Files
gbrain/src/core/upgrade-checkpoint.ts
T
dffb607ef7 v0.30.1 feat: operational hardening — make upgrades just work on Supabase (#750)
* v0.30.1 Lane A: connection-manager foundation + X1 initSchema routing

Routes Postgres queries by query type:
  - read() goes to the Supabase pooler (port 6543, fast)
  - ddl() and bulk() go to direct (port 5432, 30min stmt timeout, mwm 256MB)

Auto-detects Supabase via hostname pooler.supabase.com or port 6543.
Override with GBRAIN_DIRECT_DATABASE_URL. Kill-switch via
GBRAIN_DISABLE_DIRECT_POOL=1 falls back to single-pool legacy path.

Foundation modules (Lane A scope):
- src/core/connection-manager.ts: read/ddl/bulk/healthCheck, parent-CM
  inheritance (T5/X1), cached Promise<Sql> lazy init (A1), kill-switch
  inheritance (A2), Supabase URL auto-derivation
- src/core/url-redact.ts: redactPgUrl + redactDeep (F3)
- src/core/retry-matcher.ts: typed predicates for stmt-timeout / lock /
  conn errors (C4)
- src/core/connection-audit.ts: ~/.gbrain/audit/connection-events JSONL
  with ISO-week rotation; doctor tail-reads last 5 errors (F8)
- scripts/check-pg-url-redaction.sh: CI grep guard against unredacted
  postgresql:// URL leaks (F3)

Engine integration:
- PostgresEngine.connect: instantiates instance-owned ConnectionManager,
  inherits from parentConnectionManager when set (worker engines, sync,
  cycle), shares pool with module-singleton path
- PostgresEngine.disconnect: tears down direct pool first
- PostgresEngine.initSchema: routes DDL through connectionManager.ddl()
  when dual-pool active (X1 part 1; lock semantics replacement is Lane B)
- cli.ts:connectEngine(opts): probeOnly skips initSchema entirely (X1
  part 2 — get_health, upgrade --status will use this)

Tests added (51 new cases):
- test/url-redact.test.ts: 11 cases
- test/retry-matcher.test.ts: 13 cases
- test/connection-manager.test.ts: 27 cases (URL detection, derive,
  kill-switch, parent inheritance, dual-pool routing modes)

Foundation for Lanes B-E. Sequential lane work continues.

Plan: ~/.claude/plans/system-instruction-you-are-working-stateless-wadler.md

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

* v0.30.1 Lane B: migration runner retry + verify hooks + namespaced --force flags

Adds Migration interface fields:
  - idempotent: boolean (default true; explicit false blocks verify-hook
    re-runs on destructive migrations)
  - verify: optional post-condition probe; runs after migration claims success

Migration retry wrapper (Cherry D3 / Finding F2):
  - 3 attempts with 5s/15s/45s backoff (env GBRAIN_MIGRATE_BACKOFF_MS=0
    for tests)
  - Retries only on statement_timeout (57014) or connection-reset patterns
  - Pre-attempt: logs idle-in-transaction blockers via getIdleBlockers
  - On exhaustion: throws MigrationRetryExhausted with named PID + suggested
    pg_terminate_backend() recovery command

Verify-hook self-healing (Cherry D6 / Codex X3):
  - On verify=false + idempotent=true → re-runs migration once silently
  - On verify=false + idempotent=false → throws MigrationDriftError
  - --skip-verify CLI flag bypasses for operator override

withRefreshingLock helper (Cherry T4 / Codex A4 / X1 part 3):
  - setInterval refresh every TTL/6 ms during long-running work
  - SELECT 1 backend-alive heartbeat per refresh tick
  - Heartbeat hang past 30s → log + clear interval; lock TTL auto-expires
  - LockUnavailableError when acquire fails (caller decides retry)
  - buildTenantLockId(scope) appends current_database() suffix for
    multi-tenant safety (Cherry D4)

Namespaced --force flags (Codex T5):
  - --force-orchestrator: write 'retry' markers for ALL wedged orchestrators
  - --force-schema: re-runs runMigrations against current config.version
  - --force / --force-all: both
  - --force-retry vX.Y.Z: existing single-version reset (preserved)
  - --skip-verify: bypass verify-hook drift detection on a single run

Test additions:
  - test/migrate-extensions.test.ts: 14 cases (idempotent default,
    error envelopes, MIGRATIONS contract)
  - test/db-lock-refresh.test.ts: 10 cases (LockUnavailableError,
    buildTenantLockId multi-tenant, opts shape)
  - test/migrate.test.ts: updated 2 existing cases (PR #356 retry shape +
    function-name anchor) for v0.30.1 retry-wrapper semantics

156 unit tests passing across the v0.30.1 surface so far.

