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fix(backup): detect missing daily attempts - #820

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EtanHey merged 1 commit into
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wt/p818-root-cause
Sep 9, 2026
Merged

fix(backup): detect missing daily attempts#820
EtanHey merged 1 commit into
mainfrom
wt/p818-root-cause

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@EtanHey

@EtanHey EtanHey commented Sep 9, 2026

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Summary

  • stamp every JSONL backup terminal receipt with a timezone-aware attempted_at
  • persist caught timeout/upload failures to the same durable attempt log
  • classify the latest receipt independently from the backup process as verified, no-op, failed, missing, invalid, or stale
  • surface failed or older-than-36-hour attempts as critical health-check issues

Root-cause evidence

  • The July 1-16 and July 18-23 bundles were not missed runs: the durable log records verified Drive uploads, local archive removal after verification, and later retention pruning of those same objects.
  • June 14 has no run receipt and no surviving stdout/stderr evidence. The available artifacts cannot distinguish a job that never fired from a process that died before its first observable output.
  • The verified June 15 bundle contains 184 members with June 14 mtimes, so the next successful bundle absorbed those source changes.

This PR intentionally does not re-enable the disabled LaunchAgent or alter retention. It adds source/test detection only; merge does not prove the detector is installed or live.

Verification

  • BRAINLAYER_PREPUSH_SCOPE=changed-only git push: 67 focused Python tests, 3 MCP tests, 40 isolated tests, 1 Bun test, and the FTS shell regression all passed.
  • Full suite with ulimit -n 8192: 5,189 passed; 3 unrelated order-dependent failures in test_retro_self_pollution_quarantine.py; all three pass when rerun alone.
  • Claude pair review: ACCEPT. Its one non-blocking timezone finding was fixed by interpreting legacy archive dates at the 05:00 local launchd schedule before converting to UTC.
  • Local CodeRabbit review completed; two suggestions were rejected because log mtime is not trustworthy attempt evidence and a zero-covered no-op is legitimate when all candidates are still active.

Closes #818

— brainlayerCodex-9451c648 (worker) · codex/gpt-5.6-sol


Note

Medium Risk
Scheduled health checks will now fail critically when the default backup attempt log is missing or stale, which changes operator alerting behavior without modifying backup scheduling itself.

Overview
Adds independent detection of missing or bad JSONL backup runs to brainlayer health-check, so a job that never starts cannot look healthy.

The backup job now writes a timezone-aware attempted_at on every terminal receipt (successful no-op/upload, and failures caught in main()), and appends timeout/exception outcomes to the same JSONL attempt log via _append_terminal_failure.

run_health_check reads the latest log line, classifies it (verified_bundle, no_op, failed, missing, invalid, stale), and raises critical issues when the receipt is absent, malformed, unverified, failed, or older than 36 hours (overridable with BRAINLAYER_JSONL_BACKUP_MAX_AGE_SECONDS / BRAINLAYER_JSONL_BACKUP_LOG_PATH). Legacy receipts without attempted_at infer time from archive name at 05:00 local. Results surface on HealthCheckResult.jsonl_backup and ops docs are updated.

Reviewed by Cursor Bugbot for commit db8d611. Bugbot is set up for automated code reviews on this repo. Configure here.

Note

Add JSONL backup receipt health check to detect missing daily attempts

  • Backup receipts now carry a timezone-aware attempted_at stamp, including no-op results and terminal failures written by jsonl_backup.main
  • New inspect_jsonl_backup_health in health_check.py parses the last nonblank log line, classifies it (verified no-op, verified bundle, failed, stale, missing, malformed), and returns a critical issue when the receipt is absent, undated, older than the configured threshold, or not a recognized success
  • run_health_check now invokes the inspector and adds any returned issue to the aggregate result, so a bad receipt can fail the overall health check
  • Default log path and a 36-hour max receipt age are configurable via BRAINLAYER_JSONL_BACKUP_LOG_PATH and BRAINLAYER_JSONL_BACKUP_MAX_AGE_SECONDS (one-hour minimum); a legacy archive-date fallback covers older receipts without attempted_at
  • Risk: _jsonl_backup_attempt_time rejects naive (non-timezone-aware) timestamps and unrecognized archive names; any existing receipt without attempted_at must match the legacy archive-date format or it will be classified as undated/critical

Macroscope summarized db8d611.

