feat: replace WASM embeddings with persistent chroma-mcp MCP connection (#1176)
* feat: replace WASM embeddings with persistent chroma-mcp MCP connection Replace ChromaServerManager (npx chroma run + chromadb npm + ONNX/WASM) with ChromaMcpManager, a singleton stdio MCP client that communicates with chroma-mcp via uvx. This eliminates native binary issues, segfaults, and WASM embedding failures that plagued cross-platform installs. Key changes: - Add ChromaMcpManager: singleton MCP client with lazy connect, auto-reconnect, connection lock, and Zscaler SSL cert support - Rewrite ChromaSync to use MCP tool calls instead of chromadb npm client - Handle chroma-mcp's non-JSON responses (plain text success/error messages) - Treat "collection already exists" as idempotent success - Wire ChromaMcpManager into GracefulShutdown for clean subprocess teardown - Delete ChromaServerManager (no longer needed) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: address PR review — connection guard leak, timer leak, async reset - Clear connecting guard in finally block to prevent permanent reconnection block - Clear timeout after successful connection to prevent timer leak - Make reset() async to await stop() before nullifying instance - Delete obsolete chroma-server-manager test (imports deleted class) - Update graceful-shutdown test to use chromaMcpManager property name Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: prevent chroma-mcp spawn storm — zombie cleanup, stale onclose guard, reconnect backoff Three bugs caused chroma-mcp processes to accumulate (92+ observed): 1. Zombie on timeout: failed connections left subprocess alive because only the timer was cleared, not the transport. Now catch block explicitly closes transport+client before rethrowing. 2. Stale onclose race: old transport's onclose handler captured `this` and overwrote the current connection reference after reconnect, orphaning the new subprocess. Now guarded with reference check. 3. No backoff: every failure triggered immediate reconnect. With backfill doing hundreds of MCP calls, this created rapid-fire spawning. Added 10s backoff on both connection failure and unexpected process death. Also includes ChromaSync fixes from PR review: - queryChroma deduplication now preserves index-aligned arrays - SQL injection guard on backfill ID exclusion lists Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
Alex Newman
+120
-245
@@ -1,26 +1,21 @@
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/**
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* ChromaSync Service
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*
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* Automatically syncs observations and session summaries to ChromaDB via HTTP.
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* Automatically syncs observations and session summaries to ChromaDB via MCP.
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* This service provides real-time semantic search capabilities by maintaining
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* a vector database synchronized with SQLite.
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*
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* Uses the chromadb npm package's built-in ChromaClient for HTTP connections.
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* Supports both local server (managed by ChromaServerManager) and remote/cloud
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* servers for future claude-mem pro features.
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* Uses ChromaMcpManager to communicate with chroma-mcp over stdio MCP protocol.
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* The chroma-mcp server handles its own embedding and persistent storage,
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* eliminating the need for chromadb npm package and ONNX/WASM dependencies.
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*
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* Design: Fail-fast with no fallbacks - if Chroma is unavailable, syncing fails.
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*/
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import { ChromaClient, Collection } from 'chromadb';
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import { ChromaMcpManager } from './ChromaMcpManager.js';
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import { ParsedObservation, ParsedSummary } from '../../sdk/parser.js';
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import { SessionStore } from '../sqlite/SessionStore.js';
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import { logger } from '../../utils/logger.js';
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import { SettingsDefaultsManager } from '../../shared/SettingsDefaultsManager.js';
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import { USER_SETTINGS_PATH } from '../../shared/paths.js';
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import { ChromaServerManager } from './ChromaServerManager.js';
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import path from 'path';
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import os from 'os';
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interface ChromaDocument {
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id: string;
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@@ -75,13 +70,10 @@ interface StoredUserPrompt {
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}
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export class ChromaSync {
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private chromaClient: ChromaClient | null = null;
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private collection: Collection | null = null;
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private project: string;
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private collectionName: string;
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private readonly VECTOR_DB_DIR: string;
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private collectionCreated = false;
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private readonly BATCH_SIZE = 100;
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private modelCacheCorruptionRetried = false;
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constructor(project: string) {
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this.project = project;
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@@ -91,146 +83,36 @@ export class ChromaSync {
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.replace(/[^a-zA-Z0-9._-]/g, '_')
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.replace(/[^a-zA-Z0-9]+$/, ''); // strip trailing non-alphanumeric
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this.collectionName = `cm__${sanitized || 'unknown'}`;
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this.VECTOR_DB_DIR = path.join(os.homedir(), '.claude-mem', 'vector-db');
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}
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/**
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* Ensure HTTP client is connected to Chroma server
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* In local mode, verifies ChromaServerManager has started the server
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* In remote mode, connects directly to configured host
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* Throws error if connection fails
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* Ensure collection exists in Chroma via MCP.
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* chroma_create_collection is idempotent - safe to call multiple times.
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* Uses collectionCreated flag to avoid redundant calls within a session.
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*/
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private async ensureConnection(): Promise<void> {
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if (this.chromaClient) {
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private async ensureCollectionExists(): Promise<void> {
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if (this.collectionCreated) {
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return;
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}
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logger.info('CHROMA_SYNC', 'Connecting to Chroma HTTP server...', { project: this.project });
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const chromaMcp = ChromaMcpManager.getInstance();
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try {
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const settings = SettingsDefaultsManager.loadFromFile(USER_SETTINGS_PATH);
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const mode = settings.CLAUDE_MEM_CHROMA_MODE || 'local';
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const host = settings.CLAUDE_MEM_CHROMA_HOST || '127.0.0.1';
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const port = parseInt(settings.CLAUDE_MEM_CHROMA_PORT || '8000', 10);
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const ssl = settings.CLAUDE_MEM_CHROMA_SSL === 'true';
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// Multi-tenancy settings (used in remote/pro mode)
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const tenant = settings.CLAUDE_MEM_CHROMA_TENANT || 'default_tenant';
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const database = settings.CLAUDE_MEM_CHROMA_DATABASE || 'default_database';
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const apiKey = settings.CLAUDE_MEM_CHROMA_API_KEY || '';
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// In local mode, verify server is reachable
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if (mode === 'local') {
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const serverManager = ChromaServerManager.getInstance();
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const reachable = await serverManager.isServerReachable();
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if (!reachable) {
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throw new Error('Chroma server not reachable. Ensure worker started correctly.');
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}
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}
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// Create HTTP client
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const protocol = ssl ? 'https' : 'http';
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const chromaPath = `${protocol}://${host}:${port}`;
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// Build client options
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const clientOptions: { path: string; tenant?: string; database?: string; headers?: Record<string, string> } = {
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path: chromaPath
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};
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// In remote mode, use tenant isolation for pro users
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if (mode === 'remote') {
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clientOptions.tenant = tenant;
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clientOptions.