nlm-memory 0.11.1 → 0.13.0

package/dist/core/storage/backup-rotation.js

@@ -0,0 +1,82 @@
+/**
+ * Rolling daily backups of the canonical store.
+ *
+ * A dated snapshot (`canonical-YYYY-MM-DD.sqlite`) is written via VACUUM INTO
+ * (live-consistent, see db-restore.vacuumSnapshot) into `<dbDir>/backups/`, and
+ * snapshots older than the retention window are pruned. This is the worst-case
+ * mitigation: a bad migration that silently corrupts canonical.sqlite is
+ * recoverable from yesterday's snapshot via `nlm restore --from <date>`.
+ *
+ * The date arithmetic (which snapshots to prune, filename <-> date) is pure and
+ * unit-tested; the IO wrapper lives in `runRollingBackup`.
+ */
+import Database from "better-sqlite3";
+import { existsSync, mkdirSync, readdirSync, rmSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { vacuumSnapshot } from "./db-restore.js";
+const FILENAME_RE = /^canonical-(\d{4}-\d{2}-\d{2})\.sqlite$/;
+export function backupDir(dbPath) {
+    return join(dirname(dbPath), "backups");
+}
+export function backupFilename(date) {
+    return `canonical-${date}.sqlite`;
+}
+/** Extract the YYYY-MM-DD date from a backup filename, or null if it isn't one. */
+export function parseBackupDate(filename) {
+    const m = FILENAME_RE.exec(filename);
+    return m ? m[1] : null;
+}
+function daysBetween(fromDate, toDate) {
+    const from = Date.parse(`${fromDate}T00:00:00Z`);
+    const to = Date.parse(`${toDate}T00:00:00Z`);
+    return Math.round((to - from) / 86_400_000);
+}
+/**
+ * Given the backup filenames present, the retention window, and today's date,
+ * return the filenames to delete — those whose date is more than
+ * `retentionDays` before `today`. Non-backup filenames are ignored. Pure.
+ */
+export function backupsToPrune(filenames, retentionDays, today) {
+    return filenames.filter((name) => {
+        const date = parseBackupDate(name);
+        if (date === null)
+            return false;
+        return daysBetween(date, today) >= retentionDays;
+    });
+}
+/**
+ * Write today's snapshot and prune expired ones. `today` is injected
+ * (YYYY-MM-DD) so the rotation is deterministic and testable. Idempotent: a
+ * second call on the same day overwrites the day's snapshot.
+ */
+export function runRollingBackup(db, dbPath, today, retentionDays) {
+    const dir = backupDir(dbPath);
+    mkdirSync(dir, { recursive: true });
+    const dest = join(dir, backupFilename(today));
+    const bytes = vacuumSnapshot(db, dest);
+    const present = readdirSync(dir);
+    const pruned = backupsToPrune(present, retentionDays, today);
+    for (const name of pruned) {
+        if (name === backupFilename(today))
+            continue; // never prune the one just written
+        rmSync(join(dir, name), { force: true });
+    }
+    return { written: dest, bytes, pruned };
+}
+/** Resolve the snapshot file for a given date, or null if absent. */
+export function resolveBackup(dbPath, date) {
+    const path = join(backupDir(dbPath), backupFilename(date));
+    return existsSync(path) ? path : null;
+}
+/** List available backup dates (descending), for error messages and `--list`. */
+export function listBackupDates(dbPath) {
+    const dir = backupDir(dbPath);
+    if (!existsSync(dir))
+        return [];
+    return readdirSync(dir)
+        .map(parseBackupDate)
+        .filter((d) => d !== null)
+        .sort()
+        .reverse();
+}
+//# sourceMappingURL=backup-rotation.js.map

package/dist/core/storage/backup-rotation.js.map

@@ -0,0 +1 @@
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package/dist/core/storage/null-code-exemplar-store.d.ts

