mcp-rag-memory 2.4.1 → 2.6.0

package/dist/rag/pipeline.js

@@ -4,20 +4,53 @@ import { contentHash, getDB, newId, nowMs, packVector } from "../db/database.js"
 import { chunkText } from "./chunker.js";
 import { embedText } from "./embeddings.js";
 import { searchChunks, vectorSearch, invalidateVectorCache } from "./vector-search.js";
-/** Insert a FTS row, tolerating an unavailable FTS5 backend. */
-function insertFtsRow(docId, rowid, text) {
+let ftsWarned = false;
+/** Insert a FTS row. Only a genuinely missing FTS5 backend degrades silently —
+ * any other failure (disk full, corruption, SQLITE_BUSY) must surface, because
+ * swallowing it left every chunk permanently invisible to the keyword leg with
+ * no diagnostic and no rebuild path. */
+function insertFtsRow(rowid, text) {
     try {
         getDB().prepare("INSERT INTO chunks_fts(rowid, content) VALUES (?, ?)").run(rowid, text);
     }
-    catch {
-        // FTS missing — hybrid degrades to vector-only.
+    catch (e) {
+        const msg = e.message;
+        // Match only "the FTS table is not there". A looser /chunks_fts/ test also
+        // swallowed UNIQUE and corruption errors, which are exactly the failures
+        // this change exists to surface.
+        if (!/no such table: chunks_fts|no such module: fts5/i.test(msg))
+            throw e;
+        if (!ftsWarned) {
+            ftsWarned = true;
+            process.stderr.write("rag: chunks_fts unavailable — hybrid search degraded to vector-only\n");
+        }
     }
 }
+/** SQLite UNIQUE violation, which node:sqlite surfaces as errcode 2067. */
+function isUniqueViolation(e, column) {
+    const err = e;
+    const msg = err?.message ?? "";
+    // "." must be escaped or it matches any character.
+    return err?.errcode === 2067 || msg.includes(`UNIQUE constraint failed: ${column}`);
+}
+/** Max content accepted from a tool call or CLI, so one payload cannot stall the server for a minute. */
+export const MAX_INGEST_CHARS = 1_000_000;
 export async function ingestText(content, title, opts = {}) {
     const db = getDB();
     const ts = nowMs();
-    // Content-hash dedup: identical documents are never re-embedded.
-    const hash = contentHash(content);
+    // trim(): whitespace-only content produced a permanent 0-chunk document that
+    // could never be searched yet still occupied the content_hash unique index.
+    if (typeof content !== "string" || content.trim().length === 0) {
+        throw new Error("Ingest content must be a non-empty string");
+    }
+    if (content.length > MAX_INGEST_CHARS) {
+        throw new Error(`Ingest content too large (${content.length} chars > limit ${MAX_INGEST_CHARS}). ` +
+            `Split it, or use ingest_file / ingest_dir for large sources.`);
+    }
+    // Content-hash dedup: identical documents are never re-embedded. `dedupScope`
+    // keeps sources that legitimately repeat the same text apart (e.g. "ok" typed
+    // in two different sessions).
+    const hash = contentHash(`${opts.dedupScope ? `${opts.dedupScope}\u0000` : ""}${content}`);
     const existing = db
         .prepare("SELECT id, title, chunk_count FROM documents WHERE content_hash = ?")
         .get(hash);
@@ -35,30 +68,102 @@ export async function ingestText(content, title, opts = {}) {
     }
     const docId = newId();
     const chunks = chunkText(content);
-    db.prepare(`INSERT INTO documents (id, title, source, content_type, metadata, content_hash, chunk_count, created_at, updated_at)
-     VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`).run(docId, title, opts.source ?? null, opts.contentType ?? "text", JSON.stringify(opts.metadata ?? {}), hash, chunks.length, ts, ts);
+    if (chunks.length === 0) {
+        throw new Error("Ingest produced no indexable content (no non-whitespace text)");
+    }
     let tokens = 0;
-    const insertChunk = db.prepare(`INSERT INTO chunks (id, doc_id, idx, content, embedding, token_count, created_at) VALUES (?, ?, ?, ?, ?, ?, ?)`);
+    // Embed BEFORE opening the transaction. The MCP SDK does not serialize tool
+    // calls, so awaiting inside a transaction let a concurrent request's writes
+    // join this one — and a failure here rolled back that other request's work.
