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Author SHA1 Message Date
08f2397615 fix(webhook): extract links for incremental push syncs (#2849)
GitHub webhook + sync-trigger 'sync' jobs never opted into extraction:
the standalone sync handler defaults noExtract to TRUE, so webhook-
imported pages advanced the source bookmark with links_extracted_at
unstamped — and nothing behind a standalone job ever swept them (the
autopilot cycle's extract phase only walks that cycle's changedSlugs).

Fix, both halves of the issue:
- webhook + sync-trigger payloads pass noExtract:false so normal
  incremental pushes get sync's inline link/timeline extraction.
- >100-file deferral branch: performSync surfaces extractDeferred, and
  the sync job handler queues a source-scoped extract{stale:true}
  follow-up job (idempotent sweep; extract handler gains a stale mode
  backed by the same extractStaleFromDB core as `gbrain extract --stale`).

Tests: new sync-large-deferral-extract.serial.test.ts drives a real
101-file incremental sync end-to-end (deferral flag → queued follow-up →
stale sweep recovers links + watermark); webhook payload contract test +
sync-trigger noExtract assertion salvaged from #2850.

Fixes #2849
Takeover of #2850

Co-authored-by: patentsong <patentsong@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-21 14:38:43 -07:00
12 changed files with 229 additions and 139 deletions
+1 -1
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@@ -1651,7 +1651,7 @@ async function extractTimelineFromDB(
* make re-extraction idempotent). EVERY processed page is stamped, including
* zero-link pages — they WERE processed.
*/
async function extractStaleFromDB(
export async function extractStaleFromDB(
engine: BrainEngine,
opts: {
dryRun: boolean;
+39 -1
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@@ -1479,7 +1479,31 @@ export async function registerBuiltinHandlers(
embedSkipReason = 'auto_embed_disabled';
}
return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason };
// #2849: large-sync extract deferral follow-up. performSync skips inline
// link/timeline extraction when totalChanges > 100, leaving
// links_extracted_at unstamped. A standalone sync job (webhook push,
// sync trigger) has no autopilot extract phase behind it, so the pages
// would stay extraction-stale until a manual `gbrain extract --stale`.
// Queue a source-scoped stale sweep instead. Best-effort + idempotent:
// a duplicate sweep finds 0 stale pages and no-ops.
let extractJobId: number | null = null;
if (result.extractDeferred) {
try {
const { MinionQueue } = await import('../core/minions/queue.ts');
const queue = new MinionQueue(engine);
const followUp = await queue.add(
'extract',
{ stale: true, ...(sourceId ? { sourceId } : {}) },
{
idempotency_key: `sync-extract-stale:${sourceId ?? 'default'}:${Math.floor(Date.now() / 30_000)}`,
maxWaiting: 1,
},
);
extractJobId = followUp.id;
} catch { /* best-effort: extract --stale sweeps it later */ }
}
return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason, extract_stale_job_id: extractJobId };
});
registerBuiltinJob(worker, engine, 'embed', async (job) => {
@@ -1652,6 +1676,20 @@ export async function registerBuiltinHandlers(
});
worker.register('extract', async (job) => {
// #2849: stale-sweep mode — the sync handler's large-sync deferral
// follow-up. DB-source (reads page content from the DB, so it runs on
// checkout-less brains), source-scopable, idempotent. Same core as
// `gbrain extract --stale`.
if (job.data.stale === true) {
const { extractStaleFromDB } = await import('./extract.ts');
return await extractStaleFromDB(engine, {
dryRun: !!job.data.dryRun,
jsonMode: false,
includeFrontmatter: false,
sourceIdFilter: typeof job.data.sourceId === 'string' ? job.data.sourceId : undefined,
catchUp: false,
});
}
const { runExtractCore } = await import('./extract.ts');
const mode = (typeof job.data.mode === 'string' && ['links', 'timeline', 'all'].includes(job.data.mode))
? (job.data.mode as 'links' | 'timeline' | 'all')
+1 -5
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@@ -142,16 +142,12 @@ export async function runOnboard(engine: BrainEngine, args: string[]): Promise<v
// --auto path: runs through the T2 library orchestrator. Hooks emit CLI
// progress to stderr; the final result lands as JSON on stdout (or human
// summary). extraRemediations (gathered above from runAllOnboardChecks)
// is threaded into the runner so the onboard-check remediations
// (extract-ner, extract-timeline-from-meetings, etc.) reach the planner
// — the same wiring the --check path uses above.
