Files
gbrain/src/core/utils.ts
T
013b348c28 v0.12.3: Reliability wave — sync deadlock, search timeout scoping, wikilinks, orphans (#216)
* fix(sync): remove nested transaction that deadlocks > 10 file syncs

sync.ts wraps the add/modify loop in engine.transaction(), and each
importFromContent inside opens another one. PGLite's
_runExclusiveTransaction is a non-reentrant mutex — the second call
queues on the mutex the first is holding, and the process hangs forever
in ep_poll. Reproduced with a 15-file commit: unpatched hangs, patched
runs in 3.4s. Fix drops the outer wrap; per-file atomicity is correct
anyway (one file's failure should not roll back the others).

(cherry picked from commit 4a1ac00105)

* test(sync): regression guard for #132 top-level engine.transaction wrap

Reads src/commands/sync.ts verbatim and asserts no uncommented
engine.transaction() call appears above the add/modify loop. Protects
against silent reintroduction of the nested-mutex deadlock that hung
> 10-file syncs forever in ep_poll.

* feat(utils): tryParseEmbedding() skip+warn sibling for availability path

parseEmbedding() throws on structural corruption — right call for ingest/
migrate paths where silent skips would be data loss. Wrong call for
search/rescore paths where one corrupt row in 10K would kill every
query that touches it.

tryParseEmbedding() wraps parseEmbedding in try/catch: returns null on
any shape that would throw, warns once per session so the bad row is
visible in logs. Use it anywhere we'd rather degrade ranking than blow
up the whole query.

Retrofit postgres-engine.getEmbeddingsByChunkIds (the #175 slice call
site) — the 5-line rescore loop was the direct motivator. Keep the
throwing parseEmbedding() for everything else (pglite-engine rowToChunk,
migrate-engine round-trips, ingest).

* postgres-engine: scope search statement_timeout to the transaction

searchKeyword and searchVector run on a pooled postgres.js client
(max: 10 by default). The original code bounded each search with

  await sql`SET statement_timeout = '8s'`
  try { await sql`<query>` }
  finally { await sql`SET statement_timeout = '0'` }

but every tagged template is an independent round-trip that picks an
arbitrary connection from the pool. The SET, the query, and the reset
could all land on DIFFERENT connections. In practice the GUC sticks
to whichever connection ran the SET and then gets returned to the
pool — the next unrelated caller on that connection inherits the 8s
timeout (clipping legitimate long queries) or the reset-to-0 (disabling
the guard for whoever expected it). A crash in the middle leaves the
state set permanently.

Wrap each search in sql.begin(async sql => …). postgres.js reserves
a single connection for the transaction body, so the SET LOCAL, the
query, and the implicit COMMIT all run on the same connection. SET
LOCAL scopes the GUC to the transaction — COMMIT or ROLLBACK restores
the previous value automatically, regardless of the code path out.
Error paths can no longer leak the GUC.

No API change. Timeout value and semantics are identical (8s cap on
search queries, no effect on embed --all / bulk import which runs
outside these methods). Only one transaction per search — BEGIN +
COMMIT round-trips are negligible next to a ranked FTS or pgvector
query.

Also closes the earlier audit finding R4-F002 which reported the same
pattern on searchKeyword. This PR covers both searchKeyword and
searchVector so the pool-leak class is fully closed.

Tests (test/postgres-engine.test.ts, new file):
- No bare SET statement_timeout remains after stripping comments.
- searchKeyword and searchVector each wrap their query in sql.begin.
- Both use SET LOCAL.
- Neither explicitly clears the timeout with SET statement_timeout=0.

Source-level guardrails keep the fast unit suite DB-free. Live
Postgres coverage of the search path is in test/e2e/search-quality.test.ts,
which continues to exercise these methods end-to-end against
pgvector when DATABASE_URL is set.

(cherry picked from commit 6146c3b470)

* feat(orphans): add gbrain orphans command for finding under-connected pages

Surfaces pages with zero inbound wikilinks. Essential for content
enrichment cycles in KBs with 1000+ pages. By default filters out
auto-generated pages, raw sources, and pseudo-pages where no inbound
links is expected; --include-pseudo to disable.

Supports text (grouped by domain), --json, --count outputs.
Also exposed as find_orphans MCP operation.