+    // The yield keeps the event loop responsive: a 10 MB file is ~11k chunks and
+    // the local embedder is synchronous, so without it the stdio server could not
+    // answer any other tool call for the whole ingest.
+    const vectors = [];
     for (let i = 0; i < chunks.length; i++) {
-        const chunk = chunks[i];
-        const vec = await embedText(chunk.text);
-        tokens += chunk.tokenCount;
-        const res = insertChunk.run(newId(), docId, chunk.index, chunk.text, packVector(vec), chunk.tokenCount, ts);
-        insertFtsRow(docId, Number(res.lastInsertRowid), chunk.text);
+        vectors.push(await embedText(chunks[i].text));
+        if ((i & 15) === 15)
+            await new Promise((resolve) => setImmediate(resolve));
+    }
+    // All writes for one document are atomic, and the block below is fully
+    // synchronous, so no other request can interleave inside it.
+    db.exec("BEGIN IMMEDIATE;");
+    try {
+        db.prepare(`INSERT INTO documents (id, title, source, content_type, metadata, content_hash, chunk_count, created_at, updated_at)
+       VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`).run(docId, title, opts.source ?? null, opts.contentType ?? "text", JSON.stringify(opts.metadata ?? {}), hash, chunks.length, ts, ts);
+        const insertChunk = db.prepare(`INSERT INTO chunks (id, doc_id, idx, content, embedding, token_count, created_at) VALUES (?, ?, ?, ?, ?, ?, ?)`);
+        for (let i = 0; i < chunks.length; i++) {
+            const chunk = chunks[i];
+            tokens += chunk.tokenCount;
+            const res = insertChunk.run(newId(), docId, chunk.index, chunk.text, packVector(vectors[i]), chunk.tokenCount, ts);
+            insertFtsRow(Number(res.lastInsertRowid), chunk.text);
+        }
+        db.exec("COMMIT;");
+    }
+    catch (e) {
+        try {
+            db.exec("ROLLBACK;");
+        }
+        catch {
+            /* transaction already closed */
+        }
+        // Two identical ingests can both pass the dedup SELECT above: the check and
+        // this INSERT are separated by chunking + embedding, and MCP tool calls are
+        // not serialized. Let the unique index arbitrate and report a dedup hit
+        // rather than failing the caller with a raw driver error.
+        if (isUniqueViolation(e, "documents.content_hash")) {
+            const again = getDB()
+                .prepare("SELECT id, title, chunk_count FROM documents WHERE content_hash = ?")
+                .get(hash);
+            if (again) {
+                return {
+                    docId: again.id,
+                    title: again.title,
+                    chunks: again.chunk_count,
+                    tokens: 0,
+                    deduplicated: true,
+                };
+            }
+        }
+        throw e;
     }
     invalidateVectorCache();
     return { docId, title, chunks: chunks.length, tokens, deduplicated: false };
 }
-function assertAllowedPath(abs) {
+/** Roots are realpath'd too, so a junction/symlinked allowlist entry still matches. */
+function allowedRoots() {
     const raw = process.env.RAG_ALLOWED_DIRS;
     if (!raw)
-        return;
-    const roots = raw
+        return [];
+    return raw
         .split(/[;|,]/)
-        .map((p) => path.resolve(p.trim()))
-        .filter(Boolean);
-    if (roots.length === 0)
+        .map((p) => p.trim())
+        .filter(Boolean)
+        .map((p) => {
+        const abs = path.resolve(p);
+        try {
+            return fs.realpathSync(abs);
+        }
+        catch {
+            return abs;
+        }
+    });
+}
+let warnedOpenAllowlist = false;
+/**
+ * RAG_ALLOWED_DIRS is opt-in, so by default any readable path can be ingested
+ * and then stays retrievable from every future session sharing this store. Warn
+ * once instead of silently widening the blast radius of an agent-driven tool.
