nlm-memory 0.20.0 → 0.21.0

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

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

@@ -3,22 +3,21 @@
  *
  * Owns the connection. Builds SqliteSessionStore and SqliteFactStore over
  * that single connection so writes commit on one WAL writer (the SQLite
- * atomicity model). withTransaction wraps better-sqlite3's synchronous
- * `db.transaction()` API and re-runs it inside an async shell so callers
- * can await async work inside the callback (e.g. an embedder call) — but
- * note that the db txn itself is synchronous; do not call long-running
- * async work inside withTransaction or the txn will hold its write lock.
+ * atomicity model).
  *
  * rawDb() is a deprecated escape hatch for callers that still use direct
  * better-sqlite3 — scheduler, http actions endpoints, backfill-facts,
  * source/provider registries. Tracked for removal in #215a.
  */
 import type Database from "better-sqlite3";
-import type { Storage, StorageContext } from "../../ports/storage.js";
+import type { Storage } from "../../ports/storage.js";
 import { SqliteCodeExemplarStore } from "./sqlite-code-exemplar-store.js";
+import { SqliteEmbeddingConfigStore } from "./sqlite-embedding-config.js";
+import { SqliteEntityStore } from "./sqlite-entity-store.js";
 import { SqliteFactStore } from "./sqlite-fact-store.js";
 import { SqliteSessionStore } from "./sqlite-session-store.js";
 import { SqliteSignalStore } from "./sqlite-signal-store.js";
+import { SqliteWorkstreamStore } from "./sqlite-workstream-store.js";
 import { SourceRegistry } from "../sources/source-registry.js";
 import { ProviderRegistry } from "../providers/provider-registry.js";
 export interface SqliteStorageOptions {
@@ -30,14 +29,15 @@ export declare class SqliteStorage implements Storage {
     readonly facts: SqliteFactStore;
     readonly signals: SqliteSignalStore;
     readonly exemplars: SqliteCodeExemplarStore;
+    readonly workstreams: SqliteWorkstreamStore;
+    readonly entities: SqliteEntityStore;
+    readonly embeddingConfig: SqliteEmbeddingConfigStore;
     readonly sources: SourceRegistry;
     readonly providers: ProviderRegistry;
-    private inTxn;
     private constructor();
     static create(opts: SqliteStorageOptions): SqliteStorage;
     init(): Promise<void>;
     close(): Promise<void>;
-    withTransaction<T>(fn: (ctx: StorageContext) => T): Promise<T>;
     /**
      * @deprecated SQLite-only escape hatch for callers not yet ported to the
      * Storage interface. Tracked for removal in #215a. Do not use in new code.

