@henrychong-ai/mcp-neo4j-knowledge-graph 2.6.0 → 2.7.1

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Files changed (22) hide show
  1. package/README.md +28 -5
  2. package/dist/KnowledgeGraphManager.d.ts +42 -7
  3. package/dist/KnowledgeGraphManager.js +130 -52
  4. package/dist/KnowledgeGraphManager.js.map +1 -1
  5. package/dist/embeddings/OpenAIEmbeddingService.d.ts +6 -0
  6. package/dist/embeddings/OpenAIEmbeddingService.js +14 -2
  7. package/dist/embeddings/OpenAIEmbeddingService.js.map +1 -1
  8. package/dist/retrieval/RerankerService.d.ts +19 -6
  9. package/dist/retrieval/RerankerService.js +30 -10
  10. package/dist/retrieval/RerankerService.js.map +1 -1
  11. package/dist/schemas/index.d.ts +11 -3
  12. package/dist/schemas/index.js +12 -3
  13. package/dist/schemas/index.js.map +1 -1
  14. package/dist/server/handlers/callToolHandler.js +5 -3
  15. package/dist/server/handlers/callToolHandler.js.map +1 -1
  16. package/dist/server/handlers/listToolsHandler.js +2 -2
  17. package/dist/server/handlers/listToolsHandler.js.map +1 -1
  18. package/dist/storage/neo4j/Neo4jStorageProvider.d.ts +11 -0
  19. package/dist/storage/neo4j/Neo4jStorageProvider.js +37 -10
  20. package/dist/storage/neo4j/Neo4jStorageProvider.js.map +1 -1
  21. package/example.env +4 -2
  22. package/package.json +5 -4
package/dist/retrieval/RerankerService.d.ts CHANGED
@@ -13,7 +13,7 @@ export interface RerankConfig {
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  apiKey: string;
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  /** Candidates sent to the reranker (recall set). */
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  topN: number;
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- /** Results kept after rerank. */
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+ /** Default return count when a reranker is configured; trim applied by the caller. */
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  topK: number;
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  /** Per-passage truncation for scoring only (reranker context limits). */
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  maxPassageChars: number;
@@ -21,7 +21,12 @@ export interface RerankConfig {
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  }
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  /**
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  * Thin client for a cross-encoder reranker (default: Cloudflare Workers AI
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- * `@cf/baai/bge-reranker-base`). OpenAI-style/native HTTP; reuses `axios`.
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+ * `@cf/baai/bge-reranker-base`). OpenAI-style/native HTTP via a dedicated
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+ * axios instance with keep-alive DISABLED — the rerank call follows a
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+ * multi-second recall gap, and a pooled keep-alive socket (shared with the
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+ * embedding call) can go half-open in that gap, turning every rerank into a
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+ * timeout. A fresh connection per call is cheap relative to model latency.
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+ * (Instance is deliberately created inline here, not in a shared util.)
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  *
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  * The service itself MAY throw (transport/parse errors) — callers are expected
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  * to fail open (return the pre-rerank order). It never enables itself without a
@@ -29,8 +34,14 @@ export interface RerankConfig {
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  */
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  export declare class RerankerService {
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  private readonly cfg;
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+ private readonly client;
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  constructor(cfg: RerankConfig);
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  get enabled(): boolean;
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+ /**
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+ * Scoring-payload cap (RERANK_TOP_N) — introspection only as of v2.7.0: the
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+ * recall-widening that consumed this getter was removed; rerank() applies the
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+ * cap internally when slicing passages.
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+ */
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  get topN(): number;
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  get topK(): number;
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  get model(): string;
@@ -41,13 +52,15 @@ export declare class RerankerService {
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  * Env: RERANK_ENABLED, RERANK_MODEL (default @cf/baai/bge-reranker-base),
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  * RERANK_ENDPOINT (or derived from RERANK_ACCOUNT_ID/CF_ACCOUNT_ID + model),
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  * RERANK_API_KEY (falls back to EMBEDDING_API_KEY), RERANK_TOP_N (20),
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- * RERANK_TOP_K (10), RERANK_MAX_PASSAGE_CHARS (2000), RERANK_TIMEOUT_MS (5000).
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+ * RERANK_TOP_K (5), RERANK_MAX_PASSAGE_CHARS (2000), RERANK_TIMEOUT_MS (5000).
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  */
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  static fromEnv(): RerankerService;
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  /**
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- * Rerank `passages` against `query`. Returns candidate indices reordered
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- * descending by relevance, length <= topK. THROWS on transport/parse error —
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- * the caller fail-opens.