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

* v0.30.1 Lane C: backfill primitive + registry + X4 + X5

First-class generic backfill runner (Fix 3). Generalizes the
keyset+checkpoint+adaptive-batch pattern from
src/core/backfill-effective-date.ts so future backfills (embedding_voyage
in v0.30.2, etc.) reuse one tested runner.

NEW src/core/backfill-base.ts:
  - runBackfill() with keyset pagination, config-table checkpoint, adaptive
    batch halving on stmt timeout, conn-drop reconnect, max-errors bail
  - ensureBackfillIndex() verifies/creates partial index CONCURRENTLY (P2/X4)
  - clearBackfillCheckpoint() for --fresh path
  - T3 fix: writes go through engine.withReservedConnection so BEGIN /
    SET LOCAL / UPDATE / COMMIT execute on the SAME backend (otherwise
    SET LOCAL evaporates between pooled executeRaw calls)

NEW src/core/backfill-registry.ts:
  - effective_date: implemented (wraps existing computeEffectiveDate)
  - emotional_weight: implemented (wraps computeEmotionalWeight + stamps
    new emotional_weight_recomputed_at column)
  - embedding_voyage: declared-only in v0.30.1 (multi-column embedding
    schema lands in v0.30.2)

NEW src/commands/backfill.ts:
  - gbrain backfill <kind> [--batch-size N] [--concurrency N] [--resume]
                          [--fresh] [--dry-run] [--keep-index] [--max-errors N]
  - gbrain backfill list — shows registered backfills + status
  - X5 admission control: clampConcurrency() forces --concurrency to
    GBRAIN_DIRECT_POOL_SIZE - 1 ceiling (always reserves 1 conn for HNSW
    + heartbeat + doctor probes). Loud-warns when user requests above.

Schema migration v44 (X4 / Codex C8 fix):
  - pages.emotional_weight_recomputed_at TIMESTAMPTZ
  - emotional_weight = 0 is a VALID steady-state value per migration v40,
    so the original P2 predicate ("WHERE emotional_weight = 0") would have
    been a permanent large index over normal data. The corrected backlog
    predicate is "emotional_weight_recomputed_at IS NULL"; the partial
    index drops naturally as the cycle phase + this backfill stamp the
    column over time.
  - idempotent: true (ADD COLUMN ... NULL is metadata-only)

CLI integration:
  - src/cli.ts: registers `backfill` subcommand
  - reindex-frontmatter stays as thin alias for v0.30.1 back-compat;
    canonical entrypoint is now `gbrain backfill effective_date`

Test additions:
  - test/backfill-base.test.ts: 11 cases (keyset, checkpoint, dry-run,
    resume/fresh, maxRows cap, withReservedConnection routing, error
    paths, clearCheckpoint, ensureBackfillIndex)
  - test/backfill-concurrency-clamp.test.ts: 6 cases (X5 admission control)

173 unit tests passing across Lanes A+B+C of v0.30.1.

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

* v0.30.1 Lane D: HNSW lifecycle manager + A3 atomic-swap

Extends src/core/vector-index.ts with the v0.30.1 lifecycle layer.
The original chunkEmbeddingIndexSql / applyChunkEmbeddingIndexPolicy
contract is preserved unchanged.

New surfaces:
  - checkActiveBuild(engine, indexName): probes pg_stat_activity for an
    active CREATE INDEX or REINDEX on the named index. Used as pre-op
    guard so dropAndRebuild doesn't compete with a build already in
    flight (Supabase auto-maintenance, parallel gbrain procs).

  - dropZombieIndexes(engine, tableNames): startup sweep of
    indisvalid=false rows on gbrain tables. Drops them with
    DROP INDEX IF EXISTS, BUT skips any zombie that has an active build
    still in pg_stat_activity (codex Fix-5 in-progress-build guard).
    Wired into PostgresEngine.initSchema() — runs after migrations +
    verifySchema, best-effort, never blocks engine.connect().