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

@@ -3,20 +3,19 @@
  *
  * Owns the connection. Builds SqliteSessionStore and SqliteFactStore over
  * that single connection so writes commit on one WAL writer (the SQLite
- * atomicity model). withTransaction wraps better-sqlite3's synchronous
- * `db.transaction()` API and re-runs it inside an async shell so callers
- * can await async work inside the callback (e.g. an embedder call) — but
- * note that the db txn itself is synchronous; do not call long-running
- * async work inside withTransaction or the txn will hold its write lock.
+ * atomicity model).
  *
  * rawDb() is a deprecated escape hatch for callers that still use direct
  * better-sqlite3 — scheduler, http actions endpoints, backfill-facts,
  * source/provider registries. Tracked for removal in #215a.
  */
 import { SqliteCodeExemplarStore } from "./sqlite-code-exemplar-store.js";
+import { SqliteEmbeddingConfigStore } from "./sqlite-embedding-config.js";
+import { SqliteEntityStore } from "./sqlite-entity-store.js";
 import { SqliteFactStore } from "./sqlite-fact-store.js";
 import { SqliteSessionStore } from "./sqlite-session-store.js";
 import { SqliteSignalStore } from "./sqlite-signal-store.js";
+import { SqliteWorkstreamStore } from "./sqlite-workstream-store.js";
 import { SourceRegistry } from "../sources/source-registry.js";
 import { ProviderRegistry } from "../providers/provider-registry.js";
 export class SqliteStorage {
@@ -24,25 +23,34 @@ export class SqliteStorage {
     facts;
     signals;
     exemplars;
+    workstreams;
+    entities;
+    embeddingConfig;
     sources;
     providers;
-    inTxn = false;
-    constructor(sessions, facts, signals, exemplars, sources, providers) {
+    constructor(sessions, facts, signals, exemplars, workstreams, entities, embeddingConfig, sources, providers) {
         this.sessions = sessions;
         this.facts = facts;
         this.signals = signals;
         this.exemplars = exemplars;
+        this.workstreams = workstreams;
+        this.entities = entities;
+        this.embeddingConfig = embeddingConfig;
         this.sources = sources;
         this.providers = providers;
     }
     static create(opts) {
         const sessions = new SqliteSessionStore(opts);
-        const facts = new SqliteFactStore(sessions.rawDb());
-        const signals = new SqliteSignalStore(sessions.rawDb());
-        const exemplars = new SqliteCodeExemplarStore(sessions.rawDb());
-        const sources = new SourceRegistry(sessions.rawDb());
-        const providers = new ProviderRegistry(sessions.rawDb());
-        return new SqliteStorage(sessions, facts, signals, exemplars, sources, providers);
+        const db = sessions.rawDb();
+        const facts = new SqliteFactStore(db);
+        const signals = new SqliteSignalStore(db);
+        const exemplars = new SqliteCodeExemplarStore(db);
+        const workstreams = new SqliteWorkstreamStore(db);
+        const entities = new SqliteEntityStore(db);
+        const embeddingConfig = new SqliteEmbeddingConfigStore(db);
+        const sources = new SourceRegistry(db);
+        const providers = new ProviderRegistry(db);
+        return new SqliteStorage(sessions, facts, signals, exemplars, workstreams, entities, embeddingConfig, sources, providers);
     }
     async init() {
         // SqliteSessionStore runs migrations in its constructor today; this is
@@ -52,25 +60,6 @@ export class SqliteStorage {
     async close() {
         this.sessions.close();
     }
-    async withTransaction(fn) {
-        if (this.inTxn) {
-            throw new Error("SqliteStorage.withTransaction does not support nesting");
-        }
-        this.inTxn = true;
-        try {
-            let captured;
-            const txn = this.sessions.rawDb().transaction(() => {
-                const ctx = { facts: this.facts, sessions: this.sessions };
-                captured = fn(ctx);
-            });
-            txn();
-            // Cast is safe: a sync throw inside fn propagates out of txn() before we reach here, so the success path always assigned captured.
-            return captured;
-        }
-        finally {
-            this.inTxn = false;
-        }
-    }
     /**
      * @deprecated SQLite-only escape hatch for callers not yet ported to the
      * Storage interface. Tracked for removal in #215a. Do not use in new code.

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

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

@@ -0,0 +1,25 @@
+import type Database from "better-sqlite3";
+import type { WorkstreamStore } from "../../ports/workstream-store.js";
+import { type Workstream } from "../workstream/model.js";
+export declare class SqliteWorkstreamStore implements WorkstreamStore {
+    private readonly db;
+    constructor(db: Database.Database);
+    create(input: {
+        id: string;
+        label: string;
+        scope: string | null;
+    }): Promise<Workstream>;
+    getById(id: string): Promise<Workstream | null>;
+    findByNormalizedLabel(normalizedLabel: string): Promise<Workstream | null>;
+    listAll(): Promise<ReadonlyArray<Workstream>>;
+    touchLastSession(id: string, atIso: string): Promise<void>;
+    setLabel(id: string, label: string): Promise<void>;
+    setStatus(id: string, status: Workstream["status"]): Promise<void>;
+    merge(fromId: string, intoId: string): Promise<void>;
+    upsertEntities(workstreamId: string, entities: ReadonlyArray<string>): Promise<void>;
+    entitiesFor(workstreamIds: ReadonlyArray<string>): Promise<Map<string, string[]>>;
+    candidatesByEntityOverlap(entities: ReadonlyArray<string>, limit: number): Promise<ReadonlyArray<{
+        workstreamId: string;
+        entities: string[];
+    }>>;
+}