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+ * Rerank `passages` against `query`. Returns the FULL ordering of valid
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+ * candidate indices, best-first (defensively re-sorted by score descending —
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+ * the API's row order is not trusted). Trimming to the final return count is
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+ * the CALLER's responsibility (KnowledgeGraphManager.maybeRerank). THROWS on
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+ * transport/parse error — the caller fail-opens.
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  *
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  * @param query - Search query
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  * @param passages - Candidate passages (index-aligned with the caller's results)
package/dist/retrieval/RerankerService.js CHANGED
@@ -1,3 +1,5 @@
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+ import http from 'node:http';
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+ import https from 'node:https';
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  import axios from 'axios';
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  import { logger } from '../utils/logger.js';
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  function intEnv(name, fallback) {
@@ -9,7 +11,12 @@ function intEnv(name, fallback) {
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  }
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  /**
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  * Thin client for a cross-encoder reranker (default: Cloudflare Workers AI
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- * `@cf/baai/bge-reranker-base`). OpenAI-style/native HTTP; reuses `axios`.
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+ * `@cf/baai/bge-reranker-base`). OpenAI-style/native HTTP via a dedicated
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+ * axios instance with keep-alive DISABLED — the rerank call follows a
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+ * multi-second recall gap, and a pooled keep-alive socket (shared with the
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+ * embedding call) can go half-open in that gap, turning every rerank into a
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+ * timeout. A fresh connection per call is cheap relative to model latency.
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+ * (Instance is deliberately created inline here, not in a shared util.)
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  *
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  * The service itself MAY throw (transport/parse errors) — callers are expected
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  * to fail open (return the pre-rerank order). It never enables itself without a
@@ -17,12 +24,22 @@ function intEnv(name, fallback) {
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  */
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  export class RerankerService {
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  cfg;
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+ client;
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  constructor(cfg) {
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  this.cfg = cfg;
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+ this.client = axios.create({
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+ httpAgent: new http.Agent({ keepAlive: false }),
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+ httpsAgent: new https.Agent({ keepAlive: false }),
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+ });
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  }
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  get enabled() {
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  return this.cfg.enabled;
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  }
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+ /**
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+ * Scoring-payload cap (RERANK_TOP_N) — introspection only as of v2.7.0: the
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+ * recall-widening that consumed this getter was removed; rerank() applies the
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+ * cap internally when slicing passages.
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+ */
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  get topN() {
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  return this.cfg.topN;
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  }
@@ -39,7 +56,7 @@ export class RerankerService {
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  * Env: RERANK_ENABLED, RERANK_MODEL (default @cf/baai/bge-reranker-base),
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  * RERANK_ENDPOINT (or derived from RERANK_ACCOUNT_ID/CF_ACCOUNT_ID + model),
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  * RERANK_API_KEY (falls back to EMBEDDING_API_KEY), RERANK_TOP_N (20),
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- * RERANK_TOP_K (10), RERANK_MAX_PASSAGE_CHARS (2000), RERANK_TIMEOUT_MS (5000).
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+ * RERANK_TOP_K (5), RERANK_MAX_PASSAGE_CHARS (2000), RERANK_TIMEOUT_MS (5000).
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  */
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  static fromEnv() {
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  const requested = process.env.RERANK_ENABLED === 'true';
@@ -64,15 +81,17 @@ export class RerankerService {
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  model,
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  apiKey,
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  topN: intEnv('RERANK_TOP_N', 20),
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- topK: intEnv('RERANK_TOP_K', 10),
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+ topK: intEnv('RERANK_TOP_K', 5),
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  maxPassageChars: intEnv('RERANK_MAX_PASSAGE_CHARS', 2000),
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  timeoutMs: intEnv('RERANK_TIMEOUT_MS', 5000),
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  });
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  }
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  /**
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- * Rerank `passages` against `query`. Returns candidate indices reordered
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- * descending by relevance, length <= topK. THROWS on transport/parse error —
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- * the caller fail-opens.
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+ * Rerank `passages` against `query`. Returns the FULL ordering of valid
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+ * candidate indices, best-first (defensively re-sorted by score descending —
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+ * the API's row order is not trusted). Trimming to the final return count is
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+ * the CALLER's responsibility (KnowledgeGraphManager.maybeRerank). THROWS on
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+ * transport/parse error — the caller fail-opens.
