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* fix: 8 root-cause fixes from /investigate wave
Consolidated bundle of bug fixes from /investigate on the 8 deferred bugs.
Each fix was designed to go at the structural gap, not the symptom. Codex
verified 20 load-bearing claims on the plan; 12 triggered plan revisions.
Bug 2 — GBRAIN_POOL_SIZE env knob + init finally blocks (no auto-detect).
Covers both the singleton pool (db.ts) and instance pool (import.ts:140).
Bug 3 — Centralize migration ledger writes in apply-migrations runner.
Removed appendCompletedMigration from v0_11_0, v0_12_0, v0_12_2,
v0_13_0, v0_13_1. Added 3-partial wedge cap + --force-retry reset.
'complete wins' preserved; no partial can regress a completed migration.
Bug 5 — v0.14.0 migration registered. src/commands/migrations/v0_14_0.ts
ships Phase A (ALTER minion_jobs.max_stalled SET DEFAULT 3) + Phase B
(pending-host-work ping for shell-jobs adoption).
Bug 6/10 — jsonb_agg(DISTINCT ...) in legacy traverseGraph (both engines).
Presentation-level dedup; schema still preserves provenance rows.
Bug 7 — doctor --fast reads DB URL source via getDbUrlSource() in config.ts.
Precise message: 'Skipping DB checks (--fast mode, URL present from env)'
replaces the misleading 'No database configured'.
Bug 8 — max_stalled default bumped 1→3 in schema-embedded.ts, pglite-schema.ts,
schema.sql (new installs). v0_14_0 Phase A ALTER for existing installs.
autopilot-cycle handler yields to event loop between phases so the
worker's lock-renewal timer fires on huge brains. (Deep AbortSignal
threading through runEmbedCore/runExtractCore/runBacklinksCore/performSync
deferred to v0.15 queue polish.)
Bug 9 — Gate sync.last_commit on no-failures across all three sync paths
(incremental, full via runImport, gbrain import git continuity).
recordSyncFailures() helper + ~/.gbrain/sync-failures.jsonl with
dedup key path+commit+error-hash. New flags: --skip-failed (ack) +
--retry-failed (re-attempt). Doctor surfaces unacknowledged failures.
Bug 11 — brain_score breakdown fields on BrainHealth (embed_coverage_score,
link_density_score, timeline_coverage_score, no_orphans_score,
no_dead_links_score); sum equals brain_score by construction.
dead_links now on the type (resolves featuresTeaserForDoctor drift).
orphan_pages kept as 'islanded' (no inbound AND no outbound) and
docs updated to match — explicit semantic instead of doc drift.
New tests: test/traverse-graph-dedup.test.ts, test/sync-failures.test.ts,
test/brain-score-breakdown.test.ts, test/migration-resume.test.ts,
test/migrations-v0_14_0.test.ts. Extended: migrate, doctor, apply-migrations.
All 1696 unit tests pass locally. postgres-jsonb E2E regression unchanged
(none of these touch the JSONB write surface).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* docs: v0.14.2 CHANGELOG + CLAUDE.md; align migration-flow E2E with runner-owned ledger
CHANGELOG: v0.14.2 entry in the standard release-summary format
(two-line headline + lead + numbers table + "what this means" +
"To take advantage of v0.14.2" self-repair block + itemized
changes grouped by reliability / observability / graph correctness /
new migration / tests / deferred-to-v0.15).
CLAUDE.md: new "Key commands added in v0.14.2" section covers
--skip-failed, --retry-failed, --force-retry, GBRAIN_POOL_SIZE env,
and the new doctor checks (sync_failures, brain_score breakdown).
Migration orchestrator docs updated to describe v0_14_0.ts + the
runner-owned ledger contract from Bug 3.
test/e2e/migration-flow.test.ts: three assertions updated to match
the Bug 3 contract — orchestrators no longer append to completed.jsonl
directly, so direct-orchestrator E2E calls leave the ledger empty.