@@ -0,0 +1,21 @@
+/**
+ * NullCodeExemplarStore — no-op implementation of CodeExemplarStore.
+ *
+ * Used by PgStorage until a full PG exemplar adapter is built.
+ * All writes succeed silently; reads return empty results.
+ */
+import type { CodeExemplarSearchFilter, CodeExemplarStore } from "../../ports/code-exemplar-store.js";
+import type { CodeExemplar, CodeExemplarHit, CodeExemplarInput } from "../../shared/types.js";
+export declare class NullCodeExemplarStore implements CodeExemplarStore {
+    insert(_input: CodeExemplarInput): Promise<{
+        id: string;
+        skipped: boolean;
+    }>;
+    insertMany(_inputs: ReadonlyArray<CodeExemplarInput>): Promise<number>;
+    upsertEmbedding(_exemplarId: string, _vector: Float32Array): Promise<void>;
+    searchByVector(_v: Float32Array, _f: CodeExemplarSearchFilter): Promise<ReadonlyArray<CodeExemplarHit>>;
+    getById(_id: string): Promise<CodeExemplar | null>;
+    applyBucketCap(_installScope: string, _maxPerBucket: number): Promise<number>;
+    pruneReverted(_installScope: string): Promise<number>;
+    pruneOlderThan(_olderThanTs: string): Promise<number>;
+}

package/dist/core/storage/null-code-exemplar-store.js

@@ -0,0 +1,19 @@
+/**
+ * NullCodeExemplarStore — no-op implementation of CodeExemplarStore.
+ *
+ * Used by PgStorage until a full PG exemplar adapter is built.
+ * All writes succeed silently; reads return empty results.
+ */
+export class NullCodeExemplarStore {
+    async insert(_input) {
+        return { id: "", skipped: true };
+    }
+    async insertMany(_inputs) { return 0; }
+    async upsertEmbedding(_exemplarId, _vector) { }
+    async searchByVector(_v, _f) { return []; }
+    async getById(_id) { return null; }
+    async applyBucketCap(_installScope, _maxPerBucket) { return 0; }
+    async pruneReverted(_installScope) { return 0; }
+    async pruneOlderThan(_olderThanTs) { return 0; }
+}
+//# sourceMappingURL=null-code-exemplar-store.js.map

package/dist/core/storage/null-code-exemplar-store.js.map

@@ -0,0 +1 @@
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package/dist/core/storage/pg-fact-store.d.ts

@@ -12,11 +12,13 @@ export declare class PgFactStore implements FactStore {
     insert(fact: Fact): Promise<void>;
     insertMany(facts: ReadonlyArray<Fact>): Promise<void>;
     getById(id: string): Promise<Fact | null>;
+    getByIds(ids: ReadonlyArray<string>): Promise<ReadonlyArray<Fact>>;
     findCurrent(subject: string, predicate: string): Promise<Fact | null>;
     list(query: FactQuery): Promise<ReadonlyArray<Fact>>;
     listBySession(sessionId: string): Promise<ReadonlyArray<Fact>>;
     listForRecall(filter: FactListFilter): Promise<ReadonlyArray<Fact>>;
     markSuperseded(oldId: string, newId: string | null): Promise<void>;
+    retire(factId: string): Promise<void>;
     ingestSessionFacts(sessionId: string, facts: ReadonlyArray<Fact>): Promise<void>;
     upsertEmbedding(factId: string, vector: Float32Array): Promise<void>;
     semanticSearch(queryVector: Float32Array, limit: number): Promise<ReadonlyArray<FactSemanticNeighbor>>;

