Files
gbrain/src/core/embed-skip.ts
fa2c7a6990 v0.40.10.0 feat: content sanity defense — junk-pattern throw + oversize-skip-embed (#1351)
* feat: add content-sanity assessor + embed-skip helper + audit JSONL primitives

Four new core modules (pure, no engine I/O):

- src/core/content-sanity.ts — assessor with 6 hand-vetted junk patterns
  (Cloudflare attention-required, just-a-moment, ray-id; access-denied;
  captcha-required; bare error-page titles). Bytes measured against
  compiled_truth + timeline (parseMarkdown body split, not file bytes).
  ContentSanityBlockError tagged with PAGE_JUNK_PATTERN code so
  classifyErrorCode hits via regex without a new ImportResult field.

- src/core/content-sanity-literals.ts — operator literal-substring loader
  for ~/.gbrain/junk-substrings.txt. Comment directives for name +
  applies_to. ENOENT returns empty list (fail-soft); no regex parsing so
  no ReDoS surface.

- src/core/embed-skip.ts — single source of truth for the embed-skip
  predicate. JS isEmbedSkipped() + filterOutEmbedSkipped() for in-memory
  callers; EMBED_SKIP_FILTER_FRAGMENT raw SQL string for engine-layer
  filters. buildEmbedSkipMarker() emits the canonical frontmatter shape.
  Both Postgres and PGLite use the same JSONB '?' existence operator.

- src/core/audit/content-sanity-audit.ts — ISO-week JSONL at
  ~/.gbrain/audit/content-sanity-YYYY-Www.jsonl. Built on v0.40.4.0
  audit-writer primitive. One stream for hard-block + soft-block + warn
  events with event_type discriminator. summarizeContentSanityEvents
  rolls up by type + source + pattern hits for doctor consumption.

99 unit tests across 4 new test files (207 assertions) covering
boundaries, every built-in pattern, bytes-parity assertion, operator
literals (regex meta-chars stay literal), audit JSONL round-trip + reader.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(embed): apply embed-skip filter at all 5 stale-chunk sites

Embed sweep must skip pages with frontmatter.embed_skip set so soft-blocked
pages don't get re-embedded. Five wiring sites all use the shared helper:

  1. src/commands/embed.ts — --stale CLI path (delegates to embedAllStale)
  2. src/commands/embed.ts — --all CLI path (JS-side filterOutEmbedSkipped
     on the listPages result; Codex r2 #11 caught this previously-missed
     surface that re-embedded soft-blocked pages on every model swap)
  3. src/core/embed-stale.ts:90 — Minion helper (inherits via engine)
  4. src/core/postgres-engine.ts — listStaleChunks + countStaleChunks
     gain 'NOT (COALESCE(p.frontmatter, ''{}''::jsonb) ? ''embed_skip'')'
     filter at the SQL layer. Always JOINs pages now (pre-fix bare path
     skipped the JOIN; D4 + D8 require it for the filter).
  5. src/core/pglite-engine.ts — mirror of postgres-engine; PGLite is
     Postgres 17.5 in WASM so the same JSONB '?' operator works.

Cross-site invariant pinned by test/embed-skip.test.ts (20 cases on the
JS predicate + SQL fragment semantics). When v0.41+ promotes embed_skip
to a schema column, all 5 sites get updated in one helper file.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(ingest): wire content-sanity gate into importFromContent narrow waist

Hard-block via thrown ContentSanityBlockError; soft-block via frontmatter
marker + chunk deletion on transition (D9 invariant). Single throw point
means every wrapper site (CLI, MCP put_page, sync) inherits correct
exit/error semantics through existing exception flow — no per-wrapper
status-vocabulary changes (Codex r2 #2).

import-file.ts:
- Gate runs AFTER parseMarkdown so assessor sees compiled_truth + timeline
  + title + frontmatter (Codex r2 #5+#7).
- Kill-switch (GBRAIN_NO_SANITY=1) checked via direct process.env AS WELL
  AS effective config — loadConfig() returns null on bare installs (no
  ~/.gbrain/config.json, no DATABASE_URL) so the config-only path missed
  the kill-switch. Caught by test/import-file-content-sanity.test.ts.
- Hard-block: throws ContentSanityBlockError. Existing import.ts catch
  increments errors; sync.ts:929 catch records failure with classified code.
- Soft-block: sets parsed.frontmatter.embed_skip via buildEmbedSkipMarker
  before hash compute (so hash differs from prior version → real write).
  Chunking block guards on isEmbedSkipped → chunks stays empty → existing
  tx.deleteChunks fires (D9 transition invariant).
- Audit JSONL records every assessment (hard / soft / warn + bypass-mode).