// summary).
const result = await runRemediation(
engine,
{
targetScore,
maxUsd,
extraRemediations,
// --auto --yes opts into the prompt_required tier too; library
// doesn't distinguish auto_apply vs prompt_required, it just runs
// every remediation in the plan. The plan-building side (T12 render)
+8 -2
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@@ -2146,8 +2146,13 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
// Other event types (ping, pull_request, etc.) return 202 'ignored'
// so GitHub doesn't retry.
// D15.5: HMAC compare uses the shared safeHexEqual helper.
// D18: submits 'sync' job with auto_embed_backfill=true and priority -10
// (above autopilot's 0).
// D18: submits 'sync' job with extraction + auto_embed_backfill enabled and
// priority -10 (above autopilot's 0). noExtract:false opts normal
// incremental pushes into sync's inline link/timeline extraction (#2849
// — the standalone sync handler defaults noExtract to TRUE, which left
// webhook-imported pages permanently stale). Large (>100 file) pushes
// defer inline extract; the sync handler queues an extract --stale
// follow-up job for that branch.
// ---------------------------------------------------------------------------
const githubWebhookLimiter = rateLimit({
windowMs: 60_000,
@@ -2267,6 +2272,7 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
'sync',
{
sourceId: source.id,
noExtract: false,
auto_embed_backfill: true,
embed_reason: 'webhook',
},
+19 -1
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@@ -222,6 +222,14 @@ export interface SyncResult {
* everything," the exact misdiagnosis in the #1794 recurrence report.
*/
bankedFiles?: number;
/**
* #2849: true when extraction was REQUESTED (noExtract false) but this sync
* skipped inline link/timeline extraction because totalChanges > 100 (the
* #1794 large-sync deferral). links_extracted_at stays unstamped for the
* imported pages. The standalone `sync` job handler queues a source-scoped
* `extract --stale` follow-up when set; CLI runs print the manual hint.
*/
extractDeferred?: boolean;
}
/**
@@ -1379,6 +1387,10 @@ See also:
{
sourceId: sourceIdArg,
repoPath: source.local_path,
// #2849: opt in to inline extraction — the standalone sync handler
// defaults noExtract to TRUE (dedupe for doctor's [sync, extract]
// remediation plan), which would leave triggered syncs extraction-stale.
noExtract: false,
auto_embed_backfill: true,
embed_reason: 'sync_trigger',
},
@@ -3287,11 +3299,16 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
// the stale sweep scans the whole source, so banked-across-runs pages are
// covered regardless.
const extractOpts = opts.sourceId ? { sourceId: opts.sourceId } : undefined;
let extractDeferred = false;
if (!opts.noExtract && totalChanges > 100 && pagesAffected.length > 0) {
// #2849: surface the deferral to callers. A standalone sync job (webhook
// push, sync trigger) has no autopilot extract phase behind it, so the
// job handler queues an `extract --stale` follow-up off this flag.
extractDeferred = true;
slog(
` Large sync: deferring link/timeline extraction. ` +
`Run 'gbrain extract --stale${opts.sourceId ? ` --source-id ${opts.sourceId}` : ''}' ` +
`(or let the autopilot cycle's extract phase sweep it).`,
`(sync jobs queue this follow-up automatically).`,
);
}
if (!opts.noExtract && totalChanges <= 100 && pagesAffected.length > 0) {
@@ -3400,6 +3417,7 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
chunksCreated,
embedded,
pagesAffected,
extractDeferred,
};
}
+1 -1
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@@ -4957,7 +4957,7 @@ const run_onboard: Operation = {
// typo, the underlying queue.add would reject. Defense-in-depth.
const result = await runRemediation(
ctx.engine,
{ targetScore, maxUsd, extraRemediations: allowedExtras },
{ targetScore, maxUsd },
{},
);
+3 -10
View File
@@ -66,10 +66,9 @@ export async function runRemediation(
} = await import('../remediation-checkpoint.ts');
const ctx = await loadRecommendationContext(engine);
const extraRemediations = opts.extraRemediations ?? [];
// Pre-flight ceiling check via the shared plan computation.
const initialPlan = await computeRemediationPlan(engine, { targetScore, extraRemediations });
const initialPlan = await computeRemediationPlan(engine, { targetScore });
if (initialPlan.target_unreachable) {
hooks.onTargetUnreachable?.(targetScore, initialPlan.max_reachable_score);
return {
@@ -88,7 +87,7 @@ export async function runRemediation(
}
const initialHealth = await engine.getHealth();
let recs: RemediationStep[] = computeRecommendations(initialHealth, ctx, extraRemediations)
let recs: RemediationStep[] = computeRecommendations(initialHealth, ctx)
.filter((r) => r.status === 'remediable');
if (recs.length === 0) {
hooks.onNothingToDo?.(initialHealth.brain_score, targetScore);
@@ -306,13 +305,7 @@ export async function runRemediation(
// steps with bumped retry suffix (D1).
