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* perf(extract_atoms): batch idempotency check via atomsExistingForHashes Replaces the per-hash transcript loop (7K SQL roundtrips on big brains) with one batch query using `frontmatter->>'source_hash' = ANY($2::text[])`. Migration v104 adds the partial expression index that keeps the new query O(log n) at scale (mirrors v97 pattern: CONCURRENTLY + invalid-remnant pre-drop on Postgres, plain CREATE INDEX on PGLite). Helper exported so test/cycle/extract-atoms-batch.test.ts can drive it directly without orchestrating the full phase. Fail-open posture preserved from the prior per-hash helper. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(cycle): shorter lock TTL + active in-phase refresh + progress wiring Issue 3 + Issue 2 of the v0.41.20.0 ops-fix-wave. Codex caught during plan review that yieldBetweenPhases (the existing external hook) does NOT refresh the cycle DB lock — it's just a setImmediate() from jobs.ts:1405 / autopilot.ts:632, and lock.refresh() was never called from inside runCycle. Combined with the 30min TTL, crashed cycles wedged the lock for the full window before another worker could take over. Three coordinated changes: 1. LOCK_TTL_MINUTES 30 → 5 (src/core/cycle.ts). Crash recovers in ≤5 min instead of ≤30 min. 2. buildYieldDuringPhase(lock, outer) — exported closure that calls lock.refresh() AND the existing yieldBetweenPhases hook on every fire. Passed to both long phases (extract_atoms, synthesize_concepts) as their yieldDuringPhase opt. 3. maybeYield helper inside both phases — 30s throttle, fires inside the main work loop AND immediately after every `await chat()` LLM call (codex hardening: a single long LLM await could otherwise sit past TTL). Progress reporter wired through to both phases too (Issue 2): extract_atoms emits `[cycle.extract_atoms] N atoms / M skipped` ticks every ~1s; synthesize_concepts ticks per concept group. Cycle.ts owns start()/finish(); phases only call tick() and heartbeat() on the same reporter (NOT a child — that would produce path collision `cycle.extract_atoms.extract_atoms.work`). LockHandle interface exported for tests. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(extract): by-mention resumes from where it died Issue 4 of the v0.41.20.0 ops-fix-wave. On a 322K-page brain the sweep takes 10+ hours; if it died at 87% the user redid 87% on restart. Wires the existing `op_checkpoints` framework into extractMentionsFromDb with a flushAndCheckpoint ordering that closes the four codex-flagged correctness bugs at once: 1. Lost-links-on-crash — flush batch links to DB FIRST, commit page keys to checkpoint SECOND, persist THIRD. A crash between batch.push() and flushBatch() leaves the page un-checkpointed so resume re-scans it (no silently lost mention links). 2. Dry-run resume contradiction — dry-run does NOT load or persist the checkpoint. Verification path uses non-dry-run kill-and-resume. 3. Gazetteer hash in fingerprint — entity pages added mid-pause shift the gazetteer hash → new fingerprint → fresh scan against the new gazetteer. Without this, resumed runs would silently skip pages against a new entity set. 4. Filtered pages get checkpointed too — pages skipped by `--type` / `--since` / empty body / no-mentions all get marked completed so resume doesn't re-fetch them. Persist cadence: every 1000 items OR every 30s, whichever first (~322 persists / ~24s total overhead on the 322K-page brain). Crash window capped at 1000 pages (<0.3% loss). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(doctor): surface sync --all consolidation nudge to operators Issue 5 of the v0.41.20.0 ops-fix-wave. Multi-source brains see a paste-ready `gbrain sync --all --parallel 4 --workers 4 --skip-failed` in `gbrain doctor` output instead of maintaining two staggered per-source cron entries with manual deconfliction. New checkSyncConsolidation surfaces the recommendation when 2+ active sources exist; "not applicable" for single-source brains. Own try/catch returns warn on SQL failure — outer doctor catch wasn't a safe assumption. `skills/cron-scheduler/SKILL.md` gains a "Multi-source brains" recipe block documenting the pattern + connection-budget math (parallel × workers × 2 ≈ 32 connections at default 4/4). