agentdb 3.1.0 → 3.3.0

package/dist/src/search/conversation-retrieval.js

@@ -0,0 +1,190 @@
+/**
+ * Conversation-memory retrieval: hybrid dense + BM25 ranking of chunks, aggregated to the memory unit a caller
+ * asks for (a session, an episode). ADR-016.
+ *
+ * Pure functions over plain arrays, so the MCP search path and the LongMemEval harness run the same code.
+ * Every input that can come from a tool call is bounded: text is cut before tokenising, the token count per
+ * document and per query is capped, and the tokeniser regex has no nesting (linear time).
+ */
+/** Limits applied to untrusted text before it is tokenised. */
+export const RETRIEVAL_LIMITS = Object.freeze({
+    maxCharsPerText: 32_768,
+    maxTokensPerDoc: 4_096,
+    maxQueryTokens: 256,
+});
+const STOPWORDS = new Set(('a an and are as at be been but by can could did do does doing for from had has have having he her hers him his how i if in into is it its ' +
+    'me my myself no nor not of off on once only or other our ours out over own same she should so some such than that the their theirs them ' +
+    'then there these they this those through to too under until up very was we were what when where which while who whom why will with would you ' +
+    'your yours yourself just also about any all am again against because before being below between both down during each few further here more ' +
+    'most s t don now ll re ve d m o y')
+    .split(' '));
+/** Lower-cased word tokens without stopwords, capped at `maxTokens`. Linear in the (already capped) input. */
+export function tokenize(text, maxTokens = RETRIEVAL_LIMITS.maxTokensPerDoc) {
+    const src = text.length > RETRIEVAL_LIMITS.maxCharsPerText ? text.slice(0, RETRIEVAL_LIMITS.maxCharsPerText) : text;
+    const out = [];
+    for (const m of src.toLowerCase().matchAll(/[\p{L}\p{N}]+/gu)) {
+        const tok = m[0];
+        if (tok.length < 2 && !/\d/.test(tok))
+            continue;
+        if (STOPWORDS.has(tok))
+            continue;
+        out.push(tok.length > 6 ? lightStem(tok) : tok);
+        if (out.length >= maxTokens)
+            break;
+    }
+    return out;
+}
+/** A small suffix stripper: plural and common verb endings only, so "hiking"/"hikes"/"hiked" share a term. */
+function lightStem(tok) {
+    if (tok.endsWith('ies'))
+        return tok.slice(0, -3) + 'y';
+    if (tok.endsWith('ing'))
+        return tok.slice(0, -3);
+    if (tok.endsWith('ed'))
+        return tok.slice(0, -2);
+    if (tok.endsWith('es'))
+        return tok.slice(0, -2);
+    if (tok.endsWith('s') && !tok.endsWith('ss'))
+        return tok.slice(0, -1);
+    return tok;
+}
+/** Okapi BM25 over a document set that can grow by appending (`add`). */
+export class Bm25Index {
+    postings = new Map();
+    lengths = [];
+    total = 0;
+    k1;
+    b;
+    constructor(docs = [], k1 = 1.2, b = 0.75) {
+        this.k1 = k1;
+        this.b = b;
+        for (const tokens of docs)
+            this.add(tokens);
+    }
+    get size() {
+        return this.lengths.length;
+    }
+    /** Appends a document; its index is the previous `size`. */
+    add(tokens) {
+        const doc = this.lengths.length;
+        this.lengths.push(tokens.length);
+        this.total += tokens.length;
+        const tf = new Map();
+        for (const t of tokens)
+            tf.set(t, (tf.get(t) ?? 0) + 1);
+        for (const [term, n] of tf) {
+            let list = this.postings.get(term);
+            if (!list)
+                this.postings.set(term, (list = []));
+            list.push({ doc, tf: n });
+        }
+        return doc;
+    }
+    /**
+     * Replace document `doc` in place. `oldTokens` must be the tokens it was indexed with: their postings
+     * are removed, the new ones added, and the length statistics adjusted. O(postings of the touched terms).
+     */
+    replace(doc, oldTokens, newTokens) {
+        if (doc < 0 || doc >= this.lengths.length)
+            throw new RangeError(`no document ${doc}`);
+        for (const term of new Set(oldTokens)) {
+            const list = this.postings.get(term);