  - dropAndRebuild(engine, spec, opts): A3 atomic-swap pattern:
      1. checkActiveBuild → bail if another build is active (--force overrides)
      2. CREATE INDEX CONCURRENTLY <name>_rebuild_<unix-ms> via
         engine.withReservedConnection (CONCURRENTLY can't run in a txn)
      3. Atomic swap inside engine.transaction:
           DROP INDEX <old-name>
           ALTER INDEX <temp-name> RENAME TO <old-name>
      4. If step 2 fails (OOM, timeout, conn drop), the OLD index stays
         intact and search keeps serving queries. This is the headline
         A3 win — no production-degraded silent failure mode.

  - monitorBuild(engine, indexName, onProgress, opts): poll
    pg_stat_activity every 30s; emit elapsed_ms + size_bytes (via
    pg_relation_size) + pid. Used by gbrain backfill embedding_voyage
    when batch > 1000 triggers a rebuild.

  - isSupabaseAutoMaintenance(active): predicate on application_name
    (matches "supabase" / "postgres-meta"). Used by dropAndRebuild to
    log + back off when Supabase auto-maintenance is doing the rebuild.

Engine integration:
  - PostgresEngine.initSchema() calls dropZombieIndexes after verifySchema.
    Surfaces zombie counts via console.log.
  - Best-effort wrapped in try/catch: pg_stat_activity / pg_index access
    can be restricted on managed Postgres tiers; gbrain shouldn't fail
    engine.connect() over diagnostic queries.

Test additions (18 cases):
  - test/vector-index-lifecycle.test.ts:
    * chunkEmbeddingIndexSql contract (3 cases) — pre-existing behavior preserved
    * applyChunkEmbeddingIndexPolicy contract (1 case)
    * checkActiveBuild (4 cases, including PGLite no-op + best-effort failure)
    * isSupabaseAutoMaintenance (3 cases)
    * dropZombieIndexes (4 cases, including in-progress-build guard)
    * dropAndRebuild atomic-swap (3 cases, including PGLite + active-build bail
      + temp-name format assertion)

191 unit tests passing across Lanes A+B+C+D of v0.30.1.

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

* v0.30.1 Lane E: upgrade pipeline checkpoint + brain_id binding + get_health migrations

NEW src/core/upgrade-checkpoint.ts:
  - Cherry D5: persists step-by-step progress through gbrain post-upgrade
    so partial failures can be resumed via gbrain upgrade --resume.
    Steps: pull → install → schema → features → backfills → verify.
  - Codex X2: checkpoint binds to brain identity via sha256(database_url)
    (userinfo stripped before hashing so cred rotations don't invalidate).
    PGLite uses sha256(database_path). Cross-brain checkpoint application
    is now refused with reason='brain_mismatch'.
  - F4 fall-through: validateCheckpoint returns reason='no_checkpoint'
    when none exists, enabling silent fall-through to a full upgrade.
  - All-complete detection: stale checkpoints (every step done) return
    reason='all_complete' so the next run clears + re-runs from scratch.
  - markStepComplete + markStepFailed maintain the partial-state shape.

T2 preserved: upgrade.ts still re-execs `gbrain post-upgrade` so the NEW
binary's migration registry runs (the existing re-exec pattern is correct
per codex round 1's plan-breaking finding). The checkpoint module is the
substrate that Lane E's --resume / --status surfaces will plumb through
in v0.30.2.

D7 + C3 contract committed:
  - BrainHealth.schema_version: '1' (literal type) — additive-only contract
    pinned for MCP get_health consumers.
  - BrainHealth.migrations: { schema, orchestrator } — explicit two-ledger
    diagnostic surface (codex T5 namespacing). Both fields are OPTIONAL
    in v0.30.1 — engines can populate them in v0.30.2 without a contract
    bump. Backwards/forwards compat: clients default-handle missing fields.

VERSION: 0.30.0 → 0.30.1
package.json: synced

Test additions (18 cases):
  - test/upgrade-checkpoint.test.ts:
    * computeBrainId: userinfo strip, DB-distinct hashes, stable hex (5 cases)
    * write/load round-trip: roundtrip, missing file, malformed JSON,
      clear (4 cases)
    * validateCheckpoint: F4 no_checkpoint, X2 brain_mismatch, partial
      → resumeAt, all_complete, first-step pending (5 cases)
    * markStepComplete/markStepFailed: append, idempotent, clear-failed,
      failed-state shape (4 cases)

209 unit tests passing across all 5 lanes of v0.30.1 (Lanes A-E core
foundations). Plumbing into upgrade.ts CLI + doctor checks +
get_health() implementation is layered in via follow-up commits within
this PR.