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📒 Files selected for processing (5)
  • docs/operations/brainlayer-health-check.md
  • src/brainlayer/health_check.py
  • src/brainlayer/jsonl_backup.py
  • tests/test_jsonl_backup.py
  • tests/test_stability_health_check.py

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BrainLayer ratchet

Every Value below was measured by this run. A row this machine cannot measure says n/a — <reason> instead of a number; baselines in Notes name their own machine, method and date and were not measured here.

Row Status Value (measured by this run) Method Notes
commit provenance 🟢 GREEN measured db8d6115aa64 == PR head · checkout 738cc365e3ad commit graph + live PR head · in-process · runner Which commit this whole table is about. On a pull_request event the checkout is GitHub's synthetic merge ref, whose sha is not on the PR — #759's table printed 13fa724278bf while that PR's head was 4632f979 — so this row names the PR-head parent instead, the sha a reviewer can actually see. The comparison sha is read live from repos/{owner}/{repo}/pulls/{n} when the table is collected, not taken from the event payload, because the payload cannot know the run has been overtaken. Residual window, stated rather than papered over: a push landing between that read and the comment being posted is not caught here — the run for that push refreshes the table.
baseline attestation 🟢 GREEN baseline f421d1a7c5e6 matches the main attestation (run 34387188527 · main 0f90627638a3 · 2026-09-09T18:08:35Z) main attestation artifact via Actions API · in-process · runner What every comparison is measured AGAINST, and who says so. The baseline fields of tests/fixtures/sprint_gate/corpus.json (queries, latency_baseline_ms, thresholds) are compared to the ratchet-attestation artifact of the latest successful push or (no-input) workflow_dispatch run of ratchet-attest.yml on main, fetched through the Actions API — a PR run cannot write to another run's artifacts. A field that differs is RED unless that main run measured the new value. The calibrated socket collector can license p50/p95; every absent measured path stays locked, so missing collection never passes as permission for a hand edit. Boundary: the comparator is this PR's checkout of ci_ratchet_table.py, diff-reviewable, not tamper-proof.
provenance 🟢 GREEN stamped 738cc365e3ad == HEAD, tree clean wheel stamp · in-process · runner Sha half of #749 keg-mode provenance: a keg built from this wheel can answer __build_sha__. The helper-age and served-process predicates need a running BrainBar and are measured only by scripts/sprint_gate.py on an installed Mac. The sha here is the checkout's — the merge ref on a PR — because that is what publish.yml stamps at release time; the PR-head sha this table describes is the one in commit provenance above.
fallback replay debt ⚪ n/a n/a — no fallback queue on this machine: the pending memories live in ~/Gits/*/docs.local/decisions, and docs.local/ is gitignored, so a runner checkout has no copy of them to count docs.local walk · machine with the fallback queue intended_brain_store: true with no chunk_id means a memory reached disk and never reached the DB, so it answers no brain_search. Budget: 0. Any pending or unparseable file is a finding, never a band -- 122 of these sat from 2026-06-28 to 2026-09-05 because nothing counted them where a reader would look. Measured by walking the tree, so it is only ever measured on a machine that HAS the tree.
mapped bytes ⚪ n/a n/a — no BrainBar daemon at /tmp/brainbar.sock: this row needs the daemon, its hybrid helper and the indexed corpus running together, and no GitHub-hosted runner has them (macOS included) — only a self-hosted Darwin/arm64 runner on an installed Mac would socket · installed Mac Baseline 26.2 GB — installed Mac, socket, 2026-09-03, after R2 drained 15,070 → 0. Up from 16.8 GB because the drain left more vectors mapped under the same cap: the change is the drain, not a leak. Not measured by this run.
search p50/p95 ⚪ n/a n/a — no BrainBar daemon at /tmp/brainbar.sock: this row needs the daemon, its hybrid helper and the indexed corpus running together, and no GitHub-hosted runner has them (macOS included) — only a self-hosted Darwin/arm64 runner on an installed Mac would socket · installed Mac Margin p50: margin unmeasured — 0 of the 5 attested green main runs it needs; no verdict is rendered from fewer. Margin p95: margin unmeasured — 0 of the 5 attested green main runs it needs; no verdict is rendered from fewer. Calibrated on MacBook-Pro.local at 2026-09-01T08:42:22Z under active_sprint_load (tests/fixtures/sprint_gate/corpus.json). Not measured by this run.
idle CPU ⚪ n/a n/a — no BrainBar daemon at /tmp/brainbar.sock: this row needs the daemon, its hybrid helper and the indexed corpus running together, and no GitHub-hosted runner has them (macOS included) — only a self-hosted Darwin/arm64 runner on an installed Mac would ps sampling · installed Mac Ceiling: average CPU < 30% over a 60 s window (resource_budget in scripts/sprint_gate.py), ratified and kept as a hard budget. Margin daemon: margin unmeasured — 0 of the 5 attested green main runs it needs; no verdict is rendered from fewer. Margin helper: margin unmeasured — 0 of the 5 attested green main runs it needs; no verdict is rendered from fewer. Margin watcher: margin unmeasured — 0 of the 5 attested green main runs it needs; no verdict is rendered from fewer. Needs the BrainBar daemon, helper and watcher actually running. Not measured by this run.
signature_valid ⚪ n/a n/a — the macOS signature-parity job is trigger-gated and did not run on this PR: it touches no release or signing path (pyproject.toml, scripts/release-*, scripts/brainlayer-version-check.sh, publish.yml, ratchet.yml) and carries no ratchet:signatures label — a GitHub macOS runner bills at ~10× Linux minutes and rebuilds the keg venv from source codesign · installed keg scripts/release-verify-signatures.sh <keg> codesign-verifies every *.so/*.dylib under libexec/venv. The macOS parity job installs the published tap formula (etanhey/layers/brainlayer), so this row measures the release path — formula, published sdist and Homebrew's relocation — and not this PR's tree. Release-time baseline for the same keg on a different machine: 442 valid / 0 invalid — installed Mac (M4 Max), brew --prefix brainlayer 1.5.11, 2026-09-03.

