.md §VI.23: change from "upheld at the writer-trait
surface for inserts/updates/etc., per-table commit_staged → manifest
publish window remains" to "upheld at the writer-trait surface AND
across process boundaries". The MR-847 sweep closes the residual on
the next Omnigraph::open. The "continuous in-process" property
(no ExpectedVersionMismatch surfacing to subsequent writers between
Phase B failure and process restart) is honest follow-up at MR-856.
- docs/runs.md: replace "Finalize → publisher residual" section with
"Open-time recovery sweep (MR-847)" — describes the sidecar protocol
lifecycle (Phases A-D), the sweep's classifier + decision dispatch,
the audit trail, and the operator-facing query
(omnigraph commit list --filter actor=omnigraph:recovery).
- AGENTS.md capability matrix "Atomic single-dataset commits" row:
drop the "Layer (3) is not yet shipped — tracked in MR-847" caveat;
describe the three layers as all shipping; reference MR-856 for the
background-reconciler follow-up.
- docs/storage.md: add _graph_commit_recoveries.lance and
__recovery/{ulid}.json to the on-disk layout (mermaid + prose).
- docs/branches-commits.md: new "Recovery audit trail (MR-847)"
subsection describing the join from
_graph_commits.lance:actor_id="omnigraph:recovery" to
_graph_commit_recoveries.lance:graph_commit_id for operator
post-mortem.
- docs/maintenance.md: note the MR-847 recovery floor on cleanup —
--keep < 3 may garbage-collect Lance versions the recovery sweep
needs as a rollback target. Default --keep 10 is safe.
- docs/testing.md: add tests/recovery.rs to the engine integration-test
table; expand the failpoints.rs row to mention the four MR-847
per-writer Phase B → recovery integration tests.
- .context/mr-847-design.md: prepend a "Status: DONE" stanza listing
every commit hash + scope across phases 1-10.
AGENTS.md ↔ docs/ cross-link check passes (26 links, 26 docs).
Full workspace test sweep passes with --features failpoints (361 tests
across 20 binaries).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Closes MR-793 acceptance §1 via option (b): every inline-commit method
remaining on the trait surface is named, the upstream blocker or
internal phase that closes it is cited, and the call-site residual
comment is mandated.
Reframes the criterion text in the MR-793 ticket comment from "either
full sealing OR all residuals enumerated" — this commit ships the
"enumerated" path. The "full sealing" path (Phase 1b + Phase 9 + the
two Lance upstream tickets) closes the matrix entirely.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Hoists Lance's stage+commit two-phase write pattern from "discipline at
each writer" to a sealed trait surface (`TableStorage`). New engine code
that needs to advance Lance HEAD MUST go through `stage_*` + `commit_staged`;
the trait's opaque `SnapshotHandle` / `StagedHandle` types keep
`lance::Dataset` and `lance::Transaction` out of trait signatures.
Phases landed (see .context/mr-793-design.md for the full plan):
* 1a: `crates/omnigraph/src/storage_layer.rs` — `TableStorage` trait,
sealed (only in-tree types can impl), single impl on `TableStore`
delegating to existing inherent methods; `Omnigraph::storage()`
accessor returns `&dyn TableStorage`.
* 2: three new staged primitives — `stage_overwrite`,
`stage_create_btree_index`, `stage_create_inverted_index` —
implementing the simple branch of Lance's `CreateIndexBuilder::execute`
(scalar indices only; vector indices stay inline because
`build_index_metadata_from_segments` is `pub(crate)` in lance-4.0.0).
Six new tests in `tests/staged_writes.rs` pin both the new primitives
and the inline residuals (`delete_where`, `create_vector_index`).
* 3: `tests/forbidden_apis.rs` — defense-in-depth integration test
walks engine source, fails on direct lance::* inline-commit API use
outside `table_store.rs` / `db/manifest/`. Skips comment lines and
honors `// forbidden-api-allow:` sentinels.
