nlm-memory 0.20.0 → 0.21.0

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

@@ -0,0 +1,79 @@
+/**
+ * PgEntityStore -- EntityStore implementation over pg.Pool.
+ *
+ * All merge operations run inside a single pg transaction.
+ */
+export class PgEntityStore {
+    pool;
+    constructor(pool) {
+        this.pool = pool;
+    }
+    async merge(source, target) {
+        const client = await this.pool.connect();
+        try {
+            await client.query("BEGIN");
+            const targetRes = await client.query("SELECT status FROM entities WHERE canonical = $1", [target]);
+            if (targetRes.rowCount === 0) {
+                throw new Error(`merge: target entity not found: ${target}`);
+            }
+            if (targetRes.rows[0].status === "retired") {
+                throw new Error(`merge: target entity is retired: ${target}`);
+            }
+            const sourceRes = await client.query("SELECT status FROM entities WHERE canonical = $1", [source]);
+            if (sourceRes.rowCount === 0) {
+                throw new Error(`merge: source entity not found: ${source}`);
+            }
+            // Step 1: copy source session_entities to target, dedup on composite PK.
+            await client.query(`INSERT INTO session_entities (session_id, entity_canonical)
+         SELECT session_id, $1 FROM session_entities WHERE entity_canonical = $2
+         ON CONFLICT DO NOTHING`, [target, source]);
+            // Step 2: delete source's session_entities rows.
+            await client.query("DELETE FROM session_entities WHERE entity_canonical = $1", [source]);
+            // Step 3: recompute target.session_count exactly from session_entities.
+            await client.query(`UPDATE entities
+           SET session_count = (SELECT COUNT(*) FROM session_entities WHERE entity_canonical = $1),
+               updated_at    = NOW()
+         WHERE canonical = $1`, [target]);
+            // Step 4: widen first_seen_session / last_seen_session.
+            // first_seen and last_seen are session IDs (text FK to sessions.id).
+            // Join to sessions to order by started_at and pick earliest / latest.
+            const seenRes = await client.query(`SELECT id, started_at FROM sessions
+         WHERE id IN (
+           SELECT first_seen_session FROM entities WHERE canonical = ANY($1)
+           UNION
+           SELECT last_seen_session  FROM entities WHERE canonical = ANY($1)
+         )`, [[source, target]]);
+            if (seenRes.rows.length > 0) {
+                const sorted = seenRes.rows.slice().sort((a, b) => a.started_at.localeCompare(b.started_at));
+                const earliest = sorted[0].id;
+                const latest = sorted[sorted.length - 1].id;
+                await client.query(`UPDATE entities
+             SET first_seen_session = $1,
+                 last_seen_session  = $2,
+                 updated_at         = NOW()
+           WHERE canonical = $3`, [earliest, latest, target]);
+            }
+            // Step 5: insert the variant record so future ingest resolves source -> target.
+            await client.query(`INSERT INTO entity_variants (variant, canonical, source_session_id)
+         VALUES ($1, $2, NULL)
+         ON CONFLICT DO NOTHING`, [source, target]);
+            // Step 6: re-point existing variants of source to target.
+            await client.query(`UPDATE entity_variants SET canonical = $1 WHERE canonical = $2 AND variant != $2`, [target, source]);
+            // Step 7: retire the source entity row in place.
+            await client.query(`UPDATE entities
+           SET status        = 'retired',
+               session_count = 0,
+               updated_at    = NOW()
+         WHERE canonical = $1`, [source]);
+            await client.query("COMMIT");
+        }
+        catch (err) {
+            await client.query("ROLLBACK");
+            throw err;
+        }
+        finally {
+            client.release();
+        }
+    }
+}
+//# sourceMappingURL=pg-entity-store.js.map

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

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

@@ -0,0 +1,15 @@
+/**
+ * Single source of truth for pg fact-ingest. Caller owns the transaction:
+ * this function MUST run on a client that already issued BEGIN.
+ *
+ * Mirrors SqliteFactStore.ingestSessionFactsInTxn semantics (NLM #351):
+ *  - re-ingest clears prior facts for the session (fact_embeddings rows for
+ *    DELETED facts self-clean via the FK ON DELETE CASCADE; UPDATE-superseded
+ *    facts below need an explicit embedding delete)
+ *  - one winner per (subject, predicate) per batch (last in batch wins), so an
+ *    intra-batch duplicate can never create a mutual supersedence cycle
+ *  - every fact the collapse supersedes leaves the ANN index immediately
+ */
+import type { PoolClient } from "pg";
+import type { Fact } from "../../shared/types.js";
+export declare function ingestSessionFactsOnClient(client: PoolClient, sessionId: string, facts: ReadonlyArray<Fact>, scope?: string | null): Promise<void>;