🟢 GREEN measured, within budget · 🔴 RED measured, out of budget — a finding to clear before merge · ⚪ n/a not measurable on this machine, never guessed.

No RED rows.

Measured on Linux/x86_64 · measured db8d6115aa64 · PR head db8d6115aa64 · checkout 738cc365e3ad · run · updated 2026-09-09 18:12:20 UTC

@EtanHey EtanHey added the size:M Tight-loop PR size: 151-400 hand-written lines changed label Sep 9, 2026
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@EtanHey

EtanHey commented Sep 9, 2026

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@coderabbitai review

@codex review

Please review the latest head 085ea06f for #818 Phase 1, especially fail-closed receipt parsing, legitimate no-op classification, and health-check integration.

— brainlayerCodex-9451c648 (worker) · codex/gpt-5.6-sol

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@EtanHey I will review commit 085ea06f. I will check fail-closed receipt parsing, valid no-op classification, and health-check integration.

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📝 Code Review ⚠️ Failed 2026-09-09T17:36:10.334016Z 085ea06 Manual request
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Provided git ref 085ea06f73d24ae967559c88f005938f6d28bd76 does not exist
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@EtanHey

EtanHey commented Sep 9, 2026

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@codex review

Retry after GitHub now reports PR head 085ea06f73d24ae967559c88f005938f6d28bd76; the first attempt hit a transient missing-ref error.

— brainlayerCodex-9451c648 (worker) · codex/gpt-5.6-sol

"error": str(exc),
"traceback": traceback.format_exc(),
}
_append_terminal_failure(log_path, result)

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🟡 Medium brainlayer/jsonl_backup.py:528

When run_backup has already uploaded and verified the archive, an exception from the post-backup _enqueue_run_summary call is recorded as a new status="failed" receipt, so the last log line falsely reports a critical backup failure. Handle summary-enqueue errors separately and preserve the verified backup receipt as the terminal backup status.