+ */
+function assertAllowedPath(abs) {
+    const roots = allowedRoots();
+    if (roots.length === 0) {
+        if (!warnedOpenAllowlist) {
+            warnedOpenAllowlist = true;
+            process.stderr.write("rag: RAG_ALLOWED_DIRS is not set — any readable path can be ingested and stays " +
+                `retrievable from this store. Set RAG_ALLOWED_DIRS to restrict it.\n`);
+        }
         return;
+    }
     const real = fs.realpathSync(abs);
     if (!roots.some((r) => real === r || real.startsWith(r + path.sep))) {
         throw new Error(`Path not allowed by RAG_ALLOWED_DIRS: ${abs}`);
@@ -71,7 +176,8 @@ export async function ingestFile(filePath, opts = {}) {
     const st = fs.statSync(abs);
     if (!st.isFile())
         throw new Error(`Not a file: ${abs}`);
-    const maxMb = Number(process.env.RAG_MAX_FILE_MB ?? 10);
+    const maxMbRaw = Number(process.env.RAG_MAX_FILE_MB ?? 10);
+    const maxMb = Number.isFinite(maxMbRaw) && maxMbRaw > 0 ? maxMbRaw : 10;
     const maxBytes = Math.max(1024, Math.floor(maxMb * 1024 * 1024));
     if (st.size > maxBytes) {
         throw new Error(`File too large (${st.size} bytes > limit ${maxBytes}): ${abs}. Raise RAG_MAX_FILE_MB to allow bigger files.`);
@@ -79,25 +185,53 @@ export async function ingestFile(filePath, opts = {}) {
     assertAllowedPath(abs);
     const content = fs.readFileSync(abs, "utf-8");
     const title = path.basename(abs);
-    return ingestText(content, title, {
+    return ingestText(stripBom(content), title, {
         source: abs,
         contentType: opts.contentType ?? guessContentType(abs),
         metadata: opts.metadata ?? { path: abs },
     });
 }
+/**
+ * Drop a UTF-8 BOM. It survives readFileSync as U+FEFF, so a Windows-authored
+ * .md file's first heading indexed as "\ufeff# Title" — the FTS trigram tokenizer
+ * keyed on it and the title never matched a plain "Title" query.
+ */
+function stripBom(text) {
+    return text.charCodeAt(0) === 0xfeff ? text.slice(1) : text;
+}
 /** Let the event loop breathe every N files during large directory ingests. */
 function yieldLoop() {
     return new Promise((resolve) => setImmediate(resolve));
 }
+/** Cap the payload: a big directory must not return one line per file. */
+const DIR_REPORT_LIMIT = 50;
+/**
+ * Hard ceiling on files actually ingested. DIR_REPORT_LIMIT only truncated the
+ * response, so pointing this at a large tree still embedded every file and held
+ * the server hostage; the cap is reported explicitly instead of silently
+ * dropping the remainder.
+ */
+const DIR_MAX_FILES = 500;
 export async function ingestDirectory(dirPath, opts = {}) {
     const root = path.resolve(dirPath);
     if (!fs.existsSync(root) || !fs.statSync(root).isDirectory()) {
         throw new Error(`Not a directory: ${dirPath}`);
     }
     assertAllowedPath(root);
-    const exts = opts.extensions?.map((e) => (e.startsWith(".") ? e : `.${e}`)) ?? [
+    if (opts.extensions !== undefined) {
+        if (opts.extensions.length === 0)
+            throw new Error("extensions must not be empty");
+        for (const e of opts.extensions) {
+            if (typeof e !== "string" || e.trim() === "")
+                throw new Error(`Invalid extension: ${JSON.stringify(e)}`);
+        }
+    }
+    // Lowercase once: `full.endsWith(e)` is case-sensitive, so an explicit
+    // extensions: [".TS"] silently matched nothing on a Windows-authored tree
+    // (or a request for ".Md" against README.MD).