if (recs.length === 0 || stepCount >= maxJobs) break;
const freshHealth = await engine.getHealth();
// Extras carry a static status:'remediable' — a fresh health snapshot
// never ages them out the way health-derived steps drop. Filter out
// ids this run already processed (any terminal status), or the recheck
// would resubmit completed extras every iteration, forever.
const processedIds = new Set(submitted.map((s) => s.id));
const pendingExtras = extraRemediations.filter((r) => !processedIds.has(r.id));
recs = computeRecommendations(freshHealth, ctx, pendingExtras).filter((r) => r.status === 'remediable');
recs = computeRecommendations(freshHealth, ctx).filter((r) => r.status === 'remediable');
}
};
-10
View File
@@ -63,16 +63,6 @@ export interface RemediationOpts {
resumePlanHash?: string;
/** Whether to attempt resume at all (default false). */
resume?: boolean;
/**
* Caller-supplied RemediationStep entries threaded into the planner.
* Mirrors RemediationPlanOpts.extraRemediations so onboard's --apply
* --auto path (and MCP run_onboard auto modes) forward the same
* onboard-check remediations the --check path already passes through
* computeRemediationPlan. Without this the runner saw only generic
* brain_score remediations and reported "Nothing to do" whenever the
* only applicable work was an extra (e.g. extract-ner).
*/
extraRemediations?: RemediationStep[];
}
/**
-108
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@@ -1,108 +0,0 @@
// test/remediation-run-extras.serial.test.ts
// Regression for PR #2161 takeover: `gbrain onboard --apply --auto` dropped
// onboard-check extraRemediations. Two distinct halves of the bug:
// 1. runRemediation built the pre-flight plan + initial recs WITHOUT the
// extras, so an extras-only plan reported "Nothing to do".
// 2. The D7 mid-run recheck rebuilt recs WITHOUT the extras after every
// completed step, so with 2+ plannable steps all remaining extras were
// dropped after step 1. The recheck must also filter out extras this
// run already processed — extras carry static status:'remediable', so
// unfiltered threading would resubmit completed extras forever.
//
// SERIAL: mock.module (queue + wait-for-completion stubs, R2) + GBRAIN_HOME
// env mutation so checkpoint files land in a tmpdir, not ~/.gbrain.
import { describe, expect, test, beforeAll, afterAll, mock } from 'bun:test';
import { mkdtempSync, rmSync } from 'node:fs';
import { tmpdir } from 'node:os';
import { join } from 'node:path';
import { PGLiteEngine } from '../src/core/pglite-engine.ts';
import { makeRemediationStep } from '../src/core/remediation-step.ts';
// Stub the Minion queue: every submitted job is immediately 'completed'.
// runRemediation only calls queue.add + waitForCompletion(queue, id).
let nextJobId = 1;
const submittedJobs: Array<{ name: string }> = [];
mock.module('../src/core/minions/queue.ts', () => ({
MinionQueue: class {
async add(name: string) {
submittedJobs.push({ name });
return { id: nextJobId++, status: 'completed' };
}
},
}));
mock.module('../src/core/minions/wait-for-completion.ts', () => ({
waitForCompletion: async () => ({ status: 'completed' }),
}));
let engine: PGLiteEngine;
let home: string;
const prevHome = process.env.GBRAIN_HOME;
beforeAll(async () => {
home = mkdtempSync(join(tmpdir(), 'gbrain-remextras-'));
process.env.GBRAIN_HOME = home;
engine = new PGLiteEngine();
await engine.connect({});
await engine.initSchema();
}, 120_000);
afterAll(async () => {
await engine.disconnect();
if (prevHome === undefined) delete process.env.GBRAIN_HOME;
else process.env.GBRAIN_HOME = prevHome;
rmSync(home, { recursive: true, force: true });
});
function extra(id: string, job: string) {
return makeRemediationStep({
id,
job,
params: {},
severity: 'medium',
est_seconds: 5,
est_usd_cost: 0,
rationale: 'synthetic onboard-check extra',
status: 'remediable',
});
}
describe('runRemediation extraRemediations threading', () => {
test('extras-only plan runs BOTH extras and terminates (no Nothing-to-do, no resubmit loop)', async () => {
// Empty PGLite brain → zero health-derived recommendations. Without the
// fix, half 1 makes this run return submitted: [] via onNothingToDo.