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

@@ -0,0 +1,99 @@
+import { normalizeLabel } from "../workstream/model.js";
+function rowToWorkstream(r) {
+    return {
+        id: r.id, label: r.label, status: r.status, mergedInto: r.merged_into,
+        createdAt: r.created_at, updatedAt: r.updated_at, lastSessionAt: r.last_session_at,
+        scope: r.scope,
+    };
+}
+export class SqliteWorkstreamStore {
+    db;
+    constructor(db) {
+        this.db = db;
+    }
+    async create(input) {
+        this.db.prepare("INSERT INTO workstreams (id, label, scope) VALUES (?, ?, ?)").run(input.id, input.label, input.scope);
+        return (await this.getById(input.id));
+    }
+    async getById(id) {
+        const r = this.db.prepare("SELECT * FROM workstreams WHERE id = ?").get(id);
+        return r ? rowToWorkstream(r) : null;
+    }
+    async findByNormalizedLabel(normalizedLabel) {
+        // Small set; normalize in JS to match normalizeLabel semantics exactly.
+        const rows = this.db.prepare("SELECT * FROM workstreams").all();
+        const hit = rows.find((r) => normalizeLabel(r.label) === normalizedLabel);
+        return hit ? rowToWorkstream(hit) : null;
+    }
+    async listAll() {
+        return this.db.prepare("SELECT * FROM workstreams").all().map(rowToWorkstream);
+    }
+    async touchLastSession(id, atIso) {
+        this.db.prepare("UPDATE workstreams SET last_session_at = ?, updated_at = datetime('now') WHERE id = ?").run(atIso, id);
+    }
+    async setLabel(id, label) {
+        this.db.prepare("UPDATE workstreams SET label = ?, updated_at = datetime('now') WHERE id = ?").run(label, id);
+    }
+    async setStatus(id, status) {
+        this.db.prepare("UPDATE workstreams SET status = ?, updated_at = datetime('now') WHERE id = ?").run(status, id);
+    }
+    async merge(fromId, intoId) {
+        const tx = this.db.transaction(() => {
+            this.db.prepare("UPDATE workstreams SET merged_into = ?, status = 'merged', updated_at = datetime('now') WHERE id = ?").run(intoId, fromId);
+            // Union from's entities into into (sum session_count on PK conflict).
+            this.db.prepare(`
+        INSERT INTO workstream_entities (workstream_id, entity_canonical, session_count)
+        SELECT ?, entity_canonical, session_count FROM workstream_entities WHERE workstream_id = ?
+        ON CONFLICT(workstream_id, entity_canonical)
+        DO UPDATE SET session_count = session_count + excluded.session_count
+      `).run(intoId, fromId);
+            this.db.prepare("DELETE FROM workstream_entities WHERE workstream_id = ?").run(fromId);
+        });
+        tx();
+    }
+    async upsertEntities(workstreamId, entities) {
+        const stmt = this.db.prepare(`
+      INSERT INTO workstream_entities (workstream_id, entity_canonical, session_count)
+      VALUES (?, ?, 1)
+      ON CONFLICT(workstream_id, entity_canonical)
+      DO UPDATE SET session_count = session_count + 1
+    `);
+        const tx = this.db.transaction((names) => {
+            for (const n of names) {
+                const e = n.trim();
+                if (e)
+                    stmt.run(workstreamId, e);
+            }
+        });
+        tx(entities);
+    }
+    async entitiesFor(workstreamIds) {
+        const out = new Map();
+        if (workstreamIds.length === 0)
+            return out;
+        const ph = workstreamIds.map(() => "?").join(",");
+        const rows = this.db.prepare(`SELECT workstream_id, entity_canonical FROM workstream_entities WHERE workstream_id IN (${ph})`).all(...workstreamIds);
+        for (const r of rows) {
+            const list = out.get(r.workstream_id);
+            if (list)
+                list.push(r.entity_canonical);
+            else
+                out.set(r.workstream_id, [r.entity_canonical]);
+        }
+        return out;
+    }
+    async candidatesByEntityOverlap(entities, limit) {
+        const names = entities.map((e) => e.trim()).filter(Boolean);
+        if (names.length === 0)
+            return [];
+        const ph = names.map(() => "?").join(",");
+        const ids = this.db.prepare(`SELECT workstream_id, COUNT(*) AS overlap FROM workstream_entities
+       WHERE entity_canonical IN (${ph})
+       GROUP BY workstream_id ORDER BY overlap DESC LIMIT ?`).all(...names, limit).map((r) => r.workstream_id);
+        if (ids.length === 0)
+            return [];
+        const map = await this.entitiesFor(ids);
+        return ids.map((id) => ({ workstreamId: id, entities: map.get(id) ?? [] }));
+    }
+}
+//# sourceMappingURL=sqlite-workstream-store.js.map

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

@@ -0,0 +1 @@
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package/dist/core/storage/supersedence-log.js

@@ -24,6 +24,7 @@ export async function readSupersedenceLog() {
         raw = await readFile(path, "utf8");
     }
     catch {
+        // Log file missing or unreadable - no supersedence history recovered.
         return [];
     }
     const results = [];
@@ -44,6 +45,7 @@ export async function readSupersedenceLog() {
             });
         }
         catch {
+            // Malformed entry in log - skip and continue parsing.
             continue;
         }
     }

package/dist/core/storage/supersedence-log.js.map

@@ -1 +1 @@
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package/dist/core/telemetry/probe-filter.d.ts