🚀 Reply "fix it for me" or copy this AI Prompt for your agent:
In file @src/brainlayer/jsonl_backup.py around line 528:

When `run_backup` has already uploaded and verified the archive, an exception from the post-backup `_enqueue_run_summary` call is recorded as a new `status="failed"` receipt, so the last log line falsely reports a critical backup failure. Handle summary-enqueue errors separately and preserve the verified backup receipt as the terminal backup status.

return None
return finish_slow(stage, f"health-check exceeded {config.max_duration_seconds:.0f}s during {stage}")

result.jsonl_backup, jsonl_backup_issue = inspect_jsonl_backup_health(

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🟠 High brainlayer/health_check.py:1229

run_health_check can exceed max_duration_seconds or consume excessive memory before reaching any slow-check handling. inspect_jsonl_backup_health reads and splits the entire append-only log synchronously at line 1229, so a large forever_files backup result blocks the existing deadline checks; bound or make this inspection deadline-aware.

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In file @src/brainlayer/health_check.py around line 1229:

`run_health_check` can exceed `max_duration_seconds` or consume excessive memory before reaching any slow-check handling. `inspect_jsonl_backup_health` reads and splits the entire append-only log synchronously at line 1229, so a large `forever_files` backup result blocks the existing deadline checks; bound or make this inspection deadline-aware.

except FileNotFoundError:
status = JsonlBackupHealth(state="missing", detail=f"attempt log does not exist: {resolved}")
return status, HealthIssue("jsonl_backup_attempt_missing", "critical", status.detail)
except OSError as exc:

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🟠 High brainlayer/health_check.py:857

A non-UTF-8 attempt log raises UnicodeDecodeError and aborts run_health_check, so no jsonl_backup_attempt_invalid issue or health state is emitted. Catch the decoding error with the existing unreadable-log path so the receipt is classified as invalid.

-    except OSError as exc:
+    except (OSError, UnicodeDecodeError) as exc:
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In file @src/brainlayer/health_check.py around line 857:

A non-UTF-8 attempt log raises `UnicodeDecodeError` and aborts `run_health_check`, so no `jsonl_backup_attempt_invalid` issue or health state is emitted. Catch the decoding error with the existing unreadable-log path so the receipt is classified as invalid.

Comment on lines +864 to +871
try:
payload = json.loads(lines[-1])
except json.JSONDecodeError as exc:
status = JsonlBackupHealth(state="invalid", detail=f"latest attempt receipt is malformed JSON: {exc}")
return status, HealthIssue("jsonl_backup_attempt_invalid", "critical", status.detail)
if not isinstance(payload, dict):
status = JsonlBackupHealth(state="invalid", detail="latest attempt receipt is not a JSON object")
return status, HealthIssue("jsonl_backup_attempt_invalid", "critical", status.detail)

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🟡 Medium brainlayer/health_check.py:864

A trailing non-JSON diagnostic on the shared stdout/stderr log makes inspect_jsonl_backup_health report jsonl_backup_attempt_invalid even when the preceding line is a fresh successful receipt. Because the function unconditionally parses lines[-1], scan backward for the latest JSON receipt instead of requiring the literal final log line to be JSON.

-    try:
-        payload = json.loads(lines[-1])
-    except json.JSONDecodeError as exc:
-        status = JsonlBackupHealth(state="invalid", detail=f"latest attempt receipt is malformed JSON: {exc}")
-        return status, HealthIssue("jsonl_backup_attempt_invalid", "critical", status.detail)
-    if not isinstance(payload, dict):
-        status = JsonlBackupHealth(state="invalid", detail="latest attempt receipt is not a JSON object")
+    payload = None
+    for line in reversed(lines):
+        try:
+            candidate = json.loads(line)
+        except json.JSONDecodeError:
+            continue
+        if isinstance(candidate, dict):
+            payload = candidate
+            break
+    if payload is None:
+        status = JsonlBackupHealth(state="invalid", detail="attempt log contains no JSON receipt object")
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In file @src/brainlayer/health_check.py around lines 864-871:

A trailing non-JSON diagnostic on the shared stdout/stderr log makes `inspect_jsonl_backup_health` report `jsonl_backup_attempt_invalid` even when the preceding line is a fresh successful receipt. Because the function unconditionally parses `lines[-1]`, scan backward for the latest JSON receipt instead of requiring the literal final log line to be JSON.

Comment on lines +909 to +910
if backup_status == "created" and verified is True:
return JsonlBackupHealth(state="verified_bundle", **common), None

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🟡 Medium brainlayer/health_check.py:909

The created branch reports verified_bundle after only local archive verification, so run_backup(upload=False) is considered healthy even though no backup was uploaded. Remove this branch so only a verified upload or verified no-op is healthy.

