nlm-memory 0.20.0 → 0.20.1

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

@@ -0,0 +1,96 @@
+/**
+ * SqliteEntityStore -- EntityStore implementation over better-sqlite3.
+ *
+ * All merge operations run inside a single synchronous transaction so
+ * the database is never left in a partially-merged state.
+ */
+export class SqliteEntityStore {
+    db;
+    constructor(db) {
+        this.db = db;
+    }
+    async merge(source, target) {
+        const txn = this.db.transaction(() => {
+            const targetRow = this.db
+                .prepare("SELECT status FROM entities WHERE canonical = ?")
+                .get(target);
+            if (!targetRow)
+                throw new Error(`merge: target entity not found: ${target}`);
+            if (targetRow.status === "retired") {
+                throw new Error(`merge: target entity is retired: ${target}`);
+            }
+            const sourceRow = this.db
+                .prepare("SELECT status FROM entities WHERE canonical = ?")
+                .get(source);
+            if (!sourceRow)
+                throw new Error(`merge: source entity not found: ${source}`);
+            // Step 1: copy source session_entities to target, dedup on composite PK.
+            this.db
+                .prepare(`INSERT OR IGNORE INTO session_entities (session_id, entity_canonical)
+           SELECT session_id, ? FROM session_entities WHERE entity_canonical = ?`)
+                .run(target, source);
+            // Step 2: delete source's session_entities rows.
+            this.db
+                .prepare("DELETE FROM session_entities WHERE entity_canonical = ?")
+                .run(source);
+            // Step 3: recompute target.session_count exactly from session_entities.
+            this.db
+                .prepare(`UPDATE entities
+             SET session_count = (SELECT COUNT(*) FROM session_entities WHERE entity_canonical = ?),
+                 updated_at    = datetime('now')
+           WHERE canonical = ?`)
+                .run(target, target);
+            // Step 4: widen first_seen_session / last_seen_session.
+            // first_seen and last_seen are session IDs (text), not timestamps.
+            // We use sessions.started_at to order them chronologically and pick
+            // the earliest / latest. This is correct as long as session IDs are
+            // stable references (they are -- FK to sessions(id)).
+            const bothSeenSessions = this.db
+                .prepare(`SELECT id, started_at FROM sessions
+           WHERE id IN (
+             SELECT first_seen_session FROM entities WHERE canonical IN (?, ?)
+             UNION
+             SELECT last_seen_session  FROM entities WHERE canonical IN (?, ?)
+           )`)
+                .all(source, target, source, target);
+            if (bothSeenSessions.length > 0) {
+                bothSeenSessions.sort((a, b) => a.started_at.localeCompare(b.started_at));
+                const earliest = bothSeenSessions[0].id;
+                const latest = bothSeenSessions[bothSeenSessions.length - 1].id;
+                this.db
+                    .prepare(`UPDATE entities
+               SET first_seen_session = ?,
+                   last_seen_session  = ?,
+                   updated_at         = datetime('now')
+             WHERE canonical = ?`)
+                    .run(earliest, latest, target);
+            }
+            // Step 5: insert the variant record so future ingest resolves source -> target.
+            this.db
+                .prepare(`INSERT OR IGNORE INTO entity_variants (variant, canonical, source_session_id)
+           VALUES (?, ?, NULL)`)
+                .run(source, target);
+            // Step 6: re-point existing variants of source to target.
+            const sourceVariants = this.db
+                .prepare("SELECT variant FROM entity_variants WHERE canonical = ?")
+                .all(source);
+            for (const { variant } of sourceVariants) {
+                if (variant === source)
+                    continue;
+                this.db
+                    .prepare("UPDATE entity_variants SET canonical = ? WHERE variant = ?")
+                    .run(target, variant);
+            }
+            // Step 7: retire the source entity row in place.
+            this.db
+                .prepare(`UPDATE entities
+             SET status        = 'retired',
+                 session_count = 0,
+                 updated_at    = datetime('now')
+           WHERE canonical = ?`)
+                .run(source);
+        });
+        txn();
+    }
+}
+//# sourceMappingURL=sqlite-entity-store.js.map