Preferences assertions remain (that's still the orchestrator's side
of the contract). Runner's ledger write is covered by the unit suite
(test/apply-migrations.test.ts + test/migration-resume.test.ts).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
250 lines
11 KiB
TypeScript
250 lines
11 KiB
TypeScript
import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
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import { LATEST_VERSION, runMigrations, MIGRATIONS } from '../src/core/migrate.ts';
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import { PGLiteEngine } from '../src/core/pglite-engine.ts';
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describe('migrate', () => {
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test('LATEST_VERSION is a number >= 1', () => {
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expect(typeof LATEST_VERSION).toBe('number');
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expect(LATEST_VERSION).toBeGreaterThanOrEqual(1);
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});
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test('runMigrations is exported and callable', async () => {
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expect(typeof runMigrations).toBe('function');
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});
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// Integration tests for actual migration execution require DATABASE_URL
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// and are covered in the E2E suite (test/e2e/mechanical.test.ts)
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});
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// ─────────────────────────────────────────────────────────────────
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// REGRESSION TESTS — migrations v8 + v9 perf on duplicate-heavy tables
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// ─────────────────────────────────────────────────────────────────
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//
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// Garry's production brain hit Supabase Management API's 60s ceiling because
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// the DELETE...USING self-join in migrations v8 + v9 was O(n²) without an
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// index on the dedup columns. The fix pre-creates a btree helper index
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// before the DELETE, then drops it. These tests guard against any future
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// change that re-introduces the missing helper index.
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//
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// Two-layer guard:
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// 1. Structural — assert the migration SQL literally contains the helper
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// CREATE INDEX + DROP INDEX (deterministic, fast, catches the regression
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// even at 0-row scale where wall-clock can't distinguish O(n²) from O(1)).
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// 2. Behavioral — populate 1000 duplicates and assert the migration completes
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// under the wall-clock cap. Sanity check at small scale; the structural
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// assertion is the real guard.
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describe('migrations v8 + v9 — structural guard for helper-index fix', () => {
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test('migration v8 SQL contains idx_links_dedup_helper CREATE+DROP around the DELETE', () => {
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const v8 = MIGRATIONS.find(m => m.version === 8);
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expect(v8).toBeDefined();
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const sql = v8!.sql;
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// The fix must: (a) create the helper btree, (b) DELETE...USING, (c) drop the helper, (d) add the unique constraint.
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// If anyone reorders or removes the helper-index lines, this fails.
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expect(sql).toContain('CREATE INDEX IF NOT EXISTS idx_links_dedup_helper');
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expect(sql).toContain('ON links(from_page_id, to_page_id, link_type)');
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expect(sql).toContain('DROP INDEX IF EXISTS idx_links_dedup_helper');
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expect(sql).toContain('DELETE FROM links a USING links b');
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expect(sql).toContain('ALTER TABLE links ADD CONSTRAINT links_from_to_type_unique');
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// Order matters: CREATE INDEX before DELETE, DROP INDEX after DELETE, before ADD CONSTRAINT.
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const createIdx = sql.indexOf('CREATE INDEX IF NOT EXISTS idx_links_dedup_helper');
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const deleteUsing = sql.indexOf('DELETE FROM links a USING links b');
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const dropIdx = sql.indexOf('DROP INDEX IF EXISTS idx_links_dedup_helper');
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const addConstraint = sql.indexOf('ALTER TABLE links ADD CONSTRAINT links_from_to_type_unique');
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expect(createIdx).toBeLessThan(deleteUsing);
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expect(deleteUsing).toBeLessThan(dropIdx);
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expect(dropIdx).toBeLessThan(addConstraint);
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});
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test('migration v9 SQL contains idx_timeline_dedup_helper CREATE+DROP around the DELETE', () => {