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(test): isolate GBRAIN_HOME in cycle-LFCA + schema-cli tests Two pre-existing tests assumed a clean ~/.gbrain/config.json and a free ~/.gbrain/cycle.lock — both shared across all gbrain processes on the machine. Sibling Conductor worktrees running their own gbrain tests poisoned the shared state, causing flakes: - test/cycle-last-full-cycle-at.test.ts test 5 timed out at 5s because runCycle returned 'skipped' (file lock held by a parallel test process), and last_full_cycle_at exit hook silently no-oped. Fix: each test wraps its body in `withEnv({GBRAIN_HOME: tmpdir})` so the file lock path becomes per-test. - test/schema-cli.test.ts `schema active reports default resolution` failed exit 1 because another worktree had set `schema_pack: gbrain-base-v2` in the shared config (a pack that doesn't exist in the bundle). Fix: gbrain() helper defaults GBRAIN_HOME to a per-file tempdir (beforeAll-owned), so subprocess invocations get an isolated config dir unless tests explicitly override. Both fixes confirmed via deliberate pollution + retest: 12/12 schema-cli tests pass under simulated `schema_pack: gbrain-base-v2` contamination; cycle-LFCA test 5 completes <2s with isolated home. Discovered during v0.41.20.0 ship while investigating parallel-worktree flake. Not caused by the ops-fix-wave but found via it. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: bump version and changelog (v0.41.20.0) Five daily-driver ops pains fixed in one wave: 1. extract_atoms 7K-roundtrip overhead → 1 batch query + index 2. silent long-running phases → progress ticks every ~1s 3. 30-min crashed-cycle lock TTL → 5 min + active in-phase refresh 4. by-mention restarts from page 0 → resumes via op_checkpoints 5. multi-source cron → doctor surfaces `sync --all --parallel` nudge Two follow-up TODOs filed under v0.41.19.0 ops-fix-wave block (will be renamed at follow-up time): - `gbrain sync print-cron` subcommand (P2 ergonomics) - Lock-loss detection in DbLockHandle.refresh() (P2 contract change) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: update CLAUDE.md key files for v0.41.20.0 ops-fix-wave Folds the v0.41.20.0 wave annotations into the cycle/extract/op-checkpoint key-files block: batch idempotency via atomsExistingForHashes, shorter cycle lock TTL with buildYieldDuringPhase active refresh, progress wiring through extract_atoms + synthesize_concepts, by-mention resume via mentionsFingerprint with flushAndCheckpoint ordering, sync_consolidation doctor check, and the 44-case test suite pinning every contract. Regenerated llms-full.txt to match (CLAUDE.md edit invariant). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * fix(ci): doctor categorization + facts-engine cosine ordering hardening Two CI-only failures caught on PR #1545 (v0.41.21.0 ops-fix-wave): 1. doctor-categories drift guard — new `sync_consolidation` check from T6 wasn't categorized in src/core/doctor-categories.ts. Added under OPS_CHECK_NAMES (it surfaces an operator-cron recommendation, not a brain-data quality signal). 2. facts-engine `embedding cosine ordering when both sides have embeddings` — passed locally, failed under CI's parallel shard. Bun's truncated assertion output didn't surface which expect() fired; hardened the test against unknown leak vectors by: - per-run unique entity_slug (`embed-test-<random8>`) instead of the static `embed-test`, so any future cross-test pollution is structurally impossible - `findIndex` + `aIdx < bIdx` assertion that pins the cosine RELATIONSHIP (A closer than B because cos(A,Q)=1.0 vs cos(B,Q)=0.0) instead of the brittle `result[0].fact === 'A'` position check. The new shape matches the test name's contract verbatim ("ordering when both sides have embeddings"), so any unrelated row in the result set can no longer flip the test. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
101 lines
3.5 KiB
TypeScript
101 lines
3.5 KiB
TypeScript
// v0.41.19.0 — T3 of ops-fix-wave (codex catch).
