mcp-rag-memory 2.4.1 → 2.6.0

package/dist/memory/memory.js

@@ -1,6 +1,6 @@
 import { getDB, newId, nowMs, packVector, unpackVector } from "../db/database.js";
 import { dotProduct } from "../rag/embedder.js";
-import { estimateTokens } from "../rag/chunker.js";
+import { estimateTokensFromChars } from "../rag/chunker.js";
 import { embedText } from "../rag/embeddings.js";
 import { vectorSearch, invalidateVectorCache } from "../rag/vector-search.js";
 export const MEMORY_TYPES = [
@@ -12,45 +12,93 @@ export const MEMORY_TYPES = [
     "insight",
     "conversation",
 ];
-/** Half-life in days for the recall decay curve. */
-const DECAY_HALF_LIFE_DAYS = Number(process.env.RAG_MEMORY_HALF_LIFE_DAYS ?? 14);
+/** Half-life in days for the recall decay curve (invalid values fall back to 14). */
+const DECAY_HALF_LIFE_DAYS = numEnv("RAG_MEMORY_HALF_LIFE_DAYS", 14, (n) => n > 0);
+function numEnv(name, fallback, valid) {
+    const raw = process.env[name];
+    if (raw === undefined || raw === "")
+        return fallback;
+    const n = Number(raw);
+    return Number.isFinite(n) && valid(n) ? n : fallback;
+}
 export async function remember(input) {
-    const db = getDB();
     const id = newId();
     const ts = nowMs();
     const type = input.type ?? "fact";
     const importance = clampImportance(input.importance ?? 0.5);
     const tags = JSON.stringify(input.tags ?? []);
     const vec = await embedText(input.content);
+    // Re-acquire after the await: nothing below should use a handle captured
+    // before a yield point, where closeDB() could have invalidated it.
+    const db = getDB();
     db.prepare(`INSERT INTO memories (id, type, content, importance, embedding, tags, recall_count, last_recalled, created_at, updated_at)
      VALUES (?, ?, ?, ?, ?, ?, 0, NULL, ?, ?)`).run(id, type, input.content, importance, packVector(vec), tags, ts, ts);
     invalidateVectorCache();
-    return getMemory(id);
+    const rec = getMemory(id);
+    if (!rec)
+        throw new Error("Memory insert failed: row disappeared immediately after write");
+    return rec;
+}
+const MEMORY_TYPE_SET = new Set(MEMORY_TYPES);
+/** One query for the whole page — getMemory() per row used to be an N+1. */
+function toRecords(rows) {
+    return rows.map((row) => ({
+        id: row.id,
+        type: MEMORY_TYPE_SET.has(row.type) ? row.type : "fact",
+        content: row.content,
+        importance: typeof row.importance === "number" && Number.isFinite(row.importance) ? row.importance : 0.5,
+        tags: parseTags(row.tags),
+        recallCount: row.recall_count,
+        lastRecalled: row.last_recalled,
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    }));
+}
+const MEMORY_COLUMNS = "id, type, content, importance, tags, recall_count, last_recalled, created_at, updated_at";
+/** Never let a malformed row break every read path. */
+function parseTags(raw) {
+    try {
+        const parsed = JSON.parse(raw);
+        return Array.isArray(parsed) ? parsed.map((t) => String(t)) : [];
+    }
+    catch {
+        return [];
+    }
 }
 export async function recall(query, topK = 8, minScore = 0.1) {
     const db = getDB();
     const q = await embedText(query);
     const hits = vectorSearch(q, { topK: topK * 2, minScore, collection: "memories" });
+    if (hits.length === 0)
+        return [];
     const ts = nowMs();
-    const bump = db.prepare("UPDATE memories SET recall_count = recall_count + 1, last_recalled = ? WHERE id = ?");
-    const results = [];
+    const rows = db
+        .prepare(`SELECT ${MEMORY_COLUMNS} FROM memories WHERE id IN (${hits.map(() => "?").join(", ")})`)
+        .all(...hits.map((h) => h.key));
+    const byId = new Map(toRecords(rows).map((r) => [r.id, r]));
+    const scored = [];
     for (const h of hits) {
-        const rec = getMemory(h.key);
+        const rec = byId.get(h.key);
         if (!rec)
             continue;
-        bump.run(ts, rec.id);
         const ageMs = ts - (rec.lastRecalled ?? rec.createdAt);
         const decay = Math.pow(0.5, ageMs / (DECAY_HALF_LIFE_DAYS * 86_400_000));
-        results.push({
-            ...rec,
-            recallCount: rec.recallCount + 1,
-            lastRecalled: ts,
-            score: h.score * decay,
-            decay,
-        });
-    }
-    results.sort((a, b) => b.score - a.score);
-    return results.slice(0, topK);
+        // min_score gates the raw cosine inside vectorSearch; decay shrinks the
+        // score afterwards, so a stale-but-perfect match could come back at ~0.
