knowledge-mcp-server 1.0.0

package/dist/embeddings.js

@@ -0,0 +1,534 @@
+import { readFileSync, existsSync } from "node:fs";
+import { writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import { log } from "./logger.js";
+export function loadEmbeddings(knowledgeDir) {
+    const embeddingsPath = join(knowledgeDir, ".embeddings.json");
+    if (!existsSync(embeddingsPath)) {
+        return { vectors: new Map(), available: false };
+    }
+    try {
+        const raw = JSON.parse(readFileSync(embeddingsPath, "utf-8"));
+        const vectors = new Map(Object.entries(raw));
+        return { vectors, available: vectors.size > 0 };
+    }
+    catch {
+        return { vectors: new Map(), available: false };
+    }
+}
+export function cosineSimilarity(a, b) {
+    let dot = 0;
+    let normA = 0;
+    let normB = 0;
+    for (let i = 0; i < a.length; i++) {
+        dot += a[i] * b[i];
+        normA += a[i] * a[i];
+        normB += b[i] * b[i];
+    }
+    const denom = Math.sqrt(normA) * Math.sqrt(normB);
+    return denom === 0 ? 0 : dot / denom;
+}
+// --- Query embedding LRU cache (256 entries, ~512KB) ---
+const CACHE_MAX = 256;
+const queryCache = new Map();
+function normalizeQuery(q) {
+    return q.toLowerCase().trim().replace(/\s+/g, " ");
+}
+// --- Exponential backoff for Voyage API failures ---
+let backoffUntil = 0;
+let backoffMs = 0;
+const BACKOFF_MAX = 60_000;
+export async function embedQuery(query) {
+    const apiKey = process.env.VOYAGE_API_KEY;
+    if (!apiKey)
+        return null;
+    const key = normalizeQuery(query);
+    const cached = queryCache.get(key);
+    if (cached) {
+        // Move to end (most recently used)
+        queryCache.delete(key);
+        queryCache.set(key, cached);
+        return cached;
+    }
+    // Check backoff
+    if (Date.now() < backoffUntil) {
+        log.debug("embed_query_backoff", { remainingMs: backoffUntil - Date.now() });
+        return null;
+    }
+    try {
+        const response = await fetch("https://api.voyageai.com/v1/embeddings", {
+            method: "POST",
+            headers: {
+                "Content-Type": "application/json",
+                Authorization: `Bearer ${apiKey}`,
+            },
+            body: JSON.stringify({
+                model: "voyage-3-lite",
+                input: [query],
+                input_type: "query",
+            }),
+        });
+        if (!response.ok) {
+            log.warn("embed_query_failed", { status: response.status, statusText: response.statusText });
+            backoffMs = Math.min(backoffMs === 0 ? 1000 : backoffMs * 2, BACKOFF_MAX);
+            backoffUntil = Date.now() + backoffMs;
+            return null;
+        }
+        // Reset backoff on success
+        backoffMs = 0;
+        backoffUntil = 0;
+        const data = (await response.json());
+        const vector = data.data[0]?.embedding ?? null;
+        if (vector) {
+            // Evict oldest if at capacity
+            if (queryCache.size >= CACHE_MAX) {
+                const oldest = queryCache.keys().next().value;
+                queryCache.delete(oldest);
+            }
+            queryCache.set(key, vector);
+        }
+        return vector;
+    }
+    catch (err) {
+        log.warn("embed_query_error", { error: String(err) });
+        backoffMs = Math.min(backoffMs === 0 ? 1000 : backoffMs * 2, BACKOFF_MAX);
+        backoffUntil = Date.now() + backoffMs;
+        return null;
+    }
+}
+// --- Lightweight suffix stemmer (~18 rules, no dependencies) ---
+function stem(word) {
+    if (word.length < 4)
+        return word;
+    const rules = [
+        ["ization", "ize"],
+        ["ational", "ate"],
+        ["iveness", "ive"],
+        ["encies", "ency"],
+        ["ation", "ate"],
+        ["ness", ""],
+        ["ment", ""],
+        ["able", ""],
+        ["ible", ""],
+        ["ling", "le"],
+        ["ies", "y"],
+        ["ive", ""],
+        ["ing", ""],
+        ["ion", ""],
+        ["ed", ""],
+        ["ly", ""],
+        ["er", ""],
+        ["s", ""],
+    ];
+    for (const [suffix, replacement] of rules) {
+        if (word.endsWith(suffix)) {
+            const base = word.slice(0, -suffix.length) + replacement;
+            if (base.length >= 3)
+                return base;
+        }