+    const exts = (opts.extensions?.map((e) => (e.startsWith(".") ? e : `.${e}`)) ?? [
         ".ts", ".tsx", ".js", ".jsx", ".json", ".md", ".txt", ".py", ".go", ".rs", ".java", ".c", ".h", ".cpp", ".html", ".css",
-    ];
+    ]).map((e) => e.toLowerCase());
     const skipDirs = new Set([".git", "dist", "node_modules", ".rag-data", ".test-data", ".venv"]);
     const files = [];
     const walk = (dir) => {
@@ -107,26 +241,44 @@ export async function ingestDirectory(dirPath, opts = {}) {
                 if (opts.recursive && !skipDirs.has(entry.name) && !entry.name.startsWith("."))
                     walk(full);
             }
-            else if (entry.isFile() && exts.some((e) => full.endsWith(e))) {
+            else if (entry.isFile() && exts.some((e) => full.toLowerCase().endsWith(e))) {
                 files.push(full);
             }
         }
     };
     walk(root);
+    // Deterministic slice before any work: walk() order is filesystem-dependent,
+    // so capping after sorting keeps "which 500" reproducible across machines.
+    const sorted = files.sort();
+    const truncated = Math.max(0, sorted.length - DIR_MAX_FILES);
+    const targets = truncated > 0 ? sorted.slice(0, DIR_MAX_FILES) : sorted;
     const ingested = [];
     const skipped = [];
-    for (let i = 0; i < files.sort().length; i++) {
-        const f = files[i];
+    let ingestedCount = 0;
+    let skippedCount = 0;
+    for (let i = 0; i < targets.length; i++) {
+        const f = targets[i];
         try {
-            ingested.push(await ingestFile(f, { metadata: opts.metadata ?? { ingestDir: root } }));
+            const res = await ingestFile(f, { metadata: opts.metadata ?? { ingestDir: root } });
+            ingestedCount++;
+            if (ingested.length < DIR_REPORT_LIMIT)
+                ingested.push(res);
         }
         catch (e) {
-            skipped.push(`${f} (${e.message})`);
+            skippedCount++;
+            if (skipped.length < DIR_REPORT_LIMIT)
+                skipped.push(`${f} (${e.message})`);
         }
         if (i % 10 === 9)
             await yieldLoop();
     }
-    return { ingested, skipped };
+    if (truncated > 0) {
+        skippedCount += truncated;
+        if (skipped.length < DIR_REPORT_LIMIT) {
+            skipped.push(`${truncated} more file(s) matched but were not ingested: directory ingest is capped at ${DIR_MAX_FILES} per call`);
+        }
+    }
+    return { ingested, skipped, ingestedCount, skippedCount };
 }
 export async function searchDocs(query, topK = 10, minScore = 0.08, filters) {
     const q = await embedText(query);
@@ -146,19 +298,40 @@ export async function retrieve(query, topK = 6, minScore = 0.08, filters) {
         totalTokens: withTokens.reduce((acc, c) => acc + c.tokenCount, 0),
     };
 }
-export function listDocuments() {
+/** Bounded by default: a big store would otherwise dump every row into one tool result. */
+export const LIST_DOCS_DEFAULT = 100;
+export const LIST_DOCS_MAX = 1000;
+export function listDocuments(opts = {}) {
     const db = getDB();
+    const limit = Math.min(Math.max(Math.trunc(opts.limit ?? LIST_DOCS_DEFAULT), 1), LIST_DOCS_MAX);
+    const offset = Math.max(Math.trunc(opts.offset ?? 0), 0);
+    const total = db.prepare("SELECT COUNT(*) AS c FROM documents").get().c;
     const rows = db
-        .prepare(`SELECT id, title, source, content_type, chunk_count, created_at, updated_at, metadata FROM documents ORDER BY updated_at DESC`)
-        .all();
-    return rows;
+        .prepare(`SELECT id, title, source, content_type, chunk_count, created_at, updated_at, metadata