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  *
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  * @param query - Search query
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  * @param passages - Candidate passages (index-aligned with the caller's results)
@@ -82,7 +101,7 @@ export class RerankerService {
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  const contexts = passages
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  .slice(0, this.cfg.topN)
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  .map(text => ({ text: (text || '').slice(0, this.cfg.maxPassageChars) }));
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- const response = await axios.post(this.cfg.endpoint, { query: query.slice(0, this.cfg.maxPassageChars), contexts }, {
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+ const response = await this.client.post(this.cfg.endpoint, { query: query.slice(0, this.cfg.maxPassageChars), contexts }, {
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  headers: {
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  Authorization: `Bearer ${this.cfg.apiKey}`,
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  'Content-Type': 'application/json',
@@ -93,12 +112,15 @@ export class RerankerService {
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  if (!Array.isArray(ranked)) {
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  throw new Error('Reranker returned a malformed response (missing result.response array)');
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  }
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+ // Defensive: sort by score descending ourselves — do not trust the API's row order.
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+ // Rows with a missing (null/undefined) score sink to the end.
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+ const sorted = [...ranked].sort((a, b) => (b?.score ?? Number.NEGATIVE_INFINITY) - (a?.score ?? Number.NEGATIVE_INFINITY));
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  // Defensive: keep only integer, in-range, UNIQUE ids (CF returns request-array indices).
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  // Fractional / duplicate / out-of-range ids are dropped so a malformed-but-arrayed response
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  // can't corrupt ordering or duplicate results — the caller still fully fail-opens on a throw.
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  const seen = new Set();
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  const indices = [];
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- for (const row of ranked) {
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+ for (const row of sorted) {
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  const id = row?.id;
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  if (typeof id === 'number' &&
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  Number.isInteger(id) &&
@@ -107,8 +129,6 @@ export class RerankerService {
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  !seen.has(id)) {
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  seen.add(id);
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  indices.push(id);
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- if (indices.length >= this.cfg.topK)
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- break;
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  }
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  }
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  return indices;
package/dist/retrieval/RerankerService.js.map CHANGED
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package/dist/schemas/index.d.ts CHANGED
@@ -97,12 +97,20 @@ export declare const SearchNodesInputSchema: z.ZodObject<{
97
97
  }, z.core.$strip>;
98
98
  export type SearchNodesInput = z.infer<typeof SearchNodesInputSchema>;
99
99
  /**
100
- * Schema for semantic_search tool input
100
+ * Schema for semantic_search tool input.
101
+ *
102
+ * v2.7.1: aligned with the reranker-aware default semantics — `limit` and
103
+ * `minSimilarity` carry NO schema defaults so an absent value stays undefined
104
+ * through the handler and the manager resolves it reranker-aware (limit:
105
+ * 10 plain / RERANK_TOP_K reranked; minSimilarity: 0). A schema `.default()`
106
+ * here would silently resurrect pre-2.7.0 behaviour if this schema is ever
107
+ * wired into the handler path. `limit` accepts 0 (explicit empty result) and
108
+ * non-negative values; the manager floors/clamps at runtime.
101
109
  */
102
110
  export declare const SemanticSearchInputSchema: z.ZodObject<{
103
111
  query: z.ZodString;
104
- limit: z.ZodDefault<z.ZodNumber>;
105
- minSimilarity: z.ZodDefault<z.ZodNumber>;
112
+ limit: z.ZodOptional<z.ZodNumber>;
113
+ minSimilarity: z.ZodOptional<z.ZodNumber>;
106
114
  domain: z.ZodOptional<z.ZodString>;
107
115
  }, z.core.$strip>;
108
116
  export type SemanticSearchInput = z.infer<typeof SemanticSearchInputSchema>;
package/dist/schemas/index.js CHANGED
@@ -91,12 +91,21 @@ export const SearchNodesInputSchema = z.object({
91
91
  domain: z.string().optional(),
92
92
  });
93
93
  /**
94
- * Schema for semantic_search tool input
94
+ * Schema for semantic_search tool input.
95
+ *
96
+ * v2.7.1: aligned with the reranker-aware default semantics — `limit` and
97
+ * `minSimilarity` carry NO schema defaults so an absent value stays undefined
98
+ * through the handler and the manager resolves it reranker-aware (limit:
99
+ * 10 plain / RERANK_TOP_K reranked; minSimilarity: 0). A schema `.default()`
100
+ * here would silently resurrect pre-2.7.0 behaviour if this schema is ever
101
+ * wired into the handler path. `limit` accepts 0 (explicit empty result) and
102
+ * non-negative values; the manager floors/clamps at runtime.