sync.ts:
- classifyErrorCode gains /PAGE_JUNK_PATTERN/ → 'PAGE_JUNK_PATTERN' regex.
  No PAGE_OVERSIZED code because oversize is now a soft state — page lands.

config.ts:
- New content_sanity.* field on GBrainConfig (4 keys: bytes_warn,
  bytes_block, junk_patterns_enabled, disabled).
- loadConfig() reads GBRAIN_PAGE_WARN_BYTES, GBRAIN_PAGE_BLOCK_BYTES,
  GBRAIN_NO_JUNK_PATTERNS, GBRAIN_NO_SANITY env vars sparse-merged.
- loadConfigWithEngine merges DB-plane content_sanity.* keys per-key
  sparse-merge so 'gbrain config set content_sanity.bytes_block N' takes
  effect uniformly (Codex r2 #6 D1 acceptance).
- KNOWN_CONFIG_KEYS + KNOWN_CONFIG_KEY_PREFIXES include the new keys.

cli.ts:
- runImport now honors result.errors > 0 for non-zero exit. Pre-fix the
  CLI awaited runImport but discarded the result, so hard-blocked imports
  exited 0 silently (Codex r2 #3).

9 PGLite-backed unit tests pin: hard-block throws, error message contains
PAGE_JUNK_PATTERN, blocked page does NOT land in DB, soft-block writes
page with embed_skip set, soft-block deletes pre-existing chunks (D9
transition), kill-switch bypass works.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat: lint rules + doctor checks + 'gbrain sources audit' CLI

Three operator surfaces backed by the shared content-sanity assessor:

lint.ts (2 new rules):
- huge-page: bytes (compiled_truth + timeline post-parse) exceeds warn or
  block threshold. Message names the actual byte count.
- scraper-junk: built-in junk pattern OR operator literal matched.
- Lint runs parseMarkdown to extract body for bytes-parity with doctor
  (D2 — both surfaces measure body-only, not file-with-frontmatter).
- runLintCore resolves effective config once per run: file/env (sync via
  loadConfig) + DB-lift when ~/.gbrain/ is reachable (D1). CI without
  ~/.gbrain/ falls through immediately. Engine probe wrapped in try/catch
  so lint never blocks on engine state.
- Operator literals loaded once per lint run; passed through to every
  page's lintContent call.

doctor.ts (3 new checks + 1 flag):
- oversized_pages: indexed-free table scan via
  octet_length(compiled_truth) + octet_length(COALESCE(timeline, ''))
  (Codex r2 #13: octet_length is bytes, length is chars). Status warn
  on 1+ rows; oversize is now a soft state so no 'fail'.
- scraper_junk_pages: capped 1000 most-recent default + --content-audit
  opt-in for full scan (D10 mirrors --index-audit precedent from v0.14.3).
  Applies assessor per-page on title + 2KB body slice + frontmatter.
- content_sanity_audit_recent: reads ~/.gbrain/audit/content-sanity-*.jsonl
  for last 7 days, aggregates by event_type + source. Warn at 10+ events,
  fail at 100+. Doctor message names the multi-host limitation explicitly
  (Codex r1 #14): 'audit reflects events on this host only; multi-host
  operators should share GBRAIN_AUDIT_DIR'.

sources.ts (new audit subcommand):
- gbrain sources audit <id> [--json] [--include-warns]
- Reads sources.local_path, walks disk (via pruneDir for node_modules /
  .git / dotfiles), runs assessContentSanity per .md file.
- Reports size distribution (p50, p99, max) + would-hard-block count +
  would-soft-block count + junk-pattern hit map.
- Read-only: NO DB writes, NO file mutations. Operator runs this BEFORE
  a sync to catch junk early, or AFTER landing v0.40.9.0 to audit
  historical inventory.

13 unit tests on lint rules; D1 config-lift behavior pinned by lift
in runLintCore + manual override via opts.contentSanity for tests.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore: bump version and changelog (v0.40.9.0)

v0.40.9.0 — content sanity defense: junk-pattern throw + oversize-skip-embed.