+    }
+    return word;
+}
+// --- Stopword set (filtered during BM25 tokenization, not embedding text) ---
+const STOPWORDS = new Set([
+    "a",
+    "about",
+    "above",
+    "after",
+    "again",
+    "against",
+    "all",
+    "am",
+    "an",
+    "and",
+    "any",
+    "are",
+    "aren't",
+    "as",
+    "at",
+    "be",
+    "because",
+    "been",
+    "before",
+    "being",
+    "below",
+    "between",
+    "both",
+    "but",
+    "by",
+    "can",
+    "can't",
+    "cannot",
+    "could",
+    "couldn't",
+    "did",
+    "didn't",
+    "do",
+    "does",
+    "doesn't",
+    "doing",
+    "don't",
+    "down",
+    "during",
+    "each",
+    "few",
+    "for",
+    "from",
+    "further",
+    "get",
+    "got",
+    "had",
+    "hadn't",
+    "has",
+    "hasn't",
+    "have",
+    "haven't",
+    "having",
+    "he",
+    "he'd",
+    "he'll",
+    "he's",
+    "her",
+    "here",
+    "here's",
+    "hers",
+    "herself",
+    "him",
+    "himself",
+    "his",
+    "how",
+    "how's",
+    "if",
+    "in",
+    "into",
+    "is",
+    "isn't",
+    "it",
+    "it's",
+    "its",
+    "itself",
+    "let's",
+    "me",
+    "might",
+    "more",
+    "most",
+    "mustn't",
+    "my",
+    "myself",
+    "no",
+    "nor",
+    "not",
+    "of",
+    "off",
+    "on",
+    "once",
+    "only",
+    "or",
+    "other",
+    "ought",
+    "our",
+    "ours",
+    "ourselves",
+    "out",
+    "over",
+    "own",
+    "same",
+    "shan't",
+    "she",
+    "she'd",
+    "she'll",
+    "she's",
+    "should",
+    "shouldn't",
+    "so",
+    "some",
+    "such",
+    "than",
+    "that",
+    "that's",
+    "the",
+    "their",
+    "theirs",
+    "them",
+    "themselves",
+    "then",
+    "there",
+    "there's",
+    "these",
+    "they",
+    "they'd",
+    "they'll",
+    "they're",
+    "they've",
+    "this",
+    "those",
+    "through",
+    "to",
+    "too",
+    "under",
+    "until",
+    "up",
+    "us",
+    "very",
+    "was",
+    "wasn't",
+    "we",
+    "we'd",
+    "we'll",
+    "we're",
+    "we've",
+    "were",
+    "weren't",
+    "what",
+    "what's",
+    "when",
+    "when's",
+    "where",
+    "where's",
+    "which",
+    "while",
+    "who",
+    "who's",
+    "whom",
+    "why",
+    "why's",
+    "will",
+    "with",
+    "won't",
+    "would",
+    "wouldn't",
+    "you",
+    "you'd",
+    "you'll",
+    "you're",
+    "you've",
+    "your",
+    "yours",
+    "yourself",
+    "yourselves",
+]);
+// --- Tokenizer (preserves compound terms, adds stems alongside originals) ---
+export function tokenize(text) {
+    const lower = text.toLowerCase();
+    const tokens = [];
+    // Extract compound terms before stripping special chars (e.g., c++, c#)
+    const compoundRegex = /[a-z][a-z0-9]*\+\+|[a-z]#/g;
+    let match;
+    while ((match = compoundRegex.exec(lower)) !== null) {
+        tokens.push(match[0]);
+    }
+    // Standard tokenization (preserve hyphens for compound words like tf-idf)
+    const standard = lower
+        .replace(/[^a-z0-9\s-]/g, " ")
+        .split(/\s+/)
+        .filter((t) => t.length > 1);
+    for (const token of standard) {
+        if (STOPWORDS.has(token))
+            continue;
+        tokens.push(token);
+        const stemmed = stem(token);
+        if (stemmed !== token) {
+            tokens.push(stemmed);
+        }
+    }
+    return tokens;
+}
+function computeIdf(docFreq, docCount) {
+    const idf = new Map();
+    for (const [term, df] of docFreq) {
+        // Standard BM25 IDF: log((N - df + 0.5) / (df + 0.5) + 1)
+        idf.set(term, Math.log((docCount - df + 0.5) / (df + 0.5) + 1));
+    }
+    return idf;
+}
+export function buildTfIdfIndex(docs) {
+    const docTermFreqs = new Map();
+    const docFreq = new Map();
+    const docLengths = new Map();
+    const docCount = docs.size;
+    let totalLength = 0;
+    for (const doc of docs.values()) {
+        // Title tokens 3x, tag tokens 2x, body 1x for field boosting
+        const text = buildBoostedText(doc);
+        const tokens = tokenize(text);
+        const termFreq = new Map();
+        const seenTerms = new Set();
+        for (const token of tokens) {
+            termFreq.set(token, (termFreq.get(token) || 0) + 1);
+            if (!seenTerms.has(token)) {