95
103
  */
96
104
  export const SemanticSearchInputSchema = z.object({
97
105
  query: z.string().min(1, 'Search query is required'),
98
- limit: z.number().int().positive().max(100).default(10),
99
- minSimilarity: z.number().min(0).max(1).default(0.6),
106
+ // No max: the live tool contract honours any explicit limit exactly.
107
+ limit: z.number().min(0).optional(),
108
+ minSimilarity: z.number().min(0).max(1).optional(),
100
109
  domain: z.string().optional(),
101
110
  });
102
111
  // =============================================================================
package/dist/schemas/index.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/server/handlers/callToolHandler.js CHANGED
@@ -259,10 +259,12 @@ knowledgeGraphManager) {
259
259
  temporalHalfLife: hybridConfigRaw.temporal_half_life,
260
260
  }
261
261
  : undefined;
262
- // Extract search options from args
262
+ // Extract search options from args. limit and min_similarity pass through
263
+ // undefined-preserving — the manager resolves defaults (reranker-aware for
264
+ // limit), and an explicit min_similarity of 0 must not collapse to a default.
263
265
  const searchOptions = {
264
- limit: args.limit || 10,
265
- minSimilarity: args.min_similarity || 0.6,
266
+ limit: args.limit,
267
+ minSimilarity: args.min_similarity,
266
268
  entityTypes: args.entity_types || [],
267
269
  hybridSearch: args.hybrid_search === undefined ? true : args.hybrid_search,
268
270
  semanticWeight: args.semantic_weight || 0.6,
package/dist/server/handlers/callToolHandler.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/server/handlers/listToolsHandler.js CHANGED
@@ -364,11 +364,11 @@ export async function handleListToolsRequest() {
364
364
  },
365
365
  limit: {
366
366
  type: 'number',
367
- description: 'Maximum number of results to return (default: 10)',
367
+ description: 'Maximum number of results to return (default: 10; when a reranker is configured, default: 5, reranked best-first)',
368
368
  },
369
369
  min_similarity: {
370
370
  type: 'number',
371
- description: 'Minimum similarity threshold from 0.0 to 1.0 (default: 0.6)',
371
+ description: "Minimum similarity threshold 0.0-1.0 on Neo4j's normalised cosine scale, where 0.5 means unrelated and 1.0 identical (default: 0 — disabled; absolute floors are not meaningful for high-clustering embedding models)",
372
372
  },
373
373
  entity_types: {
374
374
  type: 'array',
package/dist/server/handlers/listToolsHandler.js.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/dist/storage/neo4j/Neo4jStorageProvider.d.ts CHANGED
@@ -75,6 +75,17 @@ export declare class Neo4jStorageProvider implements StorageProvider {
75
75
  * Includes all parameters that affect search results
76
76
  */
77
77
  private generateCacheKey;
78
+ /**
79
+ * Reorder a graph's entities to match a ranked name list.
80
+ *
81
+ * openNodes() hydration does not guarantee result order, so the ranked
82
+ * ordering produced by vector/hybrid search must be re-applied before the
83
+ * graph is cached or returned — callers (KnowledgeGraphManager.maybeRerank)
84
+ * rely on recall order being meaningful. Entities whose name is missing
85
+ * from the ranked list are placed last, preserving their relative order
86
+ * (Array.prototype.sort is stable).
87
+ */
88
+ private reorderEntitiesByRank;
78
89
  /**
79
90
  * Initialize Neo4j schema
80
91
  */
package/dist/storage/neo4j/Neo4jStorageProvider.js CHANGED
@@ -119,8 +119,8 @@ export class Neo4jStorageProvider {
119
119
  : '';
120
120
  const parts = [
121
121
  query,
122
- String(options.limit || 10),
123
- String(options.minSimilarity || 0.6),
122
+ String(options.limit ?? 10),
123
+ String(options.minSimilarity ?? 0),
124
124
  entityTypes.join(','),
125
125
  String(options.hybridSearch || false),
126
126
  String(options.semanticWeight || 0.6),
@@ -128,9 +128,28 @@ export class Neo4jStorageProvider {
128
128
  hybridConfigKey,
129
129
  vectorKey,
130
130
  options.domain || 'all',
131
+ // includeNullDomain changes the Cypher filter (`AND node.domain IS NULL`) —
132
+ // omitting it from the key aliased null-domain and all-domain results.
133
+ String(options.includeNullDomain ?? false),
131
134
  ];
132
135
  return parts.join(':');
133
136
  }
137
+ /**
138
+ * Reorder a graph's entities to match a ranked name list.