+        // Re-apply the floor to the score the caller actually receives.
+        const score = h.score * decay;
+        if (score < minScore)
+            continue;
+        scored.push({ ...rec, score, decay });
+    }
+    scored.sort((a, b) => b.score - a.score);
+    const results = scored.slice(0, topK);
+    // Bump only what is actually returned: a memory nobody saw is not "recalled",
+    // and phantom bumps used to feed decay and the promotion threshold.
+    const bump = db.prepare("UPDATE memories SET recall_count = recall_count + 1, last_recalled = ? WHERE id = ?");
+    for (const r of results)
+        bump.run(ts, r.id);
+    return results.map((r) => ({ ...r, recallCount: r.recallCount + 1, lastRecalled: ts }));
 }
 export function listMemories(opts = {}) {
     const db = getDB();
@@ -61,7 +109,9 @@ export function listMemories(opts = {}) {
         params.push(opts.type);
     }
     if (opts.tag) {
-        clauses.push("EXISTS (SELECT 1 FROM json_each(memories.tags) AS _tg WHERE _tg.value = ?)");
+        // json_each() raises "malformed JSON" on a corrupted column, which would
+        // break the whole listing. Feed it a guaranteed-valid array instead.
+        clauses.push("EXISTS (SELECT 1 FROM json_each(CASE WHEN json_valid(memories.tags) THEN memories.tags ELSE '[]' END) AS _tg WHERE _tg.value = ?)");
         params.push(opts.tag);
     }
     if (opts.minImportance !== undefined) {
@@ -69,133 +119,208 @@ export function listMemories(opts = {}) {
         params.push(opts.minImportance);
     }
     const where = clauses.length ? ` WHERE ${clauses.join(" AND ")}` : "";
-    const limit = Math.min(opts.limit ?? 100, 500);
+    const rawLimit = opts.limit;
+    const limit = rawLimit === undefined || !Number.isFinite(rawLimit)
+        ? 100
+        : Math.min(Math.max(Math.trunc(rawLimit), 1), 500);
+    // id as tiebreaker: updated_at is millisecond-resolution, so a bulk write
+    // leaves large tie groups and LIMIT would pick an arbitrary subset.
     const rows = db
-        .prepare(`SELECT id FROM memories${where} ORDER BY updated_at DESC LIMIT ${limit}`)
+        .prepare(`SELECT ${MEMORY_COLUMNS} FROM memories${where} ORDER BY updated_at DESC, id DESC LIMIT ${limit}`)
         .all(...params);
-    return rows.map((r) => getMemory(r.id)).filter(Boolean);
+    return toRecords(rows);
 }
 export function getMemory(id) {
     const db = getDB();
     const row = db
-        .prepare("SELECT * FROM memories WHERE id = ?")
+        .prepare(`SELECT ${MEMORY_COLUMNS} FROM memories WHERE id = ?`)
         .get(id);
     if (!row)
         return null;
-    return {
-        id: row.id,
-        type: row.type,
-        content: row.content,
-        importance: row.importance,
-        tags: JSON.parse(row.tags),
-        recallCount: row.recall_count,
-        lastRecalled: row.last_recalled,
-        createdAt: row.created_at,
-        updatedAt: row.updated_at,
-    };
+    return toRecords([row])[0];
 }
 export async function updateMemory(id, patch) {
-    const db = getDB();
     const existing = getMemory(id);
     if (!existing)
         return null;
-    const content = patch.content ?? existing.content;
-    const type = patch.type ?? existing.type;
-    const importance = patch.importance !== undefined ? clampImportance(patch.importance) : existing.importance;
-    const tags = patch.tags ?? existing.tags;
-    const vec = await embedText(content);
-    const ts = nowMs();
-    db.prepare("UPDATE memories SET content = ?, type = ?, importance = ?, tags = ?, embedding = ?, updated_at = ? WHERE id = ?").run(content, type, importance, JSON.stringify(tags), packVector(vec), ts, id);
-    invalidateVectorCache();
-    return getMemory(id);
+    // Build the SET list from the patch only. Rewriting every column from a
+    // pre-read snapshot made this a lost-update: two concurrent patches (CLI +
+    // server, or two sessions) each wrote back the other's stale values.