+            if (!list)
+                continue;
+            const kept = list.filter(p => p.doc !== doc);
+            if (kept.length)
+                this.postings.set(term, kept);
+            else
+                this.postings.delete(term);
+        }
+        this.total += newTokens.length - this.lengths[doc];
+        this.lengths[doc] = newTokens.length;
+        const tf = new Map();
+        for (const t of newTokens)
+            tf.set(t, (tf.get(t) ?? 0) + 1);
+        for (const [term, n] of tf) {
+            let list = this.postings.get(term);
+            if (!list)
+                this.postings.set(term, (list = []));
+            list.push({ doc, tf: n });
+        }
+    }
+    /** BM25 score of every document for the query tokens (0 where no term matches). */
+    score(query) {
+        const n = this.lengths.length;
+        const scores = new Float64Array(n);
+        const avgLen = n ? this.total / n || 1 : 1;
+        for (const term of new Set(query.slice(0, RETRIEVAL_LIMITS.maxQueryTokens))) {
+            const list = this.postings.get(term);
+            if (!list)
+                continue;
+            const idf = Math.log(1 + (n - list.length + 0.5) / (list.length + 0.5));
+            for (const { doc, tf } of list) {
+                const norm = tf + this.k1 * (1 - this.b + (this.b * this.lengths[doc]) / avgLen);
+                scores[doc] += idf * ((tf * (this.k1 + 1)) / norm);
+            }
+        }
+        return scores;
+    }
+}
+/** Dot product of a query vector with each row; equal to cosine when all vectors are L2-normalised. */
+export function dotScores(query, rows) {
+    const out = new Float64Array(rows.length);
+    const d = query.length;
+    for (let r = 0; r < rows.length; r++) {
+        const row = rows[r];
+        if (row.length !== d)
+            throw new Error(`dimension mismatch: query ${d}, row ${r} ${row.length}`);
+        let s = 0;
+        for (let i = 0; i < d; i++)
+            s += query[i] * row[i];
+        out[r] = s;
+    }
+    return out;
+}
+/** 1-based rank of each entry under a descending sort; entries that must not count (score <= floor) get rank Infinity. */
+export function ranksOf(scores, floor = -Infinity) {
+    const idx = Array.from({ length: scores.length }, (_, i) => i).filter(i => scores[i] > floor);
+    idx.sort((a, z) => scores[z] - scores[a] || a - z);
+    const ranks = new Float64Array(scores.length).fill(Infinity);
+    idx.forEach((doc, r) => (ranks[doc] = r + 1));
+    return ranks;
+}
+/** Weighted reciprocal-rank fusion of a dense and a lexical score list over the same documents. */
+export function fuseHybrid(dense, lexical, opts = {}) {
+    const k = opts.rrfK ?? 60;
+    const wd = opts.denseWeight ?? 1;
+    const wl = lexical ? opts.lexicalWeight ?? 1 : 0;
+    const rd = ranksOf(dense);
+    const rl = lexical && wl > 0 ? ranksOf(lexical, 0) : null;
+    const out = new Float64Array(dense.length);
+    for (let i = 0; i < dense.length; i++) {
+        out[i] = wd / (k + rd[i]) + (rl ? wl / (k + rl[i]) : 0);
+    }
+    return out;
+}
+/** Rank groups (sessions, episodes) by the scores of their chunks. Ties keep first-seen order. */
+export function rankGroups(groupOf, scores, opts = {}) {
+    const per = new Map();
+    const order = [];
+    groupOf.forEach((g, i) => {
+        let list = per.get(g);
+        if (!list) {
+            per.set(g, (list = []));
+            order.push(g);
+        }
+        list.push(scores[i]);
+    });
+    const tail = opts.tailWeight ?? 0.1;
+    const ranked = order.map((group, firstSeen) => {
+        const s = per.get(group).sort((a, z) => z - a);
+        let score = s[0];
+        if (opts.aggregation === 'max-plus')
+            for (let i = 1, w = tail; i < s.length && i < 4; i++, w /= 2)
+                score += w * s[i];
+        return { group, score, firstSeen };
+    });
+    ranked.sort((a, z) => z.score - a.score || a.firstSeen - z.firstSeen);
+    return ranked.map(({ group, score }) => ({ group, score }));
+}
+//# sourceMappingURL=conversation-retrieval.js.map