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

@@ -0,0 +1,34 @@
+/**
+ * Single source of truth for pg fact-ingest. Caller owns the transaction:
+ * this function MUST run on a client that already issued BEGIN.
+ *
+ * Mirrors SqliteFactStore.ingestSessionFactsInTxn semantics (NLM #351):
+ *  - re-ingest clears prior facts for the session (fact_embeddings rows for
+ *    DELETED facts self-clean via the FK ON DELETE CASCADE; UPDATE-superseded
+ *    facts below need an explicit embedding delete)
+ *  - one winner per (subject, predicate) per batch (last in batch wins), so an
+ *    intra-batch duplicate can never create a mutual supersedence cycle
+ *  - every fact the collapse supersedes leaves the ANN index immediately
+ */
+import { batchWinners } from "./fact-batch.js";
+export async function ingestSessionFactsOnClient(client, sessionId, facts, scope = null) {
+    await client.query("DELETE FROM facts WHERE source_session_id = $1", [sessionId]);
+    if (facts.length === 0)
+        return;
+    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, retired_at, scope)
+       VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12)`, [f.id, f.kind, f.subject, f.predicate, f.value, f.sourceSessionId,
+            f.sourceQuote, f.createdAt, f.supersededBy, f.confidence, f.retiredAt, scope]);
+    }
+    for (const f of batchWinners(facts)) {
+        const collapsed = await client.query(`UPDATE facts SET superseded_by = $1
+       WHERE subject = $2 AND predicate = $3 AND superseded_by IS NULL AND id != $1
+       RETURNING id`, [f.id, f.subject, f.predicate]);
+        const ids = collapsed.rows.map((r) => r.id);
+        if (ids.length > 0) {
+            await client.query("DELETE FROM fact_embeddings WHERE fact_id = ANY($1)", [ids]);
+        }
+    }
+}
+//# sourceMappingURL=pg-fact-ingest.js.map

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

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

@@ -16,6 +16,9 @@ export declare class PgFactStore implements FactStore {
     findCurrent(subject: string, predicate: string): Promise<Fact | null>;
     list(query: FactQuery): Promise<ReadonlyArray<Fact>>;
     listBySession(sessionId: string): Promise<ReadonlyArray<Fact>>;
+    listBySessions(sessionIds: ReadonlyArray<string>, opts?: {
+        includeSuperseded?: boolean;
+    }): Promise<ReadonlyArray<Fact>>;
     listForRecall(filter: FactListFilter): Promise<ReadonlyArray<Fact>>;
     markSuperseded(oldId: string, newId: string | null): Promise<void>;
     retire(factId: string): Promise<void>;