* 4: `ensure_indices` migration — scalar index builds now route through
`stage_create_*_index` + `commit_staged` instead of
`create_*_index(&mut Dataset)`. Vector indices stay inline (residual,
named honestly at the call site).
* 5: `branch_merge::publish_rewritten_merge_table` migration — the
merge_insert phase now uses `stage_merge_insert` + `commit_staged`;
delete phase stays inline (Lance #6658 residual, named honestly).
* 6: `schema_apply` rewritten_tables migration — non-empty rewrites
use `stage_overwrite` + `commit_staged`; empty-batch rewrites stay
inline because `InsertBuilder::execute_uncommitted` rejects empty
data. The narrow inline window is bounded by `__schema_apply_lock__`.
Verified-green test surface:
* `cargo test -p omnigraph-engine` — 68 lib + ~120 integration tests
(incl. 6 new staged_writes tests + the new forbidden_apis test).
* `cargo test -p omnigraph-engine --features failpoints --test failpoints`
— 5 tests, all green.
* `cargo test --workspace` — green.
Deferred to follow-up sessions (see design doc §17 split):
* Phase 1b — convert remaining engine call sites to `&dyn TableStorage`
(mostly READS that don't touch the staged-write invariant).
* Phase 7 — recovery-on-open reconciler (closes Phase B → Phase C
residual across process restarts; new subsystem).
* Phase 8 — index-coverage reconciler (full §VII.35 compliance —
removes synchronous index work from the publish path).
* Phase 9 — demote unused `TableStore` inherent methods to `pub(crate)`
(depends on Phase 1b).
Lance upstream blockers documented:
* lance-format/lance#6658 — two-phase delete API (open, no PRs).
* Companion: `build_index_metadata_from_segments` should be `pub` so
vector-index builds can be staged outside the lance crate.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Five fixes from PR #68 review (Cursor Bugbot + Codex + Cubic):
* **scan_with_pending gains merge-shadow semantics** (Codex P1, Cubic P1#1):
new `key_column: Option<&str>` parameter. When set, committed rows
whose key value appears in any pending batch are excluded from the
scan — making `scan_with_pending` correctly merge-semantic for chained
updates instead of naively unioning. execute_update calls with
Some("id"). Without this, a chained `update where age > 30` could
match a row whose pending value already moved out of range.
* **Multi-delete on same table no longer trips ExpectedVersionMismatch**
(Cursor Bugbot HIGH): open_table_for_mutation routes through
reopen_for_mutation when staging.inline_committed has the table,
using the post-inline-commit Lance version captured at record_inline
time. The legacy open_for_mutation_on_branch fence (Lance HEAD ==
manifest pinned) is correct cross-writer but wrong intra-query when
deletes have already advanced HEAD on this table. Branch goes away
when Lance ships two-phase delete (lance-format/lance#6658).
* **Cardinality validation consolidated** (Cursor LOW + Codex P2 +
Cubic P1#2 + Cubic P2): new exec/staging::count_src_per_edge +
enforce_cardinality_bounds shared by mutation and loader paths.
Restores the missing min-cardinality check on the engine path.
Loader Merge mode passes Some("id") to dedupe edges being updated
by id (not double-count committed + pending). Loader Append mode
and engine path pass None (ULID-generated ids never collide).
* **Dead count_rows_with_pending removed** (Cursor LOW): never called.
* **Misleading concat-helper comment fixed** (Cubic P3): claimed
schema normalization the helper doesn't implement. Updated to match
reality.
* **Documentation honesty** (Cubic P1#3): MR-794 narrows but doesn't
eliminate the "Lance HEAD ahead of __manifest" drift class. Drift is
unreachable for op-execution failures (the partial_failure test pins
this), but a residual remains at the finalize→publisher boundary
because Lance has no multi-dataset commit primitive: per-table
commit_staged calls run sequentially before manifest commit. Updated
docs/runs.md, docs/invariants.md §VI.25, docs/releases/v0.4.1.md to
scope the claim precisely.