@@ -0,0 +1,35 @@
+/**
+ * Probe and test traffic filter.
+ *
+ * Single source of truth for classifying recall queries as probe/test traffic.
+ * Used by the digest composer (to strip probes from displayed counters) and by
+ * the pull-usefulness eval script (to strip probes from the scored baseline).
+ *
+ * Two match strategies with different trade-offs:
+ *
+ * Substring match (PROBE_SUBSTRINGS / isProbe):
+ *   Catches probe traffic regardless of surrounding words. Accepted trade-off:
+ *   any query containing the word "probe" -- including "how did we probe the API"
+ *   -- will be stripped. In practice, probe traffic is always labelled with the
+ *   bare word; real agent queries rarely include "probe" as a term. The
+ *   alternative (exact-match "probe") would miss operational variants like
+ *   "system probe" and "probing X", so substring is the right default for the
+ *   digest composer path.
+ *
+ * Exact match (PROBE_EXACT_QUERIES):
+ *   Required for pull-usefulness.ts. That script was baseline-calibrated at
+ *   72.4% genuine-pull using this exact set. Switching it to substring matching
+ *   would silently change the denominator and invalidate historical comparisons.
+ *   "x" and "" cannot be substring-matched -- a single character would strip
+ *   virtually every query. They live here as exact entries only.
+ */
+/** Substrings that mark a recall query as probe/test traffic. */
+export declare const PROBE_SUBSTRINGS: ReadonlyArray<string>;
+/**
+ * Queries that are probe traffic only when the full query (trimmed, lowercased)
+ * is an exact match. "x" and "" are single-character or empty -- substring
+ * matching them would strip real queries.
+ */
+export declare const PROBE_EXACT_QUERIES: ReadonlySet<string>;
+/** True when the query is recognisably probe/test traffic by either strategy. */
+export declare function isProbe(query: string | null | undefined): boolean;

package/dist/core/telemetry/probe-filter.js

@@ -0,0 +1,56 @@
+/**
+ * Probe and test traffic filter.
+ *
+ * Single source of truth for classifying recall queries as probe/test traffic.
+ * Used by the digest composer (to strip probes from displayed counters) and by
+ * the pull-usefulness eval script (to strip probes from the scored baseline).
+ *
+ * Two match strategies with different trade-offs:
+ *
+ * Substring match (PROBE_SUBSTRINGS / isProbe):
+ *   Catches probe traffic regardless of surrounding words. Accepted trade-off:
+ *   any query containing the word "probe" -- including "how did we probe the API"
+ *   -- will be stripped. In practice, probe traffic is always labelled with the
+ *   bare word; real agent queries rarely include "probe" as a term. The
+ *   alternative (exact-match "probe") would miss operational variants like
+ *   "system probe" and "probing X", so substring is the right default for the
+ *   digest composer path.
+ *
+ * Exact match (PROBE_EXACT_QUERIES):
+ *   Required for pull-usefulness.ts. That script was baseline-calibrated at
+ *   72.4% genuine-pull using this exact set. Switching it to substring matching
+ *   would silently change the denominator and invalidate historical comparisons.
+ *   "x" and "" cannot be substring-matched -- a single character would strip
+ *   virtually every query. They live here as exact entries only.
+ */
+/** Substrings that mark a recall query as probe/test traffic. */
+export const PROBE_SUBSTRINGS = [
+    // "concurrency probe" and "test probe" are redundant: "probe" covers both.
+    "probe",
+    "beacon",
+    "smoke",
+    "path test",
+    "recall test",
+    "cutover-test",
+];
+/**
+ * Queries that are probe traffic only when the full query (trimmed, lowercased)
+ * is an exact match. "x" and "" are single-character or empty -- substring
+ * matching them would strip real queries.
+ */
+export const PROBE_EXACT_QUERIES = new Set([
+    "pgvector",
+    "hono",
+    "x",
+    "",
+]);
+/** True when the query is recognisably probe/test traffic by either strategy. */
+export function isProbe(query) {
+    if (query === null || query === undefined)
+        return false;
+    const q = query.trim().toLowerCase();
+    if (PROBE_EXACT_QUERIES.has(q))
+        return true;
+    return PROBE_SUBSTRINGS.some((p) => q.includes(p));
+}
+//# sourceMappingURL=probe-filter.js.map

package/dist/core/telemetry/probe-filter.js.map

@@ -0,0 +1 @@
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package/dist/core/update-check/check.d.ts