package/dist/core/storage/pg-fact-store.js

@@ -42,11 +42,19 @@ export class PgFactStore {
        FROM facts WHERE id = $1`, [id]);
         return result.rows[0] ? rowToFact(result.rows[0]) : null;
     }
+    async getByIds(ids) {
+        if (ids.length === 0)
+            return [];
+        const result = await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
+              source_quote, created_at, superseded_by, confidence
+       FROM facts WHERE id = ANY($1)`, [ids]);
+        return result.rows.map(rowToFact);
+    }
     async findCurrent(subject, predicate) {
         const result = await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
               source_quote, created_at, superseded_by, confidence
        FROM facts
-       WHERE subject = $1 AND predicate = $2 AND superseded_by IS NULL
+       WHERE subject = $1 AND predicate = $2 AND superseded_by IS NULL AND retired_at IS NULL
        ORDER BY created_at DESC
        LIMIT 1`, [subject, predicate]);
         return result.rows[0] ? rowToFact(result.rows[0]) : null;
@@ -61,8 +69,10 @@ export class PgFactStore {
             where.push(`predicate = $${idx++}`);
             params.push(query.predicate);
         }
-        if (!includeSuperseded)
+        if (!includeSuperseded) {
             where.push("superseded_by IS NULL");
+            where.push("retired_at IS NULL");
+        }
         params.push(limit);
         const result = await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
               source_quote, created_at, superseded_by, confidence
@@ -100,8 +110,10 @@ export class PgFactStore {
             where.push(`confidence >= $${idx++}`);
             params.push(filter.minConfidence);
         }
-        if (filter.includeSuperseded !== true)
+        if (filter.includeSuperseded !== true) {
             where.push("superseded_by IS NULL");
+            where.push("retired_at IS NULL");
+        }
         const limit = Math.max(1, Math.trunc(filter.limit ?? 500));
         params.push(limit);
         const sql = `
@@ -141,6 +153,25 @@ export class PgFactStore {
             client.release();
         }
     }
+    async retire(factId) {
+        const client = await this.pool.connect();
+        try {
+            await client.query("BEGIN");
+            const row = await client.query("SELECT id FROM facts WHERE id = $1", [factId]);
+            if (row.rows.length === 0)
+                throw new Error(`Fact ${factId} not found`);
+            await client.query("UPDATE facts SET retired_at = $1 WHERE id = $2", [new Date().toISOString(), factId]);
+            await client.query("DELETE FROM fact_embeddings WHERE fact_id = $1", [factId]);
+            await client.query("COMMIT");
+        }
+        catch (err) {
+            await client.query("ROLLBACK");
+            throw err;
+        }
+        finally {
+            client.release();
+        }
+    }
     async ingestSessionFacts(sessionId, facts) {
         const client = await this.pool.connect();
         try {

package/dist/core/storage/pg-fact-store.js.map

@@ -1 +1 @@
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package/dist/core/storage/pg-session-store.d.ts

@@ -7,10 +7,11 @@
  */
 import type { Pool } from "pg";
 import type { KeywordNeighbor, SearchOptions, SemanticNeighbor, SessionFilter, SessionStore } from "../../ports/session-store.js";
-import type { Session, SessionStatus } from "../../shared/types.js";
-import type { IngestRecord, RecentMarker, RecentWrite, Supersedes } from "./sqlite-session-store.js";
+import type { Fact, Session, SessionStatus } from "../../shared/types.js";
+import type { BackfillCandidate, BackfillCandidateFilter, IngestRecord, RecentMarker, RecentWrite, Supersedes } from "./sqlite-session-store.js";
+import type { PgFactStore } from "./pg-fact-store.js";
 export declare class PgSessionStore implements SessionStore {
-    private readonly pool;
+    readonly pool: Pool;
     constructor(pool: Pool);
     list(filter?: SessionFilter): Promise<ReadonlyArray<Session>>;
     getById(sessionId: string): Promise<Session | null>;
@@ -22,8 +23,17 @@ export declare class PgSessionStore implements SessionStore {
     markSuperseded(predecessorId: string, successorId: string): Promise<void>;
     recentWrites(limit: number): Promise<RecentWrite[]>;
     recentMarkers(limit: number): Promise<RecentMarker[]>;
-    insertSession(record: IngestRecord, embedder?: import("../../ports/llm-client.js").LLMClient | null, supersedes?: Supersedes | null): Promise<void>;
+    insertSession(record: IngestRecord, embedder?: import("../../ports/llm-client.js").LLMClient | null, supersedes?: Supersedes | null, factSink?: {
+        factStore: PgFactStore;
+        facts: ReadonlyArray<Fact>;
+    } | null): Promise<void>;
     insertSessionForTest(session: Session): Promise<void>;
+    /** PG counterpart of SqliteSessionStore.listBackfillCandidates. */
+    listBackfillCandidates(filter: BackfillCandidateFilter): Promise<BackfillCandidate[]>;
+    /** PG counterpart of SqliteSessionStore.insertFactsForSession — writes facts
+     *  for an EXISTING session row (deterministic supersedence + best-effort
+     *  embeddings) in one transaction. Used by the fact backfill. */
+    insertFactsForSession(sessionId: string, factStore: PgFactStore, facts: ReadonlyArray<Fact>, embedder?: import("../../ports/llm-client.js").LLMClient | null): Promise<void>;
     private loadEntities;
     private loadMarkers;
     private loadEdges;