+    const sets = [];
+    const params = [];
+    if (patch.content !== undefined) {
+        sets.push("content = ?");
+        params.push(patch.content);
+    }
+    if (patch.type !== undefined) {
+        sets.push("type = ?");
+        params.push(patch.type);
+    }
+    if (patch.importance !== undefined) {
+        sets.push("importance = ?");
+        params.push(clampImportance(patch.importance));
+    }
+    if (patch.tags !== undefined) {
+        sets.push("tags = ?");
+        params.push(JSON.stringify(patch.tags));
+    }
+    // An all-undefined patch must not touch the row (or re-embed) at all.
+    if (sets.length === 0)
+        return existing;
+    // Only a real text edit needs the model; metadata-only patches stay cheap.
+    if (patch.content !== undefined && patch.content !== existing.content) {
+        const vec = await embedText(patch.content);
+        sets.push("embedding = ?");
+        params.push(packVector(vec));
+        invalidateVectorCache();
+    }
+    sets.push("updated_at = ?");
+    params.push(nowMs());
+    // Re-acquire after the await above: the handle could have been closed.
+    const db = getDB();
+    const res = db
+        .prepare(`UPDATE memories SET ${sets.join(", ")} WHERE id = ?`)
+        .run(...params, id);
+    return Number(res.changes) > 0 ? getMemory(id) : null;
 }
 export function forget(id) {
     const db = getDB();
     const res = db.prepare("DELETE FROM memories WHERE id = ?").run(id);
-    invalidateVectorCache();
-    return { deleted: Number(res.changes) > 0 };
+    const deleted = Number(res.changes) > 0;
+    // A mistyped id used to force a full vector re-read on the next search.
+    if (deleted)
+        invalidateVectorCache();
+    return { deleted };
+}
+/** Above this many vectors the O(n^2) dedup pass is skipped (event-loop budget). */
+const DEDUP_MAX_VECTORS = 500;
+const DEDUP_SIMILARITY = 0.92;
+const DEDUP_TOKEN_OVERLAP = 0.8;
+function tokenSet(text) {
+    return new Set((text.toLowerCase().match(/[\p{L}\p{N}]+/gu) ?? []).filter((t) => t.length > 1));
+}
+/** Jaccard overlap of word sets — the second gate before anything is deleted. */
+function tokenOverlap(a, b) {
+    const ta = tokenSet(a);
+    const tb = tokenSet(b);
+    if (ta.size === 0 || tb.size === 0)
+        return 0;
+    let shared = 0;
+    for (const t of ta)
+        if (tb.has(t))
+            shared++;
+    return shared / (ta.size + tb.size - shared);
 }
 /**
- * - Removes near-duplicate memories (dot product > 0.92) keeping the highest-importance one.
+ * - Removes near-duplicate memories (cosine >= 0.92 AND >= 80% word overlap)
+ *   keeping the highest-importance one. The text gate matters: templated agent
+ *   memories ("The user's X is Y") sit at ~0.95 cosine while being distinct, and
+ *   deleting those is unrecoverable.
  * - Promotes importance of frequently-needed memories (recall_count >= 5) by +0.1.
  * - Optionally prunes stale, low-importance, never-recalled memories (RAG_PRUNE=1,
  *   RAG_PRUNE_IMPORTANCE=0.2, RAG_PRUNE_AGE_DAYS=90). Off by default — deletes are irreversible.
  */
 export async function consolidate() {
     const db = getDB();
-    const rows = db.prepare("SELECT id, embedding FROM memories").all();
-    const records = rows
-        .map((r) => ({ id: r.id, rec: getMemory(r.id) }))
-        .filter((r) => r.rec !== null && r.rec !== undefined);
-    const recordsById = new Map(records.map((r) => [r.id, r.rec]));
+    // ORDER BY so the dedup anchor (and therefore the survivor) is deterministic:
+    // scan order can change with the query plan and flip which memory survives.