+                seenTerms.add(token);
+                docFreq.set(token, (docFreq.get(token) || 0) + 1);
+            }
+        }
+        // Store raw term counts (no normalization — BM25 handles length internally)
+        docTermFreqs.set(doc.id, termFreq);
+        docLengths.set(doc.id, tokens.length);
+        totalLength += tokens.length;
+    }
+    const avgDocLength = docCount > 0 ? totalLength / docCount : 0;
+    const idf = computeIdf(docFreq, docCount);
+    return { docTermFreqs, docFreq, idf, docLengths, avgDocLength, docCount };
+}
+// --- Field boosting: title 3x, tags 2x, body 1x ---
+function buildBoostedText(doc) {
+    const title = doc.title;
+    const tags = doc.tags.join(" ");
+    return `${title} ${title} ${title} ${tags} ${tags} ${doc.contentBody}`;
+}
+// BM25 scoring constants
+const BM25_K1 = 1.2;
+const BM25_B = 0.75;
+export function bm25Score(query, docId, index) {
+    const queryTokens = tokenize(query);
+    const docTerms = index.docTermFreqs.get(docId);
+    if (!docTerms)
+        return 0;
+    const docLen = index.docLengths.get(docId) || 0;
+    let score = 0;
+    for (const token of queryTokens) {
+        const tf = docTerms.get(token) || 0;
+        const idf = index.idf.get(token) || 0;
+        if (tf === 0 || idf === 0)
+            continue;
+        // BM25: IDF * (tf * (k1 + 1)) / (tf + k1 * (1 - b + b * docLen / avgDocLen))
+        const numerator = tf * (BM25_K1 + 1);
+        const denominator = tf + BM25_K1 * (1 - BM25_B + (BM25_B * docLen) / (index.avgDocLength || 1));
+        score += idf * (numerator / denominator);
+    }
+    return score;
+}
+/** @deprecated Use bm25Score — kept for backward compatibility */
+export const tfidfScore = bm25Score;
+// --- Incremental Index Updates ---
+export function updateBm25Index(index, docId, doc) {
+    // Remove old document if it exists in the index
+    const oldTermFreqs = index.docTermFreqs.get(docId);
+    if (oldTermFreqs) {
+        const oldLength = index.docLengths.get(docId) || 0;
+        // Decrement document frequencies for each term
+        for (const term of oldTermFreqs.keys()) {
+            const df = index.docFreq.get(term);
+            if (df !== undefined) {
+                if (df <= 1) {
+                    index.docFreq.delete(term);
+                }
+                else {
+                    index.docFreq.set(term, df - 1);
+                }
+            }
+        }
+        index.docTermFreqs.delete(docId);
+        index.docLengths.delete(docId);
+        index.docCount--;
+        // Recalculate average document length
+        const totalLength = index.avgDocLength * (index.docCount + 1) - oldLength;
+        index.avgDocLength = index.docCount > 0 ? totalLength / index.docCount : 0;
+    }
+    // Add new document if provided
+    if (doc) {
+        const text = buildBoostedText(doc);
+        const tokens = tokenize(text);
+        const termFreq = new Map();
+        const seenTerms = new Set();
+        for (const token of tokens) {
+            termFreq.set(token, (termFreq.get(token) || 0) + 1);
+            if (!seenTerms.has(token)) {
+                seenTerms.add(token);
+                index.docFreq.set(token, (index.docFreq.get(token) || 0) + 1);
+            }
+        }
+        index.docTermFreqs.set(docId, termFreq);
+        index.docLengths.set(docId, tokens.length);
+        // Recalculate average document length
+        const totalLength = index.avgDocLength * index.docCount + tokens.length;
+        index.docCount++;
+        index.avgDocLength = totalLength / index.docCount;
+    }
+    // Rebuild IDF (fast — just iterates the docFreq map)
+    index.idf = computeIdf(index.docFreq, index.docCount);
+}
+// --- Inline Embedding ---
+export async function embedSingleDocument(embeddingsStore, knowledgeDir, doc) {
+    const apiKey = process.env.VOYAGE_API_KEY;
+    if (!apiKey)
+        return;
+    // Respect backoff for document embedding too
+    if (Date.now() < backoffUntil)
+        return;
+    try {
+        const text = `${doc.title}\n${doc.tags.join(", ")}\n${doc.contentBody}`;
+        const response = await fetch("https://api.voyageai.com/v1/embeddings", {
+            method: "POST",
+            headers: {
+                "Content-Type": "application/json",