package/dist/core/storage/pg-session-store.js

@@ -8,6 +8,8 @@
 import { chunkSessionText } from "../embedding/chunk-body.js";
 export class PgSessionStore {
     pool;
+    // `pool` is public-readonly so PG-native sibling helpers (actions-log Pg
+    // functions) can share the same connection pool. See docs/plans/2026-05-31-pg-adapter.md.
     constructor(pool) {
         this.pool = pool;
     }
@@ -213,7 +215,7 @@ export class PgSessionStore {
        LIMIT $1`, [limit]);
         return result.rows;
     }
-    async insertSession(record, embedder = null, supersedes = null) {
+    async insertSession(record, embedder = null, supersedes = null, factSink = null) {
         const client = await this.pool.connect();
         try {
             await client.query("BEGIN");
@@ -262,6 +264,35 @@ export class PgSessionStore {
            VALUES ($1, $2, $3) ON CONFLICT DO NOTHING`, [record.id, supersedes.priorSessionId, supersedes.kind]);
                 await client.query("UPDATE sessions SET status = $1, updated_at = NOW() WHERE id = $2", [predecessorStatus, supersedes.priorSessionId]);
             }
+            // Atomic session+facts ingest. Mirrors the SQLite factSink path
+            // (sqlite-session-store.insertSession) and PgFactStore.ingestSessionFacts,
+            // but runs on the session's own client so facts commit with the row.
+            // Re-ingest is idempotent: DELETE-by-session clears prior facts, then the
+            // batch UPDATE re-collapses every active (subject, predicate) sibling.
+            if (factSink !== null) {
+                await client.query("DELETE FROM facts WHERE source_session_id = $1", [record.id]);
+                if (factSink.facts.length > 0) {
+                    for (const f of factSink.facts) {
+                        await client.query(`INSERT INTO facts (id, kind, subject, predicate, value, source_session_id,
+                 source_quote, created_at, superseded_by, confidence)
+               VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10)`, [f.id, f.kind, f.subject, f.predicate, f.value, f.sourceSessionId,
+                            f.sourceQuote, f.createdAt, f.supersededBy, f.confidence]);
+                    }
+                    const values = factSink.facts
+                        .map((_, i) => `($${i * 3 + 1}, $${i * 3 + 2}, $${i * 3 + 3})`)
+                        .join(", ");
+                    const params = [];
+                    for (const f of factSink.facts)
+                        params.push(f.subject, f.predicate, f.id);
+                    await client.query(`UPDATE facts AS old
+             SET superseded_by = new_f.new_id
+             FROM (VALUES ${values}) AS new_f(subject, predicate, new_id)
+             WHERE old.subject = new_f.subject
+               AND old.predicate = new_f.predicate
+               AND old.superseded_by IS NULL
+               AND old.id != new_f.new_id`, params);
+                }
+            }
             await client.query("COMMIT");
         }
         catch (err) {
@@ -290,6 +321,23 @@ export class PgSessionStore {
                     process.stderr.write(`[nlm] embedding chunk failed session=${record.id} chunk=${chunkIdx}: ${String(err)}\n`);
                 }
             }
+            // Fact embeddings are best-effort and live outside the txn, mirroring the
+            // SQLite path. A per-fact embed failure leaves the fact current but
+            // semantically unreachable until a future re-ingest.
+            if (factSink !== null) {
+                for (const fact of factSink.facts) {
+                    const factText = `${fact.subject} ${fact.predicate} ${fact.value}`.trim();
+                    if (!factText)
+                        continue;
+                    try {
+                        const { vector } = await embedder.embed(factText, "document");
+                        await factSink.factStore.upsertEmbedding(fact.id, vector);
+                    }
+                    catch {
+                        // Tolerated; see comment above.
+                    }
+                }
+            }
         }
     }
     async insertSessionForTest(session) {
@@ -312,6 +360,76 @@ export class PgSessionStore {
             await this.pool.query("INSERT INTO markers (session_id, kind, text, position) VALUES ($1, 'open', $2, $3)", [session.id, session.open[i], i]);
         }
     }
+    /** PG counterpart of SqliteSessionStore.listBackfillCandidates. */