139
+ *
140
+ * openNodes() hydration does not guarantee result order, so the ranked
141
+ * ordering produced by vector/hybrid search must be re-applied before the
142
+ * graph is cached or returned — callers (KnowledgeGraphManager.maybeRerank)
143
+ * rely on recall order being meaningful. Entities whose name is missing
144
+ * from the ranked list are placed last, preserving their relative order
145
+ * (Array.prototype.sort is stable).
146
+ */
147
+ reorderEntitiesByRank(graph, rankedNames) {
148
+ const rankIndex = new Map(rankedNames.map((name, index) => [name, index]));
149
+ const entities = [...graph.entities].sort((a, b) => (rankIndex.get(a.name) ?? Number.MAX_SAFE_INTEGER) -
150
+ (rankIndex.get(b.name) ?? Number.MAX_SAFE_INTEGER));
151
+ return { ...graph, entities };
152
+ }
134
153
  /**
135
154
  * Initialize Neo4j schema
136
155
  */
@@ -427,8 +446,11 @@ export class Neo4jStorageProvider {
427
446
  const endTimer = metrics.startQueryTimer('searchNodes');
428
447
  try {
429
448
  const startTime = Date.now();
430
- // Prepare search parameters
431
- const rawLimit = options.limit || 10;
449
+ // Prepare search parameters — ?? (not ||) so an explicit limit of 0 is honoured.
450
+ // Direct callers: a NaN limit now yields LIMIT 0 (empty result) instead of the
451
+ // old falsy-collapse to 10; KnowledgeGraphManager normalises non-finite limits
452
+ // to undefined before they reach this method.
453
+ const rawLimit = options.limit ?? 10;
432
454
  const parameters = {
433
455
  query: `(?i).*${query}.*`, // Case-insensitive regex pattern
434
456
  limit: neo4j.int(Math.floor(rawLimit)),
@@ -2030,8 +2052,10 @@ export class Neo4jStorageProvider {
2030
2052
  timestamp: Date.now(),
2031
2053
  method: 'vectorOnly',
2032
2054
  });
2033
- const searchLimit = Math.floor(options.limit || 10);
2034
- const minSimilarity = options.minSimilarity || 0.6;
2055
+ // ?? (not ||) so an explicit limit of 0 stays 0 instead of widening to 10
2056
+ const searchLimit = Math.floor(options.limit ?? 10);
2057
+ // Default 0 (no similarity floor) — `??` so an explicit 0 is honoured
2058
+ const minSimilarity = options.minSimilarity ?? 0;
2035
2059
  diagnostics.stepsTaken.push({
2036
2060
  step: 'vectorSearch',
2037
2061
  timestamp: Date.now(),
@@ -2165,8 +2189,9 @@ export class Neo4jStorageProvider {
2165
2189
  // Continue with original vector results on error
2166
2190
  }
2167
2191
  }
2168
- // Get related relations for final entities
2169
- const finalGraph = await this.openNodes(finalEntityNames);
2192
+ // Get related relations for final entities, re-applying the
2193
+ // ranked order (openNodes does not preserve it) before caching
2194
+ const finalGraph = this.reorderEntitiesByRank(await this.openNodes(finalEntityNames), finalEntityNames);
2170
2195
  diagnostics.endTime = Date.now();
2171
2196
  diagnostics.totalTimeTaken = diagnostics.endTime - diagnostics.startTime;
2172
2197
  // Prepare result and cache it
@@ -2263,7 +2288,9 @@ export class Neo4jStorageProvider {
2263
2288
  status: 'started',
2264
2289
  entityNames,
2265
2290
  });
2266
- const finalGraph = await this.openNodes(entityNames);
2291
+ // Hydrate, then re-apply the ranked order (openNodes does not
2292
+ // preserve it) before caching
2293
+ const finalGraph = this.reorderEntitiesByRank(await this.openNodes(entityNames), entityNames);
2267
2294
  diagnostics.stepsTaken.push({
2268
2295
  step: 'openNodes',
2269
2296
  timestamp: Date.now(),
@@ -2288,7 +2315,7 @@ export class Neo4jStorageProvider {
2288
2315
  method: 'textOnly',
2289
2316
  reason: 'No query vector available',
2290
2317
  });
2291
- const textSearchLimit = Math.floor(options.limit || 10);
2318
+ const textSearchLimit = Math.floor(options.limit ?? 10);
2292
2319
  diagnostics.stepsTaken.push({
2293
2320
  step: 'textSearch',
2294
2321
  timestamp: Date.now(),