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const v9 = MIGRATIONS.find(m => m.version === 9);
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expect(v9).toBeDefined();
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const sql = v9!.sql;
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expect(sql).toContain('CREATE INDEX IF NOT EXISTS idx_timeline_dedup_helper');
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expect(sql).toContain('ON timeline_entries(page_id, date, summary)');
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expect(sql).toContain('DROP INDEX IF EXISTS idx_timeline_dedup_helper');
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expect(sql).toContain('DELETE FROM timeline_entries a USING timeline_entries b');
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expect(sql).toContain('CREATE UNIQUE INDEX IF NOT EXISTS idx_timeline_dedup');
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const createHelper = sql.indexOf('CREATE INDEX IF NOT EXISTS idx_timeline_dedup_helper');
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const deleteUsing = sql.indexOf('DELETE FROM timeline_entries a USING timeline_entries b');
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const dropHelper = sql.indexOf('DROP INDEX IF EXISTS idx_timeline_dedup_helper');
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const createUnique = sql.indexOf('CREATE UNIQUE INDEX IF NOT EXISTS idx_timeline_dedup');
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expect(createHelper).toBeLessThan(deleteUsing);
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expect(deleteUsing).toBeLessThan(dropHelper);
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expect(dropHelper).toBeLessThan(createUnique);
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});
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});
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describe('migrate: v8 (links_dedup) regression — must be fast on 1K duplicate rows', () => {
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let engine: PGLiteEngine;
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beforeAll(async () => {
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engine = new PGLiteEngine();
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await engine.connect({});
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await engine.initSchema();
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});
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afterAll(async () => {
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await engine.disconnect();
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});
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test('1000 duplicate links dedup completes in <5s and leaves table deduped', async () => {
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// Set up: drop BOTH the old (v8) and new (v11) unique constraints so
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// duplicates can be inserted, then reset version so v8 + v11 re-run.
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// v11 replaces the v8 constraint name; we drop whichever is present.
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const db = (engine as any).db;
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await db.exec(`ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_to_type_unique`);
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await db.exec(`ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_to_type_source_origin_unique`);
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// Two pages so the FK is satisfied
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await engine.putPage('p/from', { type: 'concept', title: 'F', compiled_truth: '', timeline: '' });
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await engine.putPage('p/to', { type: 'concept', title: 'T', compiled_truth: '', timeline: '' });
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const fromId = (await db.query(`SELECT id FROM pages WHERE slug = 'p/from'`)).rows[0].id;
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const toId = (await db.query(`SELECT id FROM pages WHERE slug = 'p/to'`)).rows[0].id;
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// Insert 1000 duplicates of the same (from, to, type) row
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for (let i = 0; i < 1000; i++) {
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await db.query(
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`INSERT INTO links (from_page_id, to_page_id, link_type, context) VALUES ($1, $2, $3, $4)`,
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[fromId, toId, 'mention', `dup-${i}`]
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);
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}
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const beforeCount = (await db.query(`SELECT COUNT(*)::int AS c FROM links`)).rows[0].c;
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expect(beforeCount).toBe(1000);
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// Reset version to 7 so v8 + v9 + v10 + v11 re-run
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await engine.setConfig('version', '7');
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// Run migrations and assert wall-clock + correctness
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const start = Date.now();
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await runMigrations(engine);
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const elapsedMs = Date.now() - start;
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expect(elapsedMs).toBeLessThan(5000);
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const afterCount = (await db.query(`SELECT COUNT(*)::int AS c FROM links`)).rows[0].c;
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expect(afterCount).toBe(1); // deduped to one row
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// v11 replaces v8's constraint name. Assert the current (v11) constraint
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// exists and the legacy v8 name is gone.