+    async listBackfillCandidates(filter) {
+        const params = [filter.cutoff];
+        let fromClause = "";
+        if (filter.from) {
+            params.push(filter.from);
+            fromClause = `AND s.id > $${params.length}`;
+        }
+        const existingFactsClause = filter.reprocess
+            ? ""
+            : "AND NOT EXISTS (SELECT 1 FROM facts f WHERE f.source_session_id = s.id)";
+        const result = await this.pool.query(`SELECT s.id, s.started_at, s.body FROM sessions s
+       WHERE s.started_at < $1 AND s.body IS NOT NULL AND length(s.body) > 0
+         ${existingFactsClause}
+         ${fromClause}
+       ORDER BY s.started_at ASC, s.id ASC`, params);
+        return result.rows.map((r) => ({ id: r.id, startedAt: r.started_at, body: r.body }));
+    }
+    /** PG counterpart of SqliteSessionStore.insertFactsForSession — writes facts
+     *  for an EXISTING session row (deterministic supersedence + best-effort
+     *  embeddings) in one transaction. Used by the fact backfill. */
+    async insertFactsForSession(sessionId, factStore, facts, embedder = null) {
+        const client = await this.pool.connect();
+        try {
+            await client.query("BEGIN");
+            await client.query("DELETE FROM facts WHERE source_session_id = $1", [sessionId]);
+            if (facts.length > 0) {
+                for (const f of facts) {
+                    await client.query(`INSERT INTO facts (id, kind, subject, predicate, value, source_session_id,
+               source_quote, created_at, superseded_by, confidence)
+             VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10)`, [f.id, f.kind, f.subject, f.predicate, f.value, f.sourceSessionId,
+                        f.sourceQuote, f.createdAt, f.supersededBy, f.confidence]);
+                }
+                const values = facts.map((_, i) => `($${i * 3 + 1}, $${i * 3 + 2}, $${i * 3 + 3})`).join(", ");
+                const supersedeParams = [];
+                for (const f of facts)
+                    supersedeParams.push(f.subject, f.predicate, f.id);
+                await client.query(`UPDATE facts AS old
+           SET superseded_by = new_f.new_id
+           FROM (VALUES ${values}) AS new_f(subject, predicate, new_id)
+           WHERE old.subject = new_f.subject
+             AND old.predicate = new_f.predicate
+             AND old.superseded_by IS NULL
+             AND old.id != new_f.new_id`, supersedeParams);
+            }
+            await client.query("COMMIT");
+        }
+        catch (err) {
+            await client.query("ROLLBACK");
+            throw err;
+        }
+        finally {
+            client.release();
+        }
+        if (embedder) {
+            for (const fact of facts) {
+                const factText = `${fact.subject} ${fact.predicate} ${fact.value}`.trim();
+                if (!factText)
+                    continue;
+                try {
+                    const { vector } = await embedder.embed(factText, "document");
+                    await factStore.upsertEmbedding(fact.id, vector);
+                }
+                catch {
+                    // Best-effort; a per-fact embed failure leaves the fact current but
+                    // semantically unreachable until a future re-ingest.
+                }
+            }
+        }
+    }
     async loadEntities(ids) {
         if (ids.length === 0)
             return new Map();
@@ -352,9 +470,12 @@ export class PgSessionStore {
         if (ids.length === 0)
             return new Map();
         const placeholders = ids.map((_, i) => `$${i + 1}`).join(",");
+        // Both IN clauses reference the same $1..$n placeholders, so bind `ids`
+        // once — not twice. (Passing [...ids, ...ids] over-supplies parameters and
+        // PG rejects the bind: "supplies N parameters but requires M".)
         const result = await this.pool.query(`SELECT from_session, to_session FROM session_edges
        WHERE kind = 'supersedes'
-         AND (from_session IN (${placeholders}) OR to_session IN (${placeholders}))`, [...ids, ...ids]);
+         AND (from_session IN (${placeholders}) OR to_session IN (${placeholders}))`, [...ids]);
         const out = new Map();
         for (const id of ids)
             out.set(id, { supersededBy: null, supersedes: [] });

package/dist/core/storage/pg-session-store.js.map

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package/dist/core/storage/pg-storage.d.ts