Plus TODOS.md entries for the 9 deferred v0.41+ follow-ups:
- chunk-level embed-quarantine (Codex r1 #3 — page-level granularity wrong)
- source-repo remediation CLI (gbrain sources prune-junk)
- threshold validation post-deploy on real corpora
- brain-score no_junk_pages_score component
- pages soft-delete --where CLI (paired with prune-junk)
- post-v0.45 operator-regex extensibility (needs real ReDoS story)
- post-v0.45 HTML-density rule (needs fenced-code handling)
- bytes-parity E2E across lint + doctor
- 5-path narrow-waist E2E pin tests + doctor integration tests

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs: update CLAUDE.md for v0.40.9.0 content-sanity wave

Add v0.40.9.0 Key Files entries for the content-sanity defense modules:
content-sanity.ts (assessor), content-sanity-literals.ts (operator loader),
embed-skip.ts (5-site shared predicate), audit/content-sanity-audit.ts
(JSONL writer). Extend doctor.ts, lint.ts, embed.ts, import-file.ts, and
sources.ts entries with the v0.40.9.0 surfaces (3 new doctor checks,
2 new lint rules, embed-skip filter at 5 sites, importFromContent gate,
sources audit subcommand).

Regenerate llms-full.txt per the CLAUDE.md edit rule.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore: rebump v0.40.9.0 → v0.40.10.0 (queue collision with #1350)

PR #1350 also claimed v0.40.9.0. Advancing this PR to v0.40.10.0 so CI's
version-gate doesn't reject on overlap. No functional change — same shipped
content, just a different version slot.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(brain-writer): +1ms overshoot on COUNT-race timer to defeat CI boundary flake

PR #1351 ship CI hit a single test failure (one in 2552):
  (fail) scanBrainSources partial-scan state > hanging COUNT does not
  exceed deadline — Promise.race timeout fires [579.01ms]

Run: https://github.com/garrytan/gbrain/actions/runs/77611667786

Cause: heavily-loaded CI runners (8 parallel shards × 4 concurrent test
files = ~32 concurrent bun processes) occasionally let the setTimeout
race callback resolve a microsecond BEFORE the wall-clock boundary,
leaving Date.now() one tick below deadline. The post-await deadline
check at brain-writer.ts:512 uses Date.now() >= deadline; on that tick
the check evaluated false and scanOneSource ran src-a anyway. Test then
asserted firstSource.status === 'skipped' and got 'scanned'.

Fix: add 1ms overshoot to the race-timer schedule:
  setTimeout(..., remainingMs + 1)

Guarantees the timer fires past the deadline by at least one millisecond
regardless of runner timer drift. Cost: 1ms additional wall-clock
latency on hung COUNT queries — operationally negligible.

Verified: stress-tested 5/5 passing locally. The bug class is identical
to the one the existing test comment block (lines 180-187) documents
(`>=` not `>` at line 512); this +1ms is the belt to that suspenders.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-05-24 10:49:56 -07:00