// With only half 1 (the original PR #2161 diff), the mid-run recheck
// drops the second extra after step 1 — submitted has 1 entry, not 2.
const { runRemediation } = await import('../src/core/remediation/run.ts');
let nothingToDo = false;
const result = await runRemediation(
engine,
{
targetScore: 1,
extraRemediations: [
extra('onboard.extract_ner', 'extract-ner'),
extra('onboard.extract_timeline', 'extract-timeline-from-meetings'),
],
// Safety bound: an unfiltered recheck would resubmit completed
// extras forever; maxJobs turns that regression into a fast fail
// (extra count > 1 below) instead of a hung test.
maxJobs: 5,
},
{ onNothingToDo: () => { nothingToDo = true; } },
);
expect(nothingToDo).toBe(false);
const ids = result.submitted.map((s) => s.id);
expect(ids).toContain('onboard.extract_ner');
expect(ids).toContain('onboard.extract_timeline');
// Each extra ran exactly once — the recheck must not re-plan extras the
// run already processed.
expect(ids.filter((i) => i === 'onboard.extract_ner').length).toBe(1);
expect(ids.filter((i) => i === 'onboard.extract_timeline').length).toBe(1);
expect(result.submitted.every((s) => s.status === 'completed')).toBe(true);
expect(submittedJobs.map((j) => j.name).sort()).toEqual([
'extract-ner',
'extract-timeline-from-meetings',
]);
});
});
+23
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@@ -16,6 +16,7 @@
*/
import { describe, test, expect } from 'bun:test';
import { createHmac } from 'node:crypto';
import { readFileSync } from 'node:fs';
import { safeHexEqual } from '../src/core/timing-safe.ts';
const GITHUB_SECRET = 'super-secret-webhook-key';
@@ -123,3 +124,25 @@ describe('Branch ref construction (D5)', () => {
expect(pushedRef === `refs/heads/${trackedBranch}`).toBe(false);
});
});
describe('Webhook sync job extraction contract (#2849)', () => {
test('opts into extraction before the pushed commit is consumed', () => {
const serveSource = readFileSync(
new URL('../src/commands/serve-http.ts', import.meta.url),
'utf8',
);
const routeStart = serveSource.indexOf("'/webhooks/github'");
const queueStart = serveSource.indexOf('const job = await queue.add(', routeStart);
const responseStart = serveSource.indexOf('res.status(202)', queueStart);
expect(routeStart).toBeGreaterThanOrEqual(0);
expect(queueStart).toBeGreaterThan(routeStart);
expect(responseStart).toBeGreaterThan(queueStart);
const routeSource = serveSource.slice(queueStart, responseStart);
const payload = routeSource.match(
/queue\.add\(\s*'sync',\s*\{([\s\S]*?)\}\s*,\s*\{/,
);
expect(payload).not.toBeNull();
expect(payload?.[1]).toMatch(/\bnoExtract:\s*false\b/);
});
});
@@ -0,0 +1,130 @@
/**
* #2849 large-sync extract deferral queues an `extract --stale` follow-up.
*
* performSync's incremental path skips inline link/timeline extraction when
* totalChanges > 100 (the #1794 large-sync deferral), leaving
* links_extracted_at unstamped. Pre-fix, a standalone sync job (webhook push,
* `gbrain sync trigger`) had NOTHING behind it to sweep those pages the
* autopilot cycle's extract phase only walks that cycle's changedSlugs so a
* large webhook push left extraction permanently stale until a manual
* `gbrain extract --stale`.
*
* Pins:
* (a) performSync surfaces `extractDeferred: true` on the >100 branch and
* leaves the pages unstamped/unlinked.
* (b) the `sync` job handler queues an `extract` job with
* { stale: true, sourceId? } when extractDeferred is set.
* (c) the `extract` handler's stale mode actually sweeps: links created +
* watermark stamped (end-to-end recovery, no manual step).
*
* Marked .serial.test.ts spawns git subprocesses + shares one PGLite engine.