+    const rows = db
+        .prepare(`SELECT ${MEMORY_COLUMNS}, embedding FROM memories ORDER BY importance DESC, created_at, id`)
+        .all();
     const vectors = [];
     for (const r of rows) {
-        if (!recordsById.has(r.id))
-            continue;
         const vec = unpackVector(r.embedding);
         if (vec)
             vectors.push({ id: r.id, vec });
     }
+    const records = new Map(toRecords(rows).map((r) => [r.id, r]));
     let removedDuplicates = 0;
+    const skippedDedup = vectors.length > DEDUP_MAX_VECTORS;
     const toDelete = new Set();
-    for (let i = 0; i < vectors.length; i++) {
-        if (toDelete.has(vectors[i].id))
-            continue;
-        for (let j = i + 1; j < vectors.length; j++) {
-            if (toDelete.has(vectors[j].id))
+    if (!skippedDedup) {
+        for (let i = 0; i < vectors.length; i++) {
+            if (toDelete.has(vectors[i].id))
                 continue;
-            const sim = dotProduct(vectors[i].vec, vectors[j].vec);
-            if (sim >= 0.92) {
-                const a = recordsById.get(vectors[i].id);
-                const b = recordsById.get(vectors[j].id);
+            for (let j = i + 1; j < vectors.length; j++) {
+                if (toDelete.has(vectors[j].id))
+                    continue;
+                if (dotProduct(vectors[i].vec, vectors[j].vec) < DEDUP_SIMILARITY)
+                    continue;
+                const a = records.get(vectors[i].id);
+                const b = records.get(vectors[j].id);
+                if (!a || !b || tokenOverlap(a.content, b.content) < DEDUP_TOKEN_OVERLAP)
+                    continue;
                 if (a.importance >= b.importance) {
-                    toDelete.add(vectors[j].id);
+                    toDelete.add(b.id);
                 }
                 else {
-                    toDelete.add(vectors[i].id);
-                    const tmpId = vectors[i].id;
-                    vectors[i].id = vectors[j].id;
-                    vectors[j].id = tmpId;
+                    toDelete.add(a.id);
+                    // Swap the WHOLE entry, not just the id: swapping ids alone leaves
+                    // vectors[i] holding the survivor's id with the *deleted* memory's
+                    // embedding, so a later comparison gates one memory's cosine on
+                    // another's vector and deletes distinct memories.
+                    const tmp = vectors[i];
+                    vectors[i] = vectors[j];
+                    vectors[j] = tmp;
                 }
                 removedDuplicates++;
             }
         }
     }
     const delStmt = db.prepare("DELETE FROM memories WHERE id = ?");
-    for (const id of toDelete)
-        delStmt.run(id);
-    let promoted = 0;
-    const bumpPromotion = async () => {
-        for (const rec of listMemories()) {
-            if (rec.recallCount >= 5 && rec.importance < 1) {
-                await updateMemory(rec.id, { importance: Math.min(1, rec.importance + 0.1) });
-                promoted++;
+    // One transaction for the whole destructive pass. In autocommit each delete
+    // committed on its own, so a SQLITE_BUSY or crash midway left duplicates
+    // deleted but promotion (or the prune half) unapplied — unrecoverable and
+    // unreported, because the throw propagated instead of the counts.
+    db.exec("BEGIN IMMEDIATE;");
+    try {
+        for (const id of toDelete)
+            delStmt.run(id);
+        // One UPDATE for the whole store: the old per-row updateMemory() re-embedded
+        // every candidate (a full model inference each) and only saw the newest 100.
+        const promoted = Number(db
+            .prepare("UPDATE memories SET importance = min(1, importance + 0.1) WHERE recall_count >= 5 AND importance < 1")
+            .run().changes);
+        let pruned = 0;
+        const pruneEnabled = process.env.RAG_PRUNE === "1" || process.env.RAG_PRUNE === "true";
+        if (pruneEnabled) {
+            const minImp = numEnv("RAG_PRUNE_IMPORTANCE", 0.2, (n) => n >= 0 && n <= 1);
+            const maxAgeDays = numEnv("RAG_PRUNE_AGE_DAYS", 90, (n) => n >= 0);
+            const cutoff = nowMs() - maxAgeDays * 86_400_000;
+            const stale = db
+                // <= so RAG_PRUNE_AGE_DAYS=0 means "everything is stale"; a strict <
+                // skipped rows created in the same millisecond as the cutoff, which made
+                // the prune silently no-op on a fast machine.