@@ -41,6 +41,12 @@ export interface UpdateCheckDeps {
     readonly fetchImpl?: typeof fetch;
 }
 export declare function getUpdateStatus(deps: UpdateCheckDeps): Promise<UpdateStatus>;
+/**
+ * Cache-only read: never fetches the registry, even on a miss or a stale
+ * (>24h) entry. For request paths (like GET /api/health) that must stay
+ * fast and never depend on npm being reachable.
+ */
+export declare function getCachedUpdateStatus(deps: Pick<UpdateCheckDeps, "currentVersion" | "cachePath" | "now">): Promise<UpdateStatus>;
 /**
  * Strict semver-newer check on simple `X.Y.Z` versions. Pre-release tags
  * (`-rc.1`, `-beta`) sort BEFORE the bare version per semver, which is

package/dist/core/update-check/check.js

@@ -74,6 +74,41 @@ export async function getUpdateStatus(deps) {
     });
     return status;
 }
+/**
+ * Cache-only read: never fetches the registry, even on a miss or a stale
+ * (>24h) entry. For request paths (like GET /api/health) that must stay
+ * fast and never depend on npm being reachable.
+ */
+export async function getCachedUpdateStatus(deps) {
+    const now = (deps.now ?? (() => new Date()))();
+    const current = deps.currentVersion;
+    if (isOptedOut()) {
+        return {
+            current,
+            latest: null,
+            behind: false,
+            checkedAt: now.toISOString(),
+            disabled: "user-opt-out",
+        };
+    }
+    const cachePath = deps.cachePath ?? defaultCachePath();
+    const cached = await readCache(cachePath);
+    if (!cached) {
+        return {
+            current,
+            latest: null,
+            behind: false,
+            checkedAt: now.toISOString(),
+            disabled: "unknown-error",
+        };
+    }
+    return {
+        current,
+        latest: cached.latest,
+        behind: cached.latest !== null && isStrictlyNewer(cached.latest, current),
+        checkedAt: cached.checkedAt,
+    };
+}
 async function readCache(path) {
     try {
         const raw = await readFile(path, "utf8");

package/dist/core/update-check/check.js.map

@@ -1 +1 @@
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package/dist/core/work-digest/active-spans.d.ts

@@ -0,0 +1,8 @@
+import type { Interval } from "./types.js";
+/**
+ * Collapse a session's message timestamps into activity intervals. Consecutive
+ * messages no more than `idleThresholdMin` apart belong to the same span; a
+ * larger gap means the operator was away and starts a new span. A lone message
+ * yields a zero-length span (it marks activity but adds no minutes).
+ */
+export declare function activeSpans(timestampsMs: ReadonlyArray<number>, idleThresholdMin: number): Interval[];

package/dist/core/work-digest/active-spans.js

@@ -0,0 +1,29 @@
+/**
+ * Collapse a session's message timestamps into activity intervals. Consecutive
+ * messages no more than `idleThresholdMin` apart belong to the same span; a
+ * larger gap means the operator was away and starts a new span. A lone message
+ * yields a zero-length span (it marks activity but adds no minutes).
+ */
+export function activeSpans(timestampsMs, idleThresholdMin) {
+    const ts = [...timestampsMs].sort((a, b) => a - b);
+    if (ts.length === 0)
+        return [];
+    const gapMs = idleThresholdMin * 60_000;
+    const spans = [];
+    let start = ts[0];
+    let prev = ts[0];
+    for (let i = 1; i < ts.length; i++) {
+        const t = ts[i];
+        if (t - prev <= gapMs) {
+            prev = t;
+        }
+        else {
+            spans.push({ start, end: prev });
+            start = t;
+            prev = t;
+        }
+    }
+    spans.push({ start, end: prev });
+    return spans;
+}
+//# sourceMappingURL=active-spans.js.map

package/dist/core/work-digest/active-spans.js.map

@@ -0,0 +1 @@
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package/dist/core/work-digest/attribute.d.ts

@@ -0,0 +1,15 @@
+import type { Interval, SessionActivity, TopicShare, FocusStats } from "./types.js";
+/**
+ * Attribute each merged active interval to a topic and derive attention +
+ * focus. v1 uses dominant-session attribution: the whole interval goes to the
+ * session with the most messages in it (the bounded simplification over
+ * fractional splitting documented in the design). Focus is derived from the
+ * ordered, attributed segments: adjacent same-topic segments collapse into
+ * blocks; a topic change between blocks is one context switch.
+ */
+export declare function attribute(merged: ReadonlyArray<Interval>, sessions: ReadonlyArray<SessionActivity>, opts: {
+    deepBlockMin: number;
+}): {
+    byTopic: TopicShare[];
+    focus: FocusStats;
+};