@@ -14,6 +14,9 @@ import type { Storage, StorageContext } from "../../ports/storage.js";
 import { PgFactStore } from "./pg-fact-store.js";
 import { PgSessionStore } from "./pg-session-store.js";
 import { PgSignalStore } from "./pg-signal-store.js";
+import { NullCodeExemplarStore } from "./null-code-exemplar-store.js";
+import { PgSourceRegistry } from "../sources/source-registry.js";
+import { PgProviderRegistry } from "../providers/provider-registry.js";
 export interface PgStorageOptions {
     readonly connectionString: string;
     readonly migrationsDir: string;
@@ -22,6 +25,9 @@ export declare class PgStorage implements Storage {
     readonly facts: PgFactStore;
     readonly sessions: PgSessionStore;
     readonly signals: PgSignalStore;
+    readonly exemplars: NullCodeExemplarStore;
+    readonly sources: PgSourceRegistry;
+    readonly providers: PgProviderRegistry;
     private readonly _pool;
     private readonly _migrationsDir;
     private inTxn;
@@ -31,8 +37,11 @@ export declare class PgStorage implements Storage {
     close(): Promise<void>;
     withTransaction<T>(fn: (ctx: StorageContext) => T): Promise<T>;
     /**
-     * @deprecated Escape hatch for callers not yet ported to the Storage
-     * interface. Tracked for removal in #215a (PG branch).
+     * Raw pool accessor. The #215a escape-hatch callers (registries, actions,
+     * scheduler, ingest, backfill) have all been ported to the Storage port /
+     * adapter methods. The one remaining caller is `nlm check-invariants`, which
+     * deliberately runs backend-specific invariant SQL through `runChecksOnPg` /
+     * `applyFixOnPg` — a dual-backend diagnostic API, not an un-ported leak.
      */
     pgPool(): Pool;
 }

package/dist/core/storage/pg-storage.js

@@ -15,11 +15,17 @@ import { join } from "node:path";
 import { PgFactStore } from "./pg-fact-store.js";
 import { PgSessionStore } from "./pg-session-store.js";
 import { PgSignalStore } from "./pg-signal-store.js";
+import { NullCodeExemplarStore } from "./null-code-exemplar-store.js";
 import { PgTxBoundFactStore, PgTxBoundSessionStore } from "./pg-tx-context.js";
+import { PgSourceRegistry } from "../sources/source-registry.js";
+import { PgProviderRegistry } from "../providers/provider-registry.js";
 export class PgStorage {
     facts;
     sessions;
     signals;
+    exemplars;
+    sources;
+    providers;
     _pool;
     _migrationsDir;
     // Guards against re-entrant (synchronous) nesting only. Not concurrent-call-safe.
@@ -30,6 +36,9 @@ export class PgStorage {
         this.facts = new PgFactStore(pool);
         this.sessions = new PgSessionStore(pool);
         this.signals = new PgSignalStore(pool);
+        this.exemplars = new NullCodeExemplarStore();
+        this.sources = new PgSourceRegistry(pool);
+        this.providers = new PgProviderRegistry(pool);
     }
     static create(opts) {
         const pool = new Pool({ connectionString: opts.connectionString });
@@ -80,8 +89,11 @@ export class PgStorage {
         return result;
     }
     /**
-     * @deprecated Escape hatch for callers not yet ported to the Storage
-     * interface. Tracked for removal in #215a (PG branch).
+     * Raw pool accessor. The #215a escape-hatch callers (registries, actions,
+     * scheduler, ingest, backfill) have all been ported to the Storage port /
+     * adapter methods. The one remaining caller is `nlm check-invariants`, which
+     * deliberately runs backend-specific invariant SQL through `runChecksOnPg` /
+     * `applyFixOnPg` — a dual-backend diagnostic API, not an un-ported leak.
      */
     pgPool() {
         return this._pool;