+                Authorization: `Bearer ${apiKey}`,
+            },
+            body: JSON.stringify({
+                model: "voyage-3-lite",
+                input: [text],
+                input_type: "document",
+            }),
+        });
+        if (!response.ok) {
+            log.warn("embed_doc_failed", { id: doc.id, status: response.status });
+            backoffMs = Math.min(backoffMs === 0 ? 1000 : backoffMs * 2, BACKOFF_MAX);
+            backoffUntil = Date.now() + backoffMs;
+            return;
+        }
+        backoffMs = 0;
+        backoffUntil = 0;
+        const data = (await response.json());
+        const vector = data.data[0]?.embedding;
+        if (!vector)
+            return;
+        embeddingsStore.vectors.set(doc.id, vector);
+        embeddingsStore.available = true;
+        persistEmbeddings(embeddingsStore, knowledgeDir);
+        log.debug("embed_doc", { id: doc.id });
+    }
+    catch (err) {
+        log.warn("embed_doc_error", { id: doc.id, error: String(err) });
+        backoffMs = Math.min(backoffMs === 0 ? 1000 : backoffMs * 2, BACKOFF_MAX);
+        backoffUntil = Date.now() + backoffMs;
+    }
+}
+export function removeEmbedding(embeddingsStore, knowledgeDir, docId) {
+    if (embeddingsStore.vectors.delete(docId)) {
+        embeddingsStore.available = embeddingsStore.vectors.size > 0;
+        persistEmbeddings(embeddingsStore, knowledgeDir);
+    }
+}
+// --- Debounced async embedding persistence ---
+let pendingFlush = null;
+let debounceTimer = null;
+async function flushEmbeddings() {
+    if (!pendingFlush)
+        return;
+    const { store, knowledgeDir } = pendingFlush;
+    pendingFlush = null;
+    try {
+        const embeddingsPath = join(knowledgeDir, ".embeddings.json");
+        const obj = {};
+        for (const [id, vec] of store.vectors) {
+            obj[id] = vec;
+        }
+        await writeFile(embeddingsPath, JSON.stringify(obj), "utf-8");
+    }
+    catch {
+        // Best-effort persistence
+    }
+}
+function persistEmbeddings(store, knowledgeDir) {
+    pendingFlush = { store, knowledgeDir };
+    if (debounceTimer)
+        clearTimeout(debounceTimer);
+    debounceTimer = setTimeout(() => {
+        debounceTimer = null;
+        flushEmbeddings();
+    }, 5000);
+}
+// Flush on process exit
+process.on("beforeExit", () => {
+    flushEmbeddings();
+});
+//# sourceMappingURL=embeddings.js.map

package/dist/embeddings.js.map

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package/dist/formatter.d.ts

@@ -0,0 +1,51 @@
+import type { KnowledgeDocument } from "./loader.js";
+export type DetailLevel = "summary" | "normal" | "full";
+interface FormattedDoc {
+    doc: KnowledgeDocument;
+    relevance: "primary" | "ancestor" | "graph-expanded";
+    similarity?: number;
+    matchedOn?: string;
+    scoringMethod?: string;
+    expandedFrom?: string;
+}
+export interface FacetCounts {
+    domains: Map<string, number>;
+    types: Map<string, number>;
+    phases: Map<string, number>;
+}
+export declare function formatSearchResults(query: string, results: FormattedDoc[], detailLevel?: DetailLevel, searchMethod?: string, facets?: FacetCounts): string;
+export declare function formatLookupResult(doc: KnowledgeDocument, ancestors: KnowledgeDocument[], related: KnowledgeDocument[], contentLevel?: "full" | "summary"): string;
+export declare function formatGraphResult(nodes: Array<{
+    id: string;
+    title: string;
+    type: string;
+    domain: string;
+    wordCount: number;
+    childrenCount: number;
+}>, edges: Array<{
+    source: string;
+    target: string;
+    type: "child" | "related";
+}>, totalDocs: number, rootId: string): string;
+export declare function formatWriteResult(result: {
+    id: string;
+    filePath: string;
+    parentId: string | null;
+    status: "created" | "updated";
+    warnings?: string[];
+}): string;
+export declare function formatDeleteResult(result: {
+    id: string;
+    warnings: string[];
+}): string;
+export declare function formatListResult(docs: Array<{
+    id: string;
+    title: string;
+    type: string;
+    domain: string;
+    tags: string[];
+    wordCount: number;
+    status: string;
+    lastUpdated?: string;
+}>, totalDocs: number): string;
+export type { FormattedDoc };