+         FROM documents ORDER BY updated_at DESC LIMIT ? OFFSET ?`)
+        .all(limit, offset);
+    return { documents: rows, total, limit, offset };
 }
 export function deleteDocument(docId) {
     const db = getDB();
-    db.prepare("DELETE FROM chunks_fts WHERE rowid IN (SELECT rowid FROM chunks WHERE doc_id = ?)").run(docId);
-    const res = db.prepare("DELETE FROM documents WHERE id = ?").run(docId);
+    db.exec("BEGIN IMMEDIATE;");
+    let changes = 0;
+    try {
+        db.prepare("DELETE FROM chunks_fts WHERE rowid IN (SELECT rowid FROM chunks WHERE doc_id = ?)").run(docId);
+        changes = Number(db.prepare("DELETE FROM documents WHERE id = ?").run(docId).changes);
+        db.exec("COMMIT;");
+    }
+    catch (e) {
+        try {
+            db.exec("ROLLBACK;");
+        }
+        catch {
+            /* transaction already closed */
+        }
+        throw e;
+    }
     invalidateVectorCache();
-    return { deleted: Number(res.changes) > 0 };
+    return { deleted: changes > 0 };
 }
 export function documentStats() {
     const db = getDB();

package/dist/rag/pipeline.js.map

@@ -1 +1 @@
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package/dist/rag/vector-search.d.ts

@@ -19,6 +19,9 @@ export interface SearchOptions {
     topK?: number;
     minScore?: number;
     collection?: "chunks" | "memories";
+    onlyKeys?: Set<string>;
+    /** Restrict to chunks of these documents (cheap: doc ids, not chunk ids). */
+    onlyDocIds?: Set<string>;
 }
 export declare function invalidateVectorCache(): void;
 /** Brute-force vector search over stored vectors (uses the in-memory cache). */
@@ -37,8 +40,12 @@ export interface SearchChunkOptions {
     filters?: SearchChunkFilters;
 }
 /**
- * Hybrid search: FTS5 BM25 keyword + vector, fused with RRF.
+ * Hybrid search: FTS5 BM25 keyword + vector, fused with RRF for ranking.
  * Controlled by SEARCH_MODE=hybrid|vector|keyword (default hybrid).
+ *
+ * The reported `score` is always on a 0..1 relevance scale — the vector cosine
+ * when the chunk has one, otherwise a rank-decayed keyword score — so `minScore`
+ * means the same thing in every mode (RRF only decides the order).
  */
 export declare function searchChunks(queryVec: Float64Array, opts: SearchChunkOptions): SearchHit[];
 //# sourceMappingURL=vector-search.d.ts.map

package/dist/rag/vector-search.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"vector-search.d.ts","sourceRoot":"","sources":["../../src/rag/vector-search.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,QAAQ;IACvB,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,EAAE,MAAM,CAAC;IACf,GAAG,EAAE,MAAM,CAAC;IACZ,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,UAAU,GAAG,IAAI,CAAC;IAC7B,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,SAAS;IACxB,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,aAAa;IAC5B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,QAAQ,GAAG,UAAU,CAAC;IACnC,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACvB,6EAA6E;IAC7E,UAAU,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;CAC1B;AAmBD,wBAAgB,qBAAqB,IAAI,IAAI,CAM5C;AA+DD,gFAAgF;AAChF,wBAAgB,YAAY,CAC1B,QAAQ,EAAE,YAAY,EACtB,OAAO,GAAE,aAAkB,GAC1B,KAAK,CAAC;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,CAuBvC;AAoED,MAAM,WAAW,kBAAkB;IACjC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,kBAAkB;IACjC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,kBAAkB,CAAC;CAC9B;AAED;;;;;;;GAOG;AACH,wBAAgB,YAAY,CAAC,QAAQ,EAAE,YAAY,EAAE,IAAI,EAAE,kBAAkB,GAAG,SAAS,EAAE,CAgG1F"}