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

* v0.30.1 e2e + test isolation: integration smoke + serial quarantine

NEW test/e2e/v030_1-integration-pglite.test.ts (14 cases):
  PGLite integration smoke proving Lane A-E surfaces work together.
    Lane B: migration runner applies v44 (emotional_weight_recomputed_at)
            cleanly; config.version reaches LATEST_VERSION
    Lane C: backfill registry resolves all 3 entries; emotional_weight +
            effective_date backfills on empty brain return examined=0
            cleanly
    Lane D: dropZombieIndexes / checkActiveBuild on PGLite are no-ops
    Lane E: upgrade-checkpoint round-trips with brain_id; X2 mismatch
            refused; F4 fall-through detected via reason='no_checkpoint';
            full step progression to all_complete

Test isolation hygiene (scripts/check-test-isolation.sh):
  - test/connection-manager.test.ts → connection-manager.serial.test.ts
  - test/backfill-concurrency-clamp.test.ts → .serial.test.ts
  - test/upgrade-checkpoint.test.ts → .serial.test.ts
  All three files mutate process.env (kill-switch, GBRAIN_DIRECT_POOL_SIZE,
  GBRAIN_HOME) which would race other tests in the parallel runner.
  *.serial.test.ts quarantine ensures they run at --max-concurrency=1.
  Choice between withEnv() refactor and serial quarantine made on the side
  of preserving existing well-formed test code.

E2E coverage status:
  - v030_1-integration-pglite.test.ts (this commit): 14 cases, all green
  - backfill-perf-pglite.test.ts: 1 case, green (no regression)
  - cycle-recompute-emotional-weight-pglite.test.ts: green (no regression)
  - multi-source-emotional-weight-pglite.test.ts: green (no regression)
  - dream-synthesize-pglite.test.ts: 14 cases, green (no regression)
  - anomalies-pglite.test.ts + salience-pglite.test.ts: 6 cases, green

Postgres-only E2Es (migration-flow, http-transport, hnsw-lifecycle,
connection-routing) require DATABASE_URL + a real Postgres+pgvector
container per the CLAUDE.md E2E lifecycle. They land as separate
DATABASE_URL-gated work — not regressed by v0.30.1 changes; their
preconditions just aren't met in the current run environment.

`bun run verify` (typecheck + 4 shell pre-checks + test-isolation lint)
passes cleanly.

Final v0.30.1 unit + integration test count: 4547 pass, 0 regressions.
Two pre-existing flaky failures (BrainRegistry serial test + warm-create
perf gate under shard contention) confirmed unrelated to this branch.

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

* chore: bump version and changelog (v0.30.1)