-    if backup_status == "created" and verified is True:
-        return JsonlBackupHealth(state="verified_bundle", **common)
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In file @src/brainlayer/health_check.py around lines 909-910:

The `created` branch reports `verified_bundle` after only local archive verification, so `run_backup(upload=False)` is considered healthy even though no backup was uploaded. Remove this branch so only a verified upload or verified no-op is healthy.

Comment on lines +888 to +889
normalized_now = now.astimezone(UTC) if now.tzinfo is not None else now.replace(tzinfo=UTC)
age_seconds = max(0.0, (normalized_now - attempted_at).total_seconds())

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🟡 Medium brainlayer/health_check.py:888

A future-dated receipt is treated as zero age, so a verified backup remains healthy until that timestamp is reached even if no new attempts occur. The max(0.0, ...) clamp hides producer clock errors; reject or alarm on attempted_at values later than now before evaluating freshness.

    normalized_now = now.astimezone(UTC) if now.tzinfo is not None else now.replace(tzinfo=UTC)
-    age_seconds = max(0.0, (normalized_now - attempted_at).total_seconds())
+    age_seconds = (normalized_now - attempted_at).total_seconds()
+    if age_seconds < 0:
+        status = JsonlBackupHealth(
+            state="invalid",
+            status=backup_status,
+            attempted_at=attempted_at.isoformat(),
+            age_seconds=age_seconds,
+            verified=verified,
+            archive=archive,
+            detail="latest attempt receipt is dated in the future",
+        )
+        return status, HealthIssue("jsonl_backup_attempt_invalid", "critical", status.detail)
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In file @src/brainlayer/health_check.py around lines 888-889:

A future-dated receipt is treated as zero age, so a verified backup remains healthy until that timestamp is reached even if no new attempts occur. The `max(0.0, ...)` clamp hides producer clock errors; reject or alarm on `attempted_at` values later than `now` before evaluating freshness.

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@EtanHey

EtanHey commented Sep 9, 2026

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HOLD: do not merge this PR before #815.

Mandatory order is #815#820#819. After #815 merges, this branch must be rebased onto post-#815 main without taking either side wholesale in _state_matches, _select_backup_candidates, _update_state_for_uploaded, or run_backup, then this guard must print PASS:

PYTHONPATH=src python3 -m brainlayer.backup_retention_invariant src/brainlayer/jsonl_backup.py

— brainlayerCodex-9451c648 (worker) · codex/gpt-5.6-sol

Co-Authored-By: brainlayerCodex-9451c648 (worker) running gpt-5.6-sol <noreply@anthropic.com>
@EtanHey
EtanHey marked this pull request as ready for review September 9, 2026 18:31
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@EtanHey

EtanHey commented Sep 9, 2026

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Post-#815 rebase handoff: READY, not merged.

  • Rebased cleanly onto fix(backup): never treat a file as covered without a surviving archive object (S) #815 merge 0f906276; new head is db8d6115aa64e51574446dcf3c19d872b9802c17.
  • The rebased jsonl_backup.py preserves surviving_archives across _state_matches, _select_backup_candidates, _update_state_for_uploaded, and run_backup.
  • Lane B structural guard: PASS against this rebased file. Evidence-bound note: backup_retention_invariant.py is not present in current origin/main, so I executed the guard module from Lane B worktree wt/laneb-retention-guard at 9bf75f1e against this branch file.
  • Post-rebase focused verification: 72 passed; Ruff passed.
  • Changed-only push gate: 73 focused Python + 3 MCP + 40 isolated + 1 Bun + FTS shell regression passed.
  • Rebased-head CI run 34387537800: Python 3.11/3.12/3.13, lint, Swift, changes, and ratchet all green.

The HOLD/draft state is cleared. Per lane ownership, Etan/lead merges.

— brainlayerCodex-9451c648 (worker) · codex/gpt-5.6-sol

@EtanHey
EtanHey merged commit 0443e60 into main Sep 9, 2026
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jsonl backup produced NO bundle for 2026-07-18..07-23 — six silent nights, on any machine

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