Tests cover basic detection, filtering, all output modes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
(cherry picked from commit f50954f8e0)

* feat(extract): support Obsidian wikilinks + wiki-style domain slugs in canonical extractor

extractEntityRefs now recognizes both syntaxes equally:
  [Name](people/slug)      -- upstream original
  [[people/slug|Name]]     -- Obsidian wikilink (new)

Extends DIR_PATTERN to include domain-organized wiki slugs used by
Karpathy-style knowledge bases:
  - entities  (legacy prefix some brains keep during migration)
  - projects  (gbrain canonical, was missing from regex)
  - tech, finance, personal, openclaw (domain-organized wiki roots)

Before this change, a 2,100-page brain with wikilinks throughout extracted
zero auto-links on put_page because the regex only matched markdown-style
[name](path). After: 1,377 new typed edges on a single extract --source db
pass over the same corpus.

Matches the behavior of the extract.ts filesystem walker (which already
handled wikilinks as of the wiki-markdown-compat fix wave), so the db and
fs sources now produce the same link graph from the same content.

Both patterns share the DIR_PATTERN constant so adding a new entity dir
only requires updating one string.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
(cherry picked from commit 1cfb15679a)

* feat(doctor): jsonb_integrity + markdown_body_completeness detection

Add two v0.12.1-era reliability checks to `gbrain doctor`:

- `jsonb_integrity` scans the 4 known write sites from the v0.12.0
  double-encode bug (pages.frontmatter, raw_data.data,
  ingest_log.pages_updated, files.metadata) and reports rows where
  jsonb_typeof(col) = 'string'. The fix hint points at
  `gbrain repair-jsonb` (the standalone repair command shipped in
  v0.12.1).

- `markdown_body_completeness` flags pages whose compiled_truth is
  <30% of the raw source content length when raw has multiple H2/H3
  boundaries. Heuristic only; suggests `gbrain sync --force` or
  `gbrain import --force <slug>`.

Also adds test/e2e/jsonb-roundtrip.test.ts — the regression coverage
that should have caught the original double-encode bug. Hits all four
write sites against real Postgres and asserts jsonb_typeof='object'
plus `->>'key'` returns the expected scalar.

Detection only: doctor diagnoses, `gbrain repair-jsonb` treats.
No overlap with the standalone repair path.

* chore: bump to v0.12.3 + changelog (reliability wave)

Master shipped v0.12.1 (extract N+1 + migration timeout) and v0.12.2
(JSONB double-encode + splitBody + wiki types + parseEmbedding) while
this wave was mid-flight. Ships the remaining pieces as v0.12.3:

- sync deadlock (#132, @sunnnybala)
- statement_timeout scoping (#158, @garagon)
- Obsidian wikilinks + domain patterns (#187 slice, @knee5)
- gbrain orphans command (#187 slice, @knee5)
- tryParseEmbedding() availability helper
- doctor detection for jsonb_integrity + markdown_body_completeness

No schema, no migration, no data touch.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs: update project documentation for v0.12.3

CLAUDE.md:
- Add src/commands/orphans.ts entry
- Expand src/commands/doctor.ts with v0.12.3 jsonb_integrity +
  markdown_body_completeness check descriptions
- Update src/core/link-extraction.ts to mention Obsidian wikilinks +
  extended DIR_PATTERN (entities/projects/tech/finance/personal/openclaw)
- Update src/core/utils.ts to mention tryParseEmbedding sibling
- Update src/core/postgres-engine.ts to note statement_timeout scoping +
  tryParseEmbedding usage in getEmbeddingsByChunkIds
- Add Key commands added in v0.12.3 section (orphans, doctor checks)
- Add test/orphans.test.ts, test/postgres-engine.test.ts, updated
  descriptions for test/sync.test.ts, test/doctor.test.ts,
  test/utils.test.ts
- Add test/e2e/jsonb-roundtrip.test.ts with note on intentional overlap
- Bump operation count from ~36 to ~41 (find_orphans shipped in v0.12.3)

README.md:
- Add gbrain orphans to ADMIN commands block

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

---------

Co-authored-by: sunnnybala <dhruvagarwal5018@gmail.com>
Co-authored-by: Gustavo Aragon <gustavoraularagon@gmail.com>
Co-authored-by: Clevin Canales <clevin@Clevins-MacBook-Pro.local>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Clevin Canales <clev.canales@gmail.com>
2026-04-19 18:23:02 +08:00