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

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-05-08 13:25:48 -07:00

161 lines
5.8 KiB
TypeScript

/**
* Upgrade pipeline checkpoint (v0.30.1 Cherry D5 + Codex X2).
*
* Persists step-by-step progress through `gbrain post-upgrade` so a partial
* failure can be resumed via `gbrain upgrade --resume` instead of
* re-running every step from scratch.
*
* Codex X2 fix: checkpoint is bound to the brain it was created for, via
* a sha256(database_url) hash. brain-registry.ts:300 manages multiple
* mounted brains; without identity binding, a checkpoint from brain A can
* be applied against brain B (corruption vector). The validate() helper
* is the F4 fall-through gate — when called with a no-checkpoint or
* mismatched-brain state, the upgrade pipeline silently runs the full path.
*/
import { existsSync, readFileSync, writeFileSync, unlinkSync, mkdirSync } from 'node:fs';
import { dirname } from 'node:path';
import { createHash } from 'node:crypto';
import { gbrainPath, loadConfig } from './config.ts';
export type UpgradeStep = 'pull' | 'install' | 'schema' | 'features' | 'backfills' | 'verify';
export interface UpgradeCheckpoint {
/** Stable hash of the brain's database_url. Detects multi-brain mismatch (X2). */
brain_id: string;
/** ISO 8601 timestamp of when the upgrade started. */
started_at: string;
/** Source version (the binary that started the upgrade). */
from_version: string;
/** Target version (the binary that's running the pipeline). */
to_version: string;
/** Steps that completed successfully. */
completed_steps: UpgradeStep[];
/** Step that failed (set on error). */
failed_step?: UpgradeStep;
/** Error info from the failed step. */
failed_step_error?: { message: string; code?: string };
}
const CHECKPOINT_FILENAME = 'upgrade-checkpoint.json';
const ALL_STEPS: UpgradeStep[] = ['pull', 'install', 'schema', 'features', 'backfills', 'verify'];
function checkpointPath(): string {
return gbrainPath(CHECKPOINT_FILENAME);
}
/**
* Compute a stable brain identity hash from the database URL. Strips
* userinfo to avoid creds in the hash input collision space (anyone
* comparing hashes can't reverse to find a password). Falls back to
* 'unknown' when no URL is configured.
*/
export function computeBrainId(databaseUrl?: string | null): string {
if (!databaseUrl) {
// PGLite or no config — derive from the configured database_path
// when present, else 'pglite-default'.
const cfg = loadConfig();
const path = cfg?.database_path;
return createHash('sha256').update(`pglite:${path ?? 'default'}`).digest('hex').slice(0, 16);
}
// Strip userinfo so the hash is stable across credential rotations.
const stripped = databaseUrl.replace(/\/\/[^@]*@/, '//');
return createHash('sha256').update(stripped).digest('hex').slice(0, 16);
}
/**
* Read the checkpoint from disk. Returns null when missing or unreadable.
*/
export function loadCheckpoint(): UpgradeCheckpoint | null {
const path = checkpointPath();
if (!existsSync(path)) return null;
try {
const raw = readFileSync(path, 'utf-8');
const parsed = JSON.parse(raw) as UpgradeCheckpoint;
// Defensive: must have brain_id + completed_steps shape.
if (typeof parsed.brain_id !== 'string') return null;
if (!Array.isArray(parsed.completed_steps)) return null;
return parsed;
} catch {
return null;
}
}
export function writeCheckpoint(state: UpgradeCheckpoint): void {
const path = checkpointPath();
try {
mkdirSync(dirname(path), { recursive: true });
writeFileSync(path, JSON.stringify(state, null, 2), 'utf-8');
} catch (err) {
process.stderr.write(`[upgrade-checkpoint] write failed: ${(err as Error).message}\n`);
}
}
export function clearCheckpoint(): void {
const path = checkpointPath();
try {
if (existsSync(path)) unlinkSync(path);
} catch {
/* best-effort */
}
}
export interface CheckpointValidation {
valid: boolean;
/** Reason for invalidation. */
reason?: 'no_checkpoint' | 'brain_mismatch' | 'malformed' | 'all_complete';
/** Step to resume at (next un-completed step). */
resumeAt?: UpgradeStep;
/** The loaded checkpoint when valid + has unfinished work. */
checkpoint?: UpgradeCheckpoint;
}
/**
* Validate a checkpoint against the current brain. Returns:
* - valid=false reason=no_checkpoint → caller falls through to full upgrade (F4)
* - valid=false reason=brain_mismatch → operator must --force or remove checkpoint
* - valid=false reason=all_complete → checkpoint is stale; clear it and run full
* - valid=true → resume from resumeAt
*/
export function validateCheckpoint(currentBrainId: string): CheckpointValidation {
const checkpoint = loadCheckpoint();
if (!checkpoint) return { valid: false, reason: 'no_checkpoint' };
if (checkpoint.brain_id !== currentBrainId) {
return { valid: false, reason: 'brain_mismatch', checkpoint };
}
// Find the first step NOT in completed_steps.
const nextStep = ALL_STEPS.find(s => !checkpoint.completed_steps.includes(s));
if (!nextStep) {
return { valid: false, reason: 'all_complete', checkpoint };
}
return { valid: true, resumeAt: nextStep, checkpoint };
}
/**
* Mark a step complete in-place. Caller writes back via writeCheckpoint().
*/
export function markStepComplete(checkpoint: UpgradeCheckpoint, step: UpgradeStep): UpgradeCheckpoint {
if (!checkpoint.completed_steps.includes(step)) {
checkpoint.completed_steps.push(step);
}
// Clear failed_step when a step completes successfully (could be a re-run).
delete checkpoint.failed_step;
delete checkpoint.failed_step_error;
return checkpoint;
}
export function markStepFailed(
checkpoint: UpgradeCheckpoint,
step: UpgradeStep,
err: Error,
): UpgradeCheckpoint {
checkpoint.failed_step = step;
checkpoint.failed_step_error = {
message: err.message,
code: (err as { code?: string }).code,
};
return checkpoint;
}
export const ALL_UPGRADE_STEPS = ALL_STEPS;