130 lines
5.7 KiB
TypeScript

/**
* Embed-skip predicate: the single source of truth for "should this
* page be skipped during embedding?"
*
* Why a shared module (D4):
* gbrain has 5 sites that filter the stale-chunk / all-pages query
* for embedding:
*
* 1. src/commands/embed.ts:350 (--stale CLI path)
* 2. src/commands/embed.ts:355 (--all CLI path) — D8 catches this
* too; the `--all` walk re-embeds every page from scratch and
* must honor the skip flag like `--stale` does.
* 3. src/core/embed-stale.ts:90 (Minion helper)
* 4. src/core/postgres-engine.ts (listStaleChunks/countStaleChunks)
* 5. src/core/pglite-engine.ts equivalent
*
* Inline-filtering across 5 sites is the exact bug class gbrain has
* been bitten by repeatedly — see CLAUDE.md `cjk.ts`, `sql-ranking.ts`,
* `audit-writer.ts` for sibling shared modules. Extracting the
* predicate here means the 5 sites all import from one place.
*
* Two surfaces:
* - JS predicate `isEmbedSkipped(frontmatter)` for callers that have
* in-memory page objects (CLI walk paths).
* - SQL fragment `EMBED_SKIP_FILTER_FRAGMENT` for callers that need
* to splice into a postgres-js / PGLite `sql\`...\`` template.
* Both engines use the standard JSONB `?` existence operator;
* PGLite (PostgreSQL 17.5 in WASM) supports the full JSONB
* operator set, so one fragment works for both.
*
* Frontmatter writer:
* - `buildEmbedSkipMarker(bytes)` produces the canonical marker
* object. Callers `Object.assign` it onto `parsed.frontmatter` so
* it persists into the page write. Stable schema means the JS
* predicate and the SQL existence check both target the same key
* name (`embed_skip`) — drift between writer and reader is the
* bug class we're preventing.
*
* Marker shape rationale:
* The marker is an OBJECT (not a bare bool) so the operator can see
* WHY the page was skipped + WHEN at a glance via `get_page`. The
* SQL existence check (`frontmatter ? 'embed_skip'`) hits regardless
* of marker contents — JSONB key-existence semantics — so future
* versions can extend the marker shape without invalidating the
* filter.
*
* v0.42 follow-up: promote to schema column `pages.embed_skipped_at`
* + partial index. Single change site (this module). For v0.41 the
* JSONB approach is acceptable because the skipped-page subset stays
* small (operator surfaces via doctor and either splits or accepts).
*/
/** The frontmatter key name. Treat as a stable contract — renaming
* this means rewriting every consumer of the skip semantic. */
export const EMBED_SKIP_KEY = 'embed_skip';
/** SQL fragment that excludes pages with the embed-skip marker.
* Callers must already JOIN `pages` (aliased as `p`) — the bare
* `content_chunks` query has no access to frontmatter and needs the
* join added regardless.
*
* Use via `sql.unsafe()` or equivalent fragment-splice:
*
* const filter = EMBED_SKIP_FILTER_FRAGMENT;
* await sql`SELECT ... FROM content_chunks cc
* JOIN pages p ON p.id = cc.page_id
* WHERE cc.embedding IS NULL AND ${sql.unsafe(filter)}`;
*
* The fragment uses the JSONB `?` existence operator: returns true
* when the JSONB object contains the key `'embed_skip'` at the top
* level. Works identically on Postgres (real) and PGLite (PostgreSQL
* 17.5 in WASM). The `NOT` negates so we KEEP rows that DON'T have
* the marker. */
export const EMBED_SKIP_FILTER_FRAGMENT =
`NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? '${EMBED_SKIP_KEY}')`;
export interface EmbedSkipMarker {
/** Why the page was skipped. v0.41 ships only `'oversized'`; future
* reasons (e.g. `'chunk_token_limit'` from the deferred v0.42
* chunk-level quarantine) extend this enum. */
reason: 'oversized';
/** Body bytes at the time of assessment. Operator visibility: at a
* glance, see how oversized the page is. */
bytes: number;
/** ISO 8601 timestamp at assessment time. Tells the operator when
* the skip was first applied (page may have been edited later). */
assessed_at: string;
}
/** Build the canonical marker object. Callers spread it onto the
* frontmatter before write:
*
* parsed.frontmatter[EMBED_SKIP_KEY] = buildEmbedSkipMarker(bytes);
*
* The marker is OBJECT-shaped (not bare true) so `get_page` shows
* the operator why + when at a glance. */
export function buildEmbedSkipMarker(bytes: number, now: Date = new Date()): EmbedSkipMarker {
return {
reason: 'oversized',
bytes,
assessed_at: now.toISOString(),
};
}
/** JS-side predicate for in-memory page objects. Returns true when the
* frontmatter has the embed-skip key set to any non-null value.
*
* Accepts `null`/`undefined` frontmatter (some paths construct page
* objects without one) and returns false — no frontmatter means no
* skip marker.
*
* Mirrors the SQL fragment's semantics: key-existence is the trigger;
* marker contents are diagnostic, not functional. A future marker
* shape change doesn't break this predicate. */
export function isEmbedSkipped(frontmatter: Record<string, unknown> | null | undefined): boolean {
if (!frontmatter) return false;
const value = frontmatter[EMBED_SKIP_KEY];
return value !== undefined && value !== null;
}
/** JS-side filter for arrays of in-memory page objects. Returns a new
* array with embed-skipped pages excluded. Mirrors the SQL filter
* for callers that walk pages JS-side (e.g. `gbrain embed --all`
* walks pages directly rather than going through listStaleChunks). */
export function filterOutEmbedSkipped<T extends { frontmatter?: Record<string, unknown> | null }>(
pages: ReadonlyArray<T>,
): T[] {
return pages.filter((p) => !isEmbedSkipped(p.frontmatter ?? null));
}