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//
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// Pins that buildYieldDuringPhase actually calls lock.refresh() AND the
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// outer hook on every fire. Codex caught that the prior plan's "use
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// yieldBetweenPhases" claim was false — yieldBetweenPhases is just
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// setImmediate() from jobs.ts/autopilot.ts and never refreshes the
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// cycle DB lock. Combined with TTL=5min (T2), a missing refresh would
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// lose the lock mid-phase. The closure built by buildYieldDuringPhase
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// is the active refresh path.
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import { describe, test, expect } from 'bun:test';
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import { buildYieldDuringPhase } from '../../src/core/cycle.ts';
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import type { LockHandle } from '../../src/core/cycle.ts';
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function makeMockLock(): { lock: LockHandle; refreshCount: number; releaseCount: number } {
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const state = { refreshCount: 0, releaseCount: 0 };
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const lock: LockHandle = {
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refresh: async () => { state.refreshCount++; },
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release: async () => { state.releaseCount++; },
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};
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return {
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lock,
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get refreshCount() { return state.refreshCount; },
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get releaseCount() { return state.releaseCount; },
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};
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}
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describe('buildYieldDuringPhase (T3 codex fix)', () => {
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test('returns undefined when both lock and outer are absent', () => {
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const fn = buildYieldDuringPhase(null);
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expect(fn).toBeUndefined();
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});
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test('returns a function when lock is present', () => {
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const { lock } = makeMockLock();
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const fn = buildYieldDuringPhase(lock);
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expect(typeof fn).toBe('function');
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});
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test('returns a function when only outer is present', () => {
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const fn = buildYieldDuringPhase(null, async () => {});
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expect(typeof fn).toBe('function');
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});
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test('each fire calls lock.refresh exactly once', async () => {
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const tracker = makeMockLock();
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const fn = buildYieldDuringPhase(tracker.lock);
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expect(fn).toBeDefined();
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await fn!();
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expect(tracker.refreshCount).toBe(1);
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await fn!();
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expect(tracker.refreshCount).toBe(2);
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await fn!();
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expect(tracker.refreshCount).toBe(3);
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});
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test('each fire calls the outer hook AFTER lock.refresh', async () => {
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const tracker = makeMockLock();
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const callOrder: string[] = [];
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const outer = async () => { callOrder.push('outer'); };
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const fn = buildYieldDuringPhase({
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...tracker.lock,
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refresh: async () => { callOrder.push('refresh'); tracker.lock.refresh(); },
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}, outer);
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await fn!();
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expect(callOrder).toEqual(['refresh', 'outer']);
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});
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test('lock.refresh throw is non-fatal — outer still runs', async () => {
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let outerCalled = false;
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const badLock: LockHandle = {
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refresh: async () => { throw new Error('lock stolen'); },
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release: async () => {},
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};
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const fn = buildYieldDuringPhase(badLock, async () => { outerCalled = true; });
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// Must not throw.
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await fn!();
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// Outer should still have run even though refresh threw.
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expect(outerCalled).toBe(true);
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});
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test('outer hook throw is non-fatal', async () => {
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const tracker = makeMockLock();
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const fn = buildYieldDuringPhase(tracker.lock, async () => {
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throw new Error('outer kaboom');
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});
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// Must not throw.
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await fn!();
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// Refresh still fired despite outer failure.
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expect(tracker.refreshCount).toBe(1);
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});
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test('never calls lock.release (release stays separate from refresh)', async () => {
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const tracker = makeMockLock();
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const fn = buildYieldDuringPhase(tracker.lock);
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for (let i = 0; i < 5; i++) await fn!();
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expect(tracker.refreshCount).toBe(5);
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expect(tracker.releaseCount).toBe(0);
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});
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});
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