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

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

@@ -26,20 +26,17 @@ export declare class SqliteFactStore implements FactStore {
      * other callers should reach FactStore via storage.facts.
      */
     constructor(db: Database.Database);
+    private cachedInsertStmt;
     insert(fact: Fact): Promise<void>;
     insertMany(facts: ReadonlyArray<Fact>): Promise<void>;
-    /**
-     * @internal. Sync row insert for use inside an already-open better-sqlite3
-     * transaction. Used only by SqliteSessionStore's inlined ingest blocks
-     * (which require sync execution inside the txn callback). External callers
-     * use insertMany() or ingestSessionFacts() via Storage.withTransaction.
-     */
-    insertRowInTxn(fact: Fact): 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>>;
+    listBySessions(sessionIds: ReadonlyArray<string>, opts?: {
+        includeSuperseded?: boolean;
+    }): Promise<ReadonlyArray<Fact>>;
     listForRecall(filter: FactListFilter): Promise<ReadonlyArray<Fact>>;
     semanticSearch(queryVector: Float32Array, limit: number): Promise<ReadonlyArray<FactSemanticNeighbor>>;
     getHistory(subject: string, predicate?: string): Promise<ReadonlyArray<FactHistoryChain>>;
@@ -57,6 +54,17 @@ export declare class SqliteFactStore implements FactStore {
     markSuperseded(oldId: string, newId: string | null): Promise<void>;
     retire(factId: string): Promise<void>;
     ingestSessionFacts(sessionId: string, facts: ReadonlyArray<Fact>): Promise<void>;
+    /**
+     * Sync core of ingestSessionFacts, callable from inside an existing
+     * better-sqlite3 transaction. SINGLE SOURCE OF TRUTH for the replace +
+     * deterministic-collapse + embedding-cleanup logic. The live ingest path
+     * (SqliteSessionStore.insertSession / insertFactsForSession) runs inside its
+     * own sync txn and delegates here, so it can no longer drift from this method.
+     * NLM #351's embedding-ghost (bug 1) and supersedence-cycle (bug 2) fixes
+     * originally landed only here and silently skipped the inlined copies — the
+     * path production actually uses — leaving both bugs live in production.
+     */
+    ingestSessionFactsInTxn(sessionId: string, facts: ReadonlyArray<Fact>): void;
     private insertStmt;
     private toRow;
     private rowToFact;