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const constraints = (await db.query(`
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SELECT conname FROM pg_constraint
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WHERE conrelid = 'links'::regclass AND contype = 'u'
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`)).rows;
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expect(constraints.some((c: { conname: string }) => c.conname === 'links_from_to_type_source_origin_unique')).toBe(true);
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expect(constraints.some((c: { conname: string }) => c.conname === 'links_from_to_type_unique')).toBe(false);
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// Helper index was dropped after dedup
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const helperIdx = (await db.query(`
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SELECT indexname FROM pg_indexes
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WHERE tablename = 'links' AND indexname = 'idx_links_dedup_helper'
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`)).rows;
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expect(helperIdx.length).toBe(0);
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});
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});
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describe('migrate: v9 (timeline_dedup_index) regression — must be fast on 1K duplicate rows', () => {
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let engine: PGLiteEngine;
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beforeAll(async () => {
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engine = new PGLiteEngine();
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await engine.connect({});
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await engine.initSchema();
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});
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afterAll(async () => {
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await engine.disconnect();
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});
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test('1000 duplicate timeline entries dedup completes in <5s and leaves table deduped', async () => {
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const db = (engine as any).db;
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await db.exec(`DROP INDEX IF EXISTS idx_timeline_dedup`);
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await engine.putPage('p/timeline', { type: 'concept', title: 'TL', compiled_truth: '', timeline: '' });
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const pageId = (await db.query(`SELECT id FROM pages WHERE slug = 'p/timeline'`)).rows[0].id;
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// Insert 1000 duplicates of the same (page_id, date, summary) row
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for (let i = 0; i < 1000; i++) {
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await db.query(
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`INSERT INTO timeline_entries (page_id, date, source, summary, detail) VALUES ($1, $2::date, $3, $4, $5)`,
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[pageId, '2024-01-15', `src-${i}`, 'Founded NovaMind', `detail-${i}`]
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);
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}
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const beforeCount = (await db.query(`SELECT COUNT(*)::int AS c FROM timeline_entries`)).rows[0].c;
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expect(beforeCount).toBe(1000);
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await engine.setConfig('version', '7');
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const start = Date.now();
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await runMigrations(engine);
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const elapsedMs = Date.now() - start;
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expect(elapsedMs).toBeLessThan(5000);
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const afterCount = (await db.query(`SELECT COUNT(*)::int AS c FROM timeline_entries`)).rows[0].c;
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expect(afterCount).toBe(1);
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const uniqueIdx = (await db.query(`
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SELECT indexname FROM pg_indexes
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WHERE tablename = 'timeline_entries' AND indexname = 'idx_timeline_dedup'
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`)).rows;
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expect(uniqueIdx.length).toBe(1);
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const helperIdx = (await db.query(`
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SELECT indexname FROM pg_indexes
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WHERE tablename = 'timeline_entries' AND indexname = 'idx_timeline_dedup_helper'
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`)).rows;
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expect(helperIdx.length).toBe(0);
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});
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});
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// ─────────────────────────────────────────────────────────────────
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// resolvePoolSize — GBRAIN_POOL_SIZE env override
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// ─────────────────────────────────────────────────────────────────
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//
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// Guards the Bug 2 fix: users on constrained poolers (Supabase port 6543)
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// must be able to cap the pool size via GBRAIN_POOL_SIZE. The default
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// (10) is unchanged when the env var is unset.
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describe('resolvePoolSize — env var + explicit override', () => {
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const { resolvePoolSize } = require('../src/core/db.ts');
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const original = process.env.GBRAIN_POOL_SIZE;
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afterAll(() => {
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if (original === undefined) delete process.env.GBRAIN_POOL_SIZE;
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else process.env.GBRAIN_POOL_SIZE = original;
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});
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test('returns 10 default when unset and no explicit override', () => {
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delete process.env.GBRAIN_POOL_SIZE;
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expect(resolvePoolSize()).toBe(10);
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});
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test('reads GBRAIN_POOL_SIZE as an integer', () => {
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process.env.GBRAIN_POOL_SIZE = '2';
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expect(resolvePoolSize()).toBe(2);
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process.env.GBRAIN_POOL_SIZE = '5';
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expect(resolvePoolSize()).toBe(5);
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});
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test('ignores invalid GBRAIN_POOL_SIZE values', () => {
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process.env.GBRAIN_POOL_SIZE = 'not-a-number';
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expect(resolvePoolSize()).toBe(10);
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process.env.GBRAIN_POOL_SIZE = '0';
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expect(resolvePoolSize()).toBe(10);
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process.env.GBRAIN_POOL_SIZE = '-1';
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expect(resolvePoolSize()).toBe(10);
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});
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test('explicit argument wins over env + default', () => {
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delete process.env.GBRAIN_POOL_SIZE;
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expect(resolvePoolSize(3)).toBe(3);
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process.env.GBRAIN_POOL_SIZE = '7';
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expect(resolvePoolSize(3)).toBe(3);
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});
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});
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