* **Failpoint test pinning the residual**: new
mutation.post_finalize_pre_publisher failpoint + two tests in
tests/failpoints.rs that confirm the documented residual behavior.
Catches future regressions that widen the residual.
Test additions on tests/runs.rs:
* chained_updates_with_overlapping_predicate_respects_intermediate_value
* multi_statement_delete_on_same_node_table
* cascade_delete_node_then_explicit_delete_edge_on_same_table
* mutation_insert_edge_enforces_min_cardinality
* load_merge_mode_dedupes_edge_for_cardinality_count
113/113 engine integration tests pass (runs + end_to_end + consistency
+ staged_writes + validators). Failpoints feature build runs in CI.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Refresh user-facing and agent-facing docs for the staged-write rewire
and clean up stale Run-state-machine references that survived MR-771.
MR-794-specific updates:
* docs/runs.md — remove "Known limitation: mid-query partial failure"
section; document the in-memory accumulator + D₂ rule + the
LoadMode::Overwrite residual.
* docs/invariants.md §VI.25 — flip from aspirational/open to
upheld for inserts/updates. Within-query read-your-writes is now
load-bearing for the publisher CAS contract.
* docs/architecture.md — add "Mutation atomicity — in-memory
accumulator (MR-794)" subsection with per-op flow; refresh the
engine + state diagrams to drop RunRegistry and add MutationStaging.
* docs/execution.md — rewrite the mutation flow sequence diagram
for the staged-write path; updated the LoadMode table to call
out per-mode commit semantics; rewrote load vs ingest.
* docs/query-language.md — document the D₂ parse-time rule.
* docs/errors.md — add the D₂ BadRequest rejection path.
* docs/testing.md — extend the runs.rs row to cover the new MR-794
contract tests; add the staged_writes.rs row.
* docs/releases/v0.4.1.md (new) — release note covering the rewire,
test additions, residuals, and files changed.
* AGENTS.md (CLAUDE.md symlink) — update the atomic-per-query
description and the L2 capability matrix row.
Stale-reference cleanup (MR-771 leftovers):
* docs/storage.md — drop live _graph_runs.lance / _graph_run_actors.lance
from the layout diagram and prose; mark legacy.
* docs/branches-commits.md — move __run__<id> to a legacy note;
remove publish_run from the publish-trigger list.
* docs/audit.md — refresh _as API list (drop begin_run_as / publish_run_as);
legacy RunRecord.actor_id moved to a historical note.
* docs/constants.md — mark run registry / branch-prefix rows as legacy.
* docs/cli.md — replace the legacy omnigraph run * quickstart block
with omnigraph commit list/show.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
mutate_as and load now write directly to target tables and call the
publisher once at the end with per-table expected versions; the Run
state machine, _graph_runs.lance writers, __run__ staging branches,
and server /runs/* endpoints are removed. Multi-statement mutations
remain atomic at the manifest level via an in-memory MutationStaging
accumulator that gives read-your-writes within a query and a single
publish at the end. Concurrent-writer conflicts surface as
ExpectedVersionMismatch (HTTP 409 manifest_conflict) instead of the
old DivergentUpdate merge shape. Documents one known limitation in
docs/runs.md: a multi-statement mid-query failure where op-N writes
a Lance fragment and op-N+1 fails leaves Lance HEAD ahead of the
manifest until a follow-up introduces per-table Lance branches.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Splits the 990-line AGENTS.md into a 184-line map (architecture,
where-to-find index, always-on invariants, capability matrix,
maintenance contract) plus 18 new docs/*.md files holding the deep
content per topic (storage, schema and query languages, indexes,
embeddings, branches/commits, runs, merge, changes, execution, policy,
server, CLI reference, audit, errors, CI, constants, v0.3.1 notes).
Adds scripts/check-agents-md.sh and a check_agents_md CI job that
verifies every docs/ link in AGENTS.md resolves and every doc in the
canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