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

@@ -3,6 +3,7 @@
  *
  * Receives its Pool from PgStorage. Never opens its own connection.
  */
+import { ingestSessionFactsOnClient } from "./pg-fact-ingest.js";
 export class PgFactStore {
     pool;
     constructor(pool) {
@@ -38,7 +39,7 @@ export class PgFactStore {
     }
     async getById(id) {
         const result = await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
-              source_quote, created_at, superseded_by, confidence
+              source_quote, created_at, superseded_by, confidence, retired_at
        FROM facts WHERE id = $1`, [id]);
         return result.rows[0] ? rowToFact(result.rows[0]) : null;
     }
@@ -46,13 +47,13 @@ export class PgFactStore {
         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
+              source_quote, created_at, superseded_by, confidence, retired_at
        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
+              source_quote, created_at, superseded_by, confidence, retired_at
        FROM facts
        WHERE subject = $1 AND predicate = $2 AND superseded_by IS NULL AND retired_at IS NULL
        ORDER BY created_at DESC
@@ -75,7 +76,7 @@ export class PgFactStore {
         }
         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
+              source_quote, created_at, superseded_by, confidence, retired_at
        FROM facts
        WHERE ${where.join(" AND ")}
        ORDER BY created_at DESC
@@ -84,12 +85,22 @@ export class PgFactStore {
     }
     async listBySession(sessionId) {
         const result = await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
-              source_quote, created_at, superseded_by, confidence
+              source_quote, created_at, superseded_by, confidence, retired_at
        FROM facts
        WHERE source_session_id = $1
        ORDER BY created_at ASC`, [sessionId]);
         return result.rows.map(rowToFact);
     }
+    async listBySessions(sessionIds, opts) {
+        if (sessionIds.length === 0)
+            return [];
+        const ph = sessionIds.map((_, i) => `$${i + 1}`).join(",");
+        const filter = opts?.includeSuperseded === true ? "" : " AND superseded_by IS NULL AND retired_at IS NULL";
+        const result = await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
+              source_quote, created_at, superseded_by, confidence, retired_at
+       FROM facts WHERE source_session_id IN (${ph})${filter} ORDER BY created_at ASC`, [...sessionIds]);
+        return result.rows.map(rowToFact);
+    }
     async listForRecall(filter) {
         const where = [];
         const params = [];
@@ -118,7 +129,7 @@ export class PgFactStore {
         params.push(limit);
         const sql = `
       SELECT id, kind, subject, predicate, value, source_session_id,
-             source_quote, created_at, superseded_by, confidence
+             source_quote, created_at, superseded_by, confidence, retired_at
       FROM facts
       ${where.length > 0 ? "WHERE " + where.join(" AND ") : ""}
       ORDER BY created_at DESC
@@ -143,6 +154,11 @@ export class PgFactStore {
                     throw new Error(`Fact ${newId} not found`);
             }
             await client.query("UPDATE facts SET superseded_by = $1 WHERE id = $2", [newId, oldId]);
+            // Superseded facts leave the ANN index (parity with SQLite + retire); a
+            // lingering embedding silently reduces effective recall (NLM #351).
+            if (newId !== null) {
+                await client.query("DELETE FROM fact_embeddings WHERE fact_id = $1", [oldId]);
+            }
             await client.query("COMMIT");
         }
         catch (err) {
@@ -176,28 +192,7 @@ export class PgFactStore {
         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 params = [];
-                for (const f of 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 ingestSessionFactsOnClient(client, sessionId, facts);
             await client.query("COMMIT");
         }
         catch (err) {
@@ -226,12 +221,12 @@ export class PgFactStore {
     async getHistory(subject, predicate) {
         const result = predicate
             ? await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
-                  source_quote, created_at, superseded_by, confidence
+                  source_quote, created_at, superseded_by, confidence, retired_at
            FROM facts
            WHERE subject = $1 AND predicate = $2
            ORDER BY predicate ASC, created_at DESC`, [subject, predicate])
             : await this.pool.query(`SELECT id, kind, subject, predicate, value, source_session_id,
-                  source_quote, created_at, superseded_by, confidence
+                  source_quote, created_at, superseded_by, confidence, retired_at
            FROM facts
            WHERE subject = $1
            ORDER BY predicate ASC, created_at DESC`, [subject]);
@@ -288,6 +283,7 @@ function rowToFact(row) {
         createdAt: row.created_at,
         supersededBy: row.superseded_by,
         confidence: row.confidence,
+        retiredAt: row.retired_at ?? null,
     };
 }
 //# sourceMappingURL=pg-fact-store.js.map

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

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

@@ -0,0 +1,18 @@
+/**
+ * Version-gated PostgreSQL migration runner. Reads versioned *.sql files from
+ * a directory, applies any whose integer prefix is not yet in schema_migrations,
+ * and returns the list of newly applied versions. Idempotent: re-running on an
+ * up-to-date database is a no-op.
+ *
+ * Migration files that contain their own BEGIN/COMMIT markers have those lines
+ * stripped; the runner wraps each file in a single transaction instead. A file
+ * whose first line is `-- nlm:no-wrap` is executed as-is (manages its own
+ * transaction). No pg migration files use that convention today; the check is
+ * kept for parity with the sqlite runner.
+ */
+import type { Pool } from "pg";
+export interface AppliedMigration {
+    readonly version: number;
+    readonly name: string;
+}
+export declare function runMigrationsPg(pool: Pool, migrationsDir: string): Promise<ReadonlyArray<AppliedMigration>>;