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

@@ -15,6 +15,7 @@
  *         getHistory (supersedence chain inspection)
  *   B.4 — auto-supersedence on (subject, predicate) collision (deferred)
  */
+import { batchWinners } from "./fact-batch.js";
 export class SqliteFactStore {
     db;
     /**
@@ -25,6 +26,7 @@ export class SqliteFactStore {
     constructor(db) {
         this.db = db;
     }
+    cachedInsertStmt;
     async insert(fact) {
         this.insertStmt().run(this.toRow(fact));
     }
@@ -38,19 +40,10 @@ export class SqliteFactStore {
         });
         txn(facts.map((f) => this.toRow(f)));
     }
-    /**
-     * @internal. Sync row insert for use inside an already-open better-sqlite3
-     * transaction. Used only by SqliteSessionStore's inlined ingest blocks
-     * (which require sync execution inside the txn callback). External callers
-     * use insertMany() or ingestSessionFacts() via Storage.withTransaction.
-     */
-    insertRowInTxn(fact) {
-        this.insertStmt().run(this.toRow(fact));
-    }
     async getById(id) {
         const row = this.db
             .prepare(`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 = ?`)
             .get(id);
         return row ? this.rowToFact(row) : null;
@@ -61,7 +54,7 @@ export class SqliteFactStore {
         const placeholders = ids.map(() => "?").join(",");
         const rows = this.db
             .prepare(`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 IN (${placeholders})`)
             .all(...ids);
         return rows.map((r) => this.rowToFact(r));
@@ -69,7 +62,7 @@ export class SqliteFactStore {
     async findCurrent(subject, predicate) {
         const row = this.db
             .prepare(`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 = ? AND predicate = ? AND superseded_by IS NULL AND retired_at IS NULL
          ORDER BY created_at DESC
@@ -93,7 +86,7 @@ export class SqliteFactStore {
         params.push(limit);
         const rows = this.db
             .prepare(`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 ${where.join(" AND ")}
          ORDER BY created_at DESC
@@ -104,13 +97,25 @@ export class SqliteFactStore {
     async listBySession(sessionId) {
         const rows = this.db
             .prepare(`SELECT id, kind, subject, predicate, value, source_session_id,
-                source_quote, created_at, superseded_by, confidence
+                source_quote, created_at, superseded_by, confidence, retired_at
          FROM facts
          WHERE source_session_id = ?
          ORDER BY created_at ASC`)
             .all(sessionId);
         return rows.map((r) => this.rowToFact(r));
     }
+    async listBySessions(sessionIds, opts) {
+        if (sessionIds.length === 0)
+            return [];
+        const ph = sessionIds.map(() => "?").join(",");
+        const filter = opts?.includeSuperseded === true ? "" : " AND superseded_by IS NULL AND retired_at IS NULL";
+        const rows = this.db
+            .prepare(`SELECT id, kind, subject, predicate, value, source_session_id,
+                source_quote, created_at, superseded_by, confidence, retired_at
+         FROM facts WHERE source_session_id IN (${ph})${filter} ORDER BY created_at ASC`)
+            .all(...sessionIds);
+        return rows.map((r) => this.rowToFact(r));
+    }
     async listForRecall(filter) {
         const where = [];
         const params = [];
@@ -138,7 +143,7 @@ export class SqliteFactStore {
         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
@@ -255,6 +260,12 @@ export class SqliteFactStore {
             this.db
                 .prepare("UPDATE facts SET superseded_by = ? WHERE id = ?")
                 .run(newId, oldId);
+            // A superseded fact is recall-ineligible, so its embedding must leave the
+            // ANN index (matching retire()'s behavior) — otherwise it consumes
+            // k-nearest slots and silently reduces effective recall (NLM #351).
+            if (newId !== null) {
+                this.db.prepare("DELETE FROM fact_embeddings WHERE fact_id = ?").run(oldId);
+            }
         });
         txn();
     }
@@ -273,7 +284,28 @@ export class SqliteFactStore {
         txn();
     }
     async ingestSessionFacts(sessionId, facts) {
+        this.ingestSessionFactsInTxn(sessionId, facts);
+    }
+    /**
+     * Sync core of ingestSessionFacts, callable from inside an existing
+     * better-sqlite3 transaction. SINGLE SOURCE OF TRUTH for the replace +
+     * deterministic-collapse + embedding-cleanup logic. The live ingest path
+     * (SqliteSessionStore.insertSession / insertFactsForSession) runs inside its
+     * own sync txn and delegates here, so it can no longer drift from this method.
+     * NLM #351's embedding-ghost (bug 1) and supersedence-cycle (bug 2) fixes
+     * originally landed only here and silently skipped the inlined copies — the
+     * path production actually uses — leaving both bugs live in production.
+     */
+    ingestSessionFactsInTxn(sessionId, facts) {
+        // Re-ingesting a session replaces its facts; drop the old facts' embeddings
+        // too, or they orphan in the ANN index as ghosts (NLM #351).
+        const stale = this.db
+            .prepare("SELECT id FROM facts WHERE source_session_id = ?")
+            .all(sessionId);
         this.db.prepare("DELETE FROM facts WHERE source_session_id = ?").run(sessionId);
+        const delStaleEmb = this.db.prepare("DELETE FROM fact_embeddings WHERE fact_id = ?");
+        for (const row of stale)
+            delStaleEmb.run(row.id);
         if (facts.length === 0)
             return;
         const insertStmt = this.insertStmt();
@@ -283,22 +315,39 @@ export class SqliteFactStore {
         // new fact, not just the single most-recent prior. A single-prior loop
         // cannot restore the invariant once two priors are already active and
         // leaves the duplicate live forever. See NLM #301.
+        const findSupersededStmt = this.db.prepare(`SELECT id FROM facts WHERE subject = ? AND predicate = ? AND superseded_by IS NULL AND id != ?`);
         const markSupersededStmt = this.db.prepare(`UPDATE facts SET superseded_by = ?
        WHERE subject = ? AND predicate = ? AND superseded_by IS NULL AND id != ?`);
-        for (const f of facts) {
+        const delEmbeddingStmt = this.db.prepare("DELETE FROM fact_embeddings WHERE fact_id = ?");
+        // Collapse ONCE per (subject, predicate), under a single winner. Running the
+        // collapse per-fact creates a supersedence CYCLE when a batch carries two
+        // facts for the same (subject, predicate): each supersedes the other, so
+        // both end recall-ineligible forever (NLM #351 bug 2). Last fact in the
+        // batch for a given (subject, predicate) wins; every other active fact —
+        // batch duplicates and prior facts alike — collapses under it.
+        for (const f of batchWinners(facts)) {
+            // Capture which facts this collapse supersedes BEFORE the update, then
+            // drop their embeddings — a superseded fact must not linger in the ANN
+            // index (NLM #351). Same reason markSuperseded/retire delete embeddings.
+            const collapsed = findSupersededStmt.all(f.subject, f.predicate, f.id);
             markSupersededStmt.run(f.id, f.subject, f.predicate, f.id);
+            for (const row of collapsed)
+                delEmbeddingStmt.run(row.id);
         }
     }
     insertStmt() {
-        return this.db.prepare(`
-      INSERT INTO facts (
-        id, kind, subject, predicate, value, source_session_id,
-        source_quote, created_at, superseded_by, confidence
-      ) VALUES (
-        @id, @kind, @subject, @predicate, @value, @source_session_id,
-        @source_quote, @created_at, @superseded_by, @confidence
-      )
-    `);
+        if (!this.cachedInsertStmt) {
+            this.cachedInsertStmt = this.db.prepare(`
+        INSERT INTO facts (
+          id, kind, subject, predicate, value, source_session_id,
+          source_quote, created_at, superseded_by, confidence, retired_at
+        ) VALUES (
+          @id, @kind, @subject, @predicate, @value, @source_session_id,
+          @source_quote, @created_at, @superseded_by, @confidence, @retired_at
+        )
+      `);
+        }
+        return this.cachedInsertStmt;
     }
     toRow(fact) {
         return {
@@ -312,6 +361,7 @@ export class SqliteFactStore {
             created_at: fact.createdAt,
             superseded_by: fact.supersededBy,
             confidence: fact.confidence,
+            retired_at: fact.retiredAt ?? null,
         };
     }
     rowToFact(row) {
@@ -326,6 +376,7 @@ export class SqliteFactStore {
             createdAt: row.created_at,
             supersededBy: row.superseded_by,
             confidence: row.confidence,
+            retiredAt: row.retired_at ?? null,
         };
     }
 }