*/
import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
import { mkdtempSync, writeFileSync, rmSync, mkdirSync } from 'fs';
import { execSync } from 'child_process';
import { tmpdir } from 'os';
import { join } from 'path';
import { PGLiteEngine } from '../src/core/pglite-engine.ts';
import { MinionWorker } from '../src/core/minions/worker.ts';
import { MinionQueue } from '../src/core/minions/queue.ts';
import { registerBuiltinHandlers } from '../src/commands/jobs.ts';
let engine: PGLiteEngine;
let worker: MinionWorker;
let repoPath: string;
function git(cmd: string): void { execSync(cmd, { cwd: repoPath, stdio: 'pipe' }); }
describe('#2849 — large sync defers extract and queues a stale sweep', () => {
beforeAll(async () => {
engine = new PGLiteEngine();
await engine.connect({});
await engine.initSchema();
worker = new MinionWorker(engine, { queue: 'test' });
await registerBuiltinHandlers(worker, engine, { quiet: true });
repoPath = mkdtempSync(join(tmpdir(), 'gbrain-large-defer-'));
git('git init');
git('git config user.email "t@t.com"');
git('git config user.name "T"');
mkdirSync(join(repoPath, 'people'), { recursive: true });
mkdirSync(join(repoPath, 'notes'), { recursive: true });
writeFileSync(join(repoPath, 'people/alice.md'), [
'---', 'type: person', 'title: Alice', '---', '', 'Alice is a founder.',
].join('\n'));
git('git add -A && git commit -m "initial"');
// Seed: full first sync imports the anchor page + sets last_commit.
const { performSync } = await import('../src/commands/sync.ts');
await performSync(engine, { repoPath, full: true, noPull: true, noEmbed: true });
// Second commit: 101 new pages → incremental totalChanges > 100.
for (let i = 0; i < 101; i++) {
writeFileSync(join(repoPath, `notes/n${i}.md`), [
'---', 'type: note', `title: Note ${i}`, '---', '',
`[Alice](people/alice) appears in note ${i}.`,
].join('\n'));
}
git('git add -A && git commit -m "add 101 pages"');
}, 120_000);
afterAll(async () => {
if (repoPath) rmSync(repoPath, { recursive: true, force: true });
if (engine) await engine.disconnect();
}, 60_000);
test('sync handler defers inline extract and queues extract{stale} follow-up; stale sweep recovers', async () => {
const syncHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
.handlers.get('sync');
expect(syncHandler).toBeDefined();
// Same payload shape the webhook submits (minus embed backfill noise).
const result = await syncHandler!({
data: { repoPath, noExtract: false, noPull: true, auto_embed_backfill: false },
signal: { aborted: false },
updateProgress: async () => {},
}) as { status: string; extractDeferred?: boolean; extract_stale_job_id?: number | null };
expect(result.status).toBe('synced');
// (a) inline extract was deferred, pages left stale.
expect(result.extractDeferred).toBe(true);
const staleBefore = await engine.countStalePagesForExtraction();
expect(staleBefore).toBeGreaterThan(100);
expect(await engine.getLinks('notes/n0')).toHaveLength(0);
// (b) a follow-up extract job with stale:true was queued.
expect(result.extract_stale_job_id).toBeGreaterThan(0);
const queue = new MinionQueue(engine);
const extractJobs = await queue.getJobs({ name: 'extract', limit: 5 });
expect(extractJobs.length).toBe(1);
expect((extractJobs[0].data as { stale: boolean }).stale).toBe(true);
// (c) running the extract handler's stale mode recovers: links + stamps.
const extractHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
.handlers.get('extract');
await extractHandler!({
data: extractJobs[0].data,
signal: { aborted: false },
updateProgress: async () => {},
});
const links = await engine.getLinks('notes/n0');
expect(links.some(l => l.to_slug === 'people/alice')).toBe(true);
const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
`SELECT links_extracted_at FROM pages WHERE slug = 'notes/n0'`,
);
expect(rows[0]?.links_extracted_at).not.toBeNull();
}, 180_000);
test('sub-threshold sync does NOT set extractDeferred (no spurious follow-up)', async () => {
// One more small commit → inline extract path, no deferral.
writeFileSync(join(repoPath, 'notes/small.md'), [
'---', 'type: note', 'title: Small', '---', '', 'No big deal.',
].join('\n'));
git('git add -A && git commit -m "one small page"');
const { performSync } = await import('../src/commands/sync.ts');
const result = await performSync(engine, { repoPath, noPull: true, noEmbed: true });
expect(result.status).toBe('synced');
expect(result.extractDeferred).toBeFalsy();
}, 60_000);
});
+4
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@@ -100,6 +100,10 @@ describe('runSyncTrigger', () => {
const job = jobs[0];
expect(job.priority).toBe(-10);
expect((job.data as { sourceId: string }).sourceId).toBe('default');
// #2849: opt in to inline extraction — the standalone sync handler
// defaults noExtract to TRUE, which would leave triggered syncs
// extraction-stale.
expect((job.data as { noExtract: boolean }).noExtract).toBe(false);
expect((job.data as { auto_embed_backfill: boolean }).auto_embed_backfill).toBe(true);
});