141 lines
5.2 KiB
TypeScript

import { createHash } from 'crypto';
import type { Page, PageInput, PageType, Chunk, SearchResult } from './types.ts';
/**
* Validate and normalize a slug. Slugs are lowercased repo-relative paths.
* Rejects empty slugs, path traversal (..), and leading /.
*/
export function validateSlug(slug: string): string {
if (!slug || /(^|\/)\.\.($|\/)/.test(slug) || /^\//.test(slug)) {
throw new Error(`Invalid slug: "${slug}". Slugs cannot be empty, start with /, or contain path traversal.`);
}
return slug.toLowerCase();
}
/**
* SHA-256 hash of page content, used for import idempotency.
* Hashes all PageInput fields to match importFromContent's hash algorithm.
*/
export function contentHash(page: PageInput): string {
return createHash('sha256')
.update(JSON.stringify({
title: page.title,
type: page.type,
compiled_truth: page.compiled_truth,
timeline: page.timeline || '',
frontmatter: page.frontmatter || {},
}))
.digest('hex');
}
export function rowToPage(row: Record<string, unknown>): Page {
return {
id: row.id as number,
slug: row.slug as string,
type: row.type as PageType,
title: row.title as string,
compiled_truth: row.compiled_truth as string,
timeline: row.timeline as string,
frontmatter: (typeof row.frontmatter === 'string' ? JSON.parse(row.frontmatter) : row.frontmatter) as Record<string, unknown>,
content_hash: row.content_hash as string | undefined,
created_at: new Date(row.created_at as string),
updated_at: new Date(row.updated_at as string),
};
}
/**
* Normalize an embedding value into a Float32Array.
*
* pgvector returns embeddings in different shapes depending on driver/path:
* - postgres.js (Postgres): often a string like `"[0.1,0.2,...]"`
* - pglite: typically a numeric array or Float32Array
* - pgvector node binding: numeric array
* - Some queries that JSON-aggregate embeddings: JSON-string array
*
* Without normalization, downstream cosine math sees a string and produces
* NaN scores silently. This helper guarantees a Float32Array or throws
* loudly on malformed input — never returns NaN.
*/
export function parseEmbedding(value: unknown): Float32Array | null {
if (value === null || value === undefined) return null;
if (value instanceof Float32Array) return value;
if (Array.isArray(value)) {
if (value.length === 0) return new Float32Array(0);
if (typeof value[0] !== 'number') {
throw new Error(`parseEmbedding: array contains non-numeric element (${typeof value[0]})`);
}
return Float32Array.from(value as number[]);
}
if (typeof value === 'string') {
const trimmed = value.trim();
// Plain non-vector strings: treat as "no embedding here", return null.
// Strings that LOOK like vector literals but contain garbage: throw,
// because that's a real corruption signal worth surfacing loudly.
if (!trimmed.startsWith('[') || !trimmed.endsWith(']')) return null;
const inner = trimmed.slice(1, -1).trim();
if (inner.length === 0) return new Float32Array(0);
const parts = inner.split(',');
const out = new Float32Array(parts.length);
for (let i = 0; i < parts.length; i++) {
const n = Number(parts[i].trim());
if (!Number.isFinite(n)) {
throw new Error(`parseEmbedding: non-finite value at index ${i}: ${parts[i]}`);
}
out[i] = n;
}
return out;
}
return null;
}
let _tryParseEmbeddingWarned = false;
/**
* Availability-path sibling of parseEmbedding(). Returns null + warns once
* on any shape parseEmbedding would throw on. Use this on read/rescore paths
* where one corrupt row should degrade ranking, not kill the whole query.
* Use parseEmbedding() (throws) on ingest/migrate paths where silent skips
* would be data loss.
*/
export function tryParseEmbedding(value: unknown): Float32Array | null {
try {
return parseEmbedding(value);
} catch (err) {
if (!_tryParseEmbeddingWarned) {
_tryParseEmbeddingWarned = true;
const msg = err instanceof Error ? err.message : String(err);
console.warn(`tryParseEmbedding: skipping corrupt embedding row (${msg}). Further warnings suppressed this session.`);
}
return null;
}
}
export function rowToChunk(row: Record<string, unknown>, includeEmbedding = false): Chunk {
return {
id: row.id as number,
page_id: row.page_id as number,
chunk_index: row.chunk_index as number,
chunk_text: row.chunk_text as string,
chunk_source: row.chunk_source as 'compiled_truth' | 'timeline',
embedding: includeEmbedding ? parseEmbedding(row.embedding) : null,
model: row.model as string,
token_count: row.token_count as number | null,
embedded_at: row.embedded_at ? new Date(row.embedded_at as string) : null,
};
}
export function rowToSearchResult(row: Record<string, unknown>): SearchResult {
return {
slug: row.slug as string,
page_id: row.page_id as number,
title: row.title as string,
type: row.type as PageType,
chunk_text: row.chunk_text as string,
chunk_source: row.chunk_source as 'compiled_truth' | 'timeline',
chunk_id: row.chunk_id as number,
chunk_index: row.chunk_index as number,
score: Number(row.score),
stale: Boolean(row.stale),
};
}