package/dist/src/search/conversation-retrieval.js.map

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package/dist/src/search/cross-encoder.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Opt-in cross-encoder reranking (ADR-016). A cross-encoder reads the query and a candidate together, so it ranks
+ * far better than either embedding similarity or BM25, at about 200 ms per 60 candidates on CPU for the default
+ * 22M-parameter model (q8). It is therefore applied only to a bounded candidate set, and only when a caller asks.
+ *
+ * The model is downloaded once by @huggingface/transformers. Every input is bounded: at most MAX_CANDIDATES
+ * candidates, each cut to MAX_CHARS before tokenising, and the tokenizer truncates pairs at 512 tokens.
+ */
+export declare const DEFAULT_RERANKER: string;
+/** Two candidate lists of RERANK_DEPTH (60) each, deduplicated, fit. */
+export declare const MAX_CANDIDATES = 128;
+/**
+ * Relevance logits of each candidate for the query, in input order. Throws if the model cannot be loaded;
+ * callers fall back to their unreranked order.
+ */
+export declare function crossEncoderScores(query: string, candidates: readonly string[], modelId?: string): Promise<Float64Array>;
+//# sourceMappingURL=cross-encoder.d.ts.map

package/dist/src/search/cross-encoder.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cross-encoder.d.ts","sourceRoot":"","sources":["../../../src/search/cross-encoder.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,eAAO,MAAM,gBAAgB,QAAwE,CAAC;AACtG,wEAAwE;AACxE,eAAO,MAAM,cAAc,MAAM,CAAC;AA2BlC;;;GAGG;AACH,wBAAsB,kBAAkB,CAAC,KAAK,EAAE,MAAM,EAAE,UAAU,EAAE,SAAS,MAAM,EAAE,EAAE,OAAO,SAAmB,GAAG,OAAO,CAAC,YAAY,CAAC,CAcxI"}

package/dist/src/search/cross-encoder.js

@@ -0,0 +1,52 @@
+/**
+ * Opt-in cross-encoder reranking (ADR-016). A cross-encoder reads the query and a candidate together, so it ranks
+ * far better than either embedding similarity or BM25, at about 200 ms per 60 candidates on CPU for the default
+ * 22M-parameter model (q8). It is therefore applied only to a bounded candidate set, and only when a caller asks.
+ *
+ * The model is downloaded once by @huggingface/transformers. Every input is bounded: at most MAX_CANDIDATES
+ * candidates, each cut to MAX_CHARS before tokenising, and the tokenizer truncates pairs at 512 tokens.
+ */
+export const DEFAULT_RERANKER = process.env.AGENTDB_RERANKER_MODEL || 'Xenova/ms-marco-MiniLM-L-6-v2';
+/** Two candidate lists of RERANK_DEPTH (60) each, deduplicated, fit. */
+export const MAX_CANDIDATES = 128;
+const MAX_CHARS = 4_096;
+const BATCH = 32;
+const loading = new Map();
+async function load(modelId) {
+    let p = loading.get(modelId);
+    if (!p) {
+        p = (async () => {
+            const t = await import('@huggingface/transformers');
+            const tokenizer = await t.AutoTokenizer.from_pretrained(modelId);
+            const model = await t.AutoModelForSequenceClassification.from_pretrained(modelId, { dtype: 'q8' });
+            return { tokenizer: tokenizer, model: model };
+        })();
+        // A failed load is not cached, so a later call can retry (e.g. after the network returns).
+        p.catch(() => loading.delete(modelId));
+        loading.set(modelId, p);
+    }
+    return p;
+}
+/**
+ * Relevance logits of each candidate for the query, in input order. Throws if the model cannot be loaded;
+ * callers fall back to their unreranked order.
+ */
+export async function crossEncoderScores(query, candidates, modelId = DEFAULT_RERANKER) {
+    if (candidates.length > MAX_CANDIDATES)
+        throw new RangeError(`at most ${MAX_CANDIDATES} candidates`);
+    const out = new Float64Array(candidates.length);
+    if (candidates.length === 0)
+        return out;
+    const { tokenizer, model } = await load(modelId);
+    const q = query.slice(0, MAX_CHARS);
+    for (let i = 0; i < candidates.length; i += BATCH) {
+        const docs = candidates.slice(i, i + BATCH).map(d => d.slice(0, MAX_CHARS));
+        const enc = tokenizer(new Array(docs.length).fill(q), { text_pair: docs, padding: true, truncation: true, max_length: 512 });
+        const { logits } = await model(enc);
+        const width = logits.dims[1] ?? 1;
+        for (let j = 0; j < docs.length; j++)
+            out[i + j] = Number(logits.data[j * width + (width - 1)]);
+    }
+    return out;
+}
+//# sourceMappingURL=cross-encoder.js.map

package/dist/src/search/cross-encoder.js.map

@@ -0,0 +1 @@
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package/dist/src/security/mcp-policy.d.ts.map