+                .prepare("SELECT id FROM memories WHERE importance < ? AND recall_count = 0 AND created_at <= ?")
+                .all(minImp, cutoff);
+            for (const s of stale) {
+                delStmt.run(s.id);
+                pruned++;
             }
         }
-    };
-    let pruned = 0;
-    const pruneEnabled = process.env.RAG_PRUNE === "1" || process.env.RAG_PRUNE === "true";
-    if (pruneEnabled) {
-        const minImp = Number(process.env.RAG_PRUNE_IMPORTANCE ?? 0.2);
-        const maxAgeDays = Number(process.env.RAG_PRUNE_AGE_DAYS ?? 90);
-        const cutoff = nowMs() - maxAgeDays * 86_400_000;
-        const stale = db
-            .prepare("SELECT id FROM memories WHERE importance < ? AND recall_count = 0 AND created_at < ?")
-            .all(minImp, cutoff);
-        for (const s of stale) {
-            delStmt.run(s.id);
-            pruned++;
+        db.exec("COMMIT;");
+        // Deleted rows must leave the vector cache, or the next search still scores
+        // them and can return a memory that no longer exists.
+        if (removedDuplicates > 0 || pruned > 0)
+            invalidateVectorCache();
+        const stats = memoryStats();
+        return {
+            removedDuplicates,
+            promoted,
+            pruned,
+            skippedDedup,
+            totals: { memories: stats.memories, tokens: stats.tokens },
+        };
+    }
+    catch (e) {
+        try {
+            db.exec("ROLLBACK;");
         }
+        catch {
+            /* transaction already closed */
+        }
+        throw e;
     }
-    await bumpPromotion();
-    invalidateVectorCache();
-    const stats = memoryStats();
-    return {
-        removedDuplicates,
-        promoted,
-        pruned,
-        totals: { memories: stats.memories, tokens: stats.tokens },
-    };
 }
 export function memoryStats() {
     const db = getDB();
@@ -205,10 +330,15 @@ export function memoryStats() {
     const byType = {};
     for (const r of byTypeRows)
         byType[r.type] = r.c;
-    let totalTokens = 0;
-    for (const r of db.prepare("SELECT content FROM memories").all()) {
-        totalTokens += estimateTokens(r.content);
+    // LENGTH() in SQL: loading every content blob just to count tokens was a full
+    // table pull on each system_stats / memory_stats call. Keep the char count in
+    // SQL and estimate here — materialising "x".repeat(n) per row re-allocated the
+    // very blobs this was meant to avoid.
+    let chars = 0;
+    for (const r of db.prepare("SELECT LENGTH(content) AS n FROM memories").all()) {
+        chars += Math.max(0, r.n ?? 0);
     }
+    const totalTokens = estimateTokensFromChars(chars);
     return { memories: count.c, tokens: totalTokens, avgImportance: avg.a, byType };
 }
 export async function contextPrompt(query, topK = 6) {
@@ -219,6 +349,8 @@ export async function contextPrompt(query, topK = 6) {
     return { context: lines.join("\n"), sources: hits };
 }
 function clampImportance(v) {
+    if (!Number.isFinite(v))
+        return 0.5;
     return Math.min(1, Math.max(0, v));
 }
 //# sourceMappingURL=memory.js.map

package/dist/memory/memory.js.map

@@ -1 +1 @@
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package/dist/rag/chunker.d.ts

@@ -13,4 +13,11 @@ export interface ChunkOptions {
 export declare function chunkText(text: string, options?: ChunkOptions): Chunk[];
 /** Rough token estimate: ~4 chars per token for latin, ~1.5 for CJK. */
 export declare function estimateTokens(text: string): number;
+/**
+ * Same estimate for an already-known character count. Lets a caller total
+ * LENGTH() across many rows in SQL instead of materialising each content
+ * blob just to re-count its characters. Assumes no CJK in the total, which
+ * under-counts CJK-heavy stores — the same tradeoff the SQL path already made.
+ */
+export declare function estimateTokensFromChars(chars: number): number;
 //# sourceMappingURL=chunker.d.ts.map

package/dist/rag/chunker.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"chunker.d.ts","sourceRoot":"","sources":["../../src/rag/chunker.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,MAAM,WAAW,KAAK;IACpB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAwHD,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,KAAK,EAAE,CAiF3E;AAED,wEAAwE;AACxE,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAInD;AAED;;;;;GAKG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAG7D"}