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

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

@@ -7,9 +7,9 @@
  * of core depends on the SessionStore *port*, never on this file.
  *
  * Schema parity with the Python daemon: sessions row + session_entities +
- * markers + session_embeddings (vec0). Idle-status overlay (computed from
- * transcript mtime) is deferred to a later phase — A.2 returns the persisted
- * status verbatim.
+ * markers + session_embedding_chunks (vec0). Idle-status overlay (computed
+ * from transcript mtime) is deferred to a later phase; A.2 returns the
+ * persisted status verbatim.
  */
 import Database from "better-sqlite3";
 import type { KeywordNeighbor, SearchOptions, SemanticNeighbor, SessionFilter, SessionStore } from "../../ports/session-store.js";
@@ -40,6 +40,11 @@ export interface IngestRecord {
     readonly entities: ReadonlyArray<string>;
     readonly decisions: ReadonlyArray<string>;
     readonly openQuestions: ReadonlyArray<string>;
+    readonly classifier?: {
+        readonly provider: string;
+        readonly model: string;
+        readonly confidence: number;
+    };
 }
 /**
  * Supersedence target for insertSession. `kind` selects the relation:
@@ -87,6 +92,8 @@ export interface BackfillCandidate {
 }
 export declare class SqliteSessionStore implements SessionStore {
     private readonly db;
+    private overlayCache;
+    private overlayCacheAt;
     /**
      * @internal. Construct via SqliteStorage.create(...) instead. Direct
      * construction is preserved for the SqliteStorage adapter only; all
@@ -104,6 +111,8 @@ export declare class SqliteSessionStore implements SessionStore {
     /** Raw db handle for ingest helpers (Scheduler, scanOnce). Avoid using
      *  directly from the recall path — it bypasses the SessionStore port. */
     rawDb(): Database.Database;
+    invalidateOverlayCache(): void;
+    private overlay;
     /** Recently-written sessions ordered by created_at desc. Powers /live Writes column. */
     recentWrites(limit: number): RecentWrite[];
     /** Recently-extracted markers ordered by session created_at desc. Powers /live Decisions column. */
@@ -112,8 +121,9 @@ export declare class SqliteSessionStore implements SessionStore {
      * Atomic ingest: writes the session row, markers, entity rows + links,
      * supersedes edge (if any), and the embedding (best-effort) in one
      * transaction. Idempotent on re-ingest — ON CONFLICT updates the session
-     * in place; markers are deleted and rewritten; entity links use INSERT OR
-     * IGNORE; embedding row is DELETE+INSERT (vec0 doesn't UPDATE).
+     * in place; markers are deleted and rewritten; entity links are replaced
+     * (DELETE + re-insert, session_count recomputed exactly); embedding row is
+     * DELETE+INSERT (vec0 doesn't UPDATE).
      *
      * Mirrors Python's SQLiteStore.insert_session. Markdown projection is not
      * yet ported and skipped here.
@@ -158,6 +168,7 @@ export declare class SqliteSessionStore implements SessionStore {
      * daemon. Resolved sessions carry `body: ""`.
      */
     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>>;
     /**
      * Lexical recall via the sessions_fts FTS5 index. BM25 column weights
@@ -170,6 +181,10 @@ export declare class SqliteSessionStore implements SessionStore {
     resolveSuccessors(ids: ReadonlyArray<string>): Promise<Map<string, string>>;
     updateStatus(sessionId: string, status: SessionStatus): Promise<void>;
     markSuperseded(predecessorId: string, successorId: string): Promise<void>;
+    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>>;
     /** @internal test-only helper; production callers use insertSession(). */
     insertSessionForTest(session: Session): void;
     insertEdgeForTest(fromSession: string, toSession: string, kind?: "supersedes" | "continues"): void;