@@ -1 +1 @@
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package/dist/src/security/mcp-policy.js

@@ -13,6 +13,13 @@ const READONLY_TOOLS = [
     'recall_with_certificate',
     'reflexion_retrieve',
     'skill_search',
+    // CRUD reads (ADR-017)
+    'agentdb_get',
+    'agentdb_list',
+    'agentdb_pattern_get',
+    'agentdb_pattern_list',
+    'skill_get',
+    'skill_list',
 ];
 const LEARNING_TOOLS = [
     ...READONLY_TOOLS,
@@ -38,12 +45,18 @@ const LEARNING_TOOLS = [
     'reflexion_store_batch',
     'skill_create',
     'skill_create_batch',
+    // In-place updates keep ids; deletes stay admin-only (ADR-017)
+    'agentdb_update',
+    'agentdb_pattern_update',
+    'skill_update',
 ];
 /** Tools that reset or delete data: only the admin profile (or an explicit allow) grants them. */
 export const ADMIN_ONLY_TOOLS = [
     'agentdb_init',
     'agentdb_delete',
     'agentdb_delete_batch',
+    'agentdb_pattern_delete',
+    'skill_delete',
     'agentdb_clear_cache',
 ];
 /** Profile used when AGENTDB_MCP_PROFILE is unset */

package/dist/src/security/mcp-policy.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentdb",
-  "version": "3.1.0",
+  "version": "3.3.0",
   "description": "Self-learning vector memory for AI agents — single-file .rvf cognitive container with HNSW search, episodic Reflexion memory, causal graph + Cypher, 9 RL algorithms, Thompson Sampling bandit, 41 MCP tools, hybrid (BM25 + dense) retrieval, GNN attention. 150x faster than SQLite. Up to +36% search quality from feedback. Runs in Node, browsers (WASM), edge, offline. Backs the agentic-flow / ruflo / Claude Code memory layer.",
   "type": "module",
   "main": "dist/src/index.js",
@@ -65,7 +65,7 @@
     "test": "vitest",
     "test:unit": "vitest --run",
     "test:browser": "vitest browser-bundle-unit.test.js --run",
-    "test:ci": "npm run test:unit && npm run test:browser && npm run build && npm run verify:bundle && npm run test:mcp-stdio",
+    "test:ci": "npm run test:unit && npm run test:browser && npm run build && npm run verify:bundle && npm run test:mcp-stdio && npm run test:mcp-crud",
     "test:mcp-stdio": "node tests/mcp-stdio-purity.mjs",
     "verify:bundle": "node scripts/verify-bundle.js",
     "cli": "node dist/src/cli/agentdb-cli.js",
@@ -81,7 +81,9 @@
     "benchmark:adr072:fast": "vitest run tests/benchmarks/validate-adr072.test.ts",
     "benchmark:all": "npm run benchmark:attention && npm run benchmark:backends && npm run benchmark:profile && npm run benchmark:ruvector",
     "build:model": "node scripts/build-model-rvf.mjs",
-    "prebuild": "node scripts/inline-schemas.mjs"
+    "prebuild": "node scripts/inline-schemas.mjs",
+    "test:mcp-crud": "node tests/mcp-crud-e2e.mjs",
+    "benchmark:crud": "tsx benchmarks/crud-benchmark.mts"
   },
   "keywords": [
     "agentdb",
@@ -210,7 +212,7 @@
     "commander": "^12.1.0",
     "hnswlib-node": "^3.0.0",
     "inquirer": "^9.3.8",
-    "ruvector": "^0.2.40",
+    "ruvector": "^0.3.5",
     "ruvector-attention-wasm": "^0.1.32",
     "ruvector-graph-transformer-wasm": "^2.0.4"
   },