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

@@ -0,0 +1,73 @@
+/**
+ * Version-gated PostgreSQL migration runner. Reads versioned *.sql files from
+ * a directory, applies any whose integer prefix is not yet in schema_migrations,
+ * and returns the list of newly applied versions. Idempotent: re-running on an
+ * up-to-date database is a no-op.
+ *
+ * Migration files that contain their own BEGIN/COMMIT markers have those lines
+ * stripped; the runner wraps each file in a single transaction instead. A file
+ * whose first line is `-- nlm:no-wrap` is executed as-is (manages its own
+ * transaction). No pg migration files use that convention today; the check is
+ * kept for parity with the sqlite runner.
+ */
+import { readFileSync, readdirSync } from "node:fs";
+import { join } from "node:path";
+const FILE_PATTERN = /^(\d+)_([a-z0-9_-]+)\.sql$/i;
+function stripTransactionMarkers(sql) {
+    return sql
+        .split("\n")
+        .filter((line) => !/^\s*(?:BEGIN|COMMIT)\s*;\s*$/.test(line))
+        .join("\n");
+}
+export async function runMigrationsPg(pool, migrationsDir) {
+    await pool.query(`
+    CREATE TABLE IF NOT EXISTS schema_migrations (
+      version     INTEGER PRIMARY KEY,
+      name        TEXT NOT NULL,
+      applied_at  TIMESTAMPTZ NOT NULL DEFAULT NOW()
+    )
+  `);
+    const { rows: appliedRows } = await pool.query("SELECT version FROM schema_migrations");
+    const applied = new Set(appliedRows.map((r) => r.version));
+    const files = readdirSync(migrationsDir)
+        .filter((f) => FILE_PATTERN.test(f))
+        .sort();
+    const newlyApplied = [];
+    for (const file of files) {
+        const match = FILE_PATTERN.exec(file);
+        if (!match)
+            continue;
+        const version = Number(match[1]);
+        const name = match[2] ?? file;
+        if (applied.has(version))
+            continue;
+        const rawSql = readFileSync(join(migrationsDir, file), "utf8");
+        const noWrap = rawSql.startsWith("-- nlm:no-wrap");
+        const client = await pool.connect();
+        try {
+            if (noWrap) {
+                await client.query(rawSql);
+                await client.query("INSERT INTO schema_migrations (version, name) VALUES ($1, $2) ON CONFLICT DO NOTHING", [version, name]);
+            }
+            else {
+                const sql = stripTransactionMarkers(rawSql);
+                await client.query("BEGIN");
+                try {
+                    await client.query(sql);
+                    await client.query("INSERT INTO schema_migrations (version, name) VALUES ($1, $2) ON CONFLICT DO NOTHING", [version, name]);
+                    await client.query("COMMIT");
+                }
+                catch (err) {
+                    await client.query("ROLLBACK");
+                    throw new Error(`Migration ${file} failed: ${err instanceof Error ? err.message : String(err)}`);
+                }
+            }
+        }
+        finally {
+            client.release();
+        }
+        newlyApplied.push({ version, name });
+    }
+    return newlyApplied;
+}
+//# sourceMappingURL=pg-migrate.js.map

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

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

@@ -6,21 +6,30 @@
  * insertSessionForTest() for ingest and test seeding.
  */
 import type { Pool } from "pg";
-import type { KeywordNeighbor, SearchOptions, SemanticNeighbor, SessionFilter, SessionStore } from "../../ports/session-store.js";
+import type { KeywordNeighbor, SearchOptions, SemanticNeighbor, SessionStore } from "../../ports/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 {
     readonly pool: Pool;
     constructor(pool: Pool);
-    list(filter?: SessionFilter): Promise<ReadonlyArray<Session>>;
+    private overlayCache;
+    private overlayCacheAt;
+    invalidateOverlayCache(): void;
+    private overlay;
     getById(sessionId: string): Promise<Session | null>;
     getByIds(ids: ReadonlyArray<string>): Promise<ReadonlyArray<Session>>;
+    listByDateRange(fromIso: string, toIso: string): Promise<ReadonlyArray<Session>>;
     semanticSearch(queryVector: Float32Array, limit: number, opts?: SearchOptions): Promise<ReadonlyArray<SemanticNeighbor>>;
     keywordSearch(query: string, limit: number, opts?: SearchOptions): Promise<ReadonlyArray<KeywordNeighbor>>;
     resolveSuccessors(ids: ReadonlyArray<string>): Promise<Map<string, string>>;
     updateStatus(sessionId: string, status: SessionStatus): Promise<void>;
     markSuperseded(predecessorId: string, successorId: string): Promise<void>;
+    getSessionScopeById(id: string): Promise<string | null>;
+    setWorkstreamBinding(sessionId: string, workstreamId: string | null, source: import("../workstream/model.js").BindingSource | null, confidence: number | null): Promise<void>;
+    listSessionIdsByWorkstreams(workstreamIds: ReadonlyArray<string>): Promise<ReadonlyArray<string>>;
+    getEntities(sessionId: string): Promise<ReadonlyArray<string>>;
+    getWorkstreamIds(sessionIds: ReadonlyArray<string>): Promise<Map<string, string | null>>;
     recentWrites(limit: number): Promise<RecentWrite[]>;
     recentMarkers(limit: number): Promise<RecentMarker[]>;
     insertSession(record: IngestRecord, embedder?: import("../../ports/llm-client.js").LLMClient | null, supersedes?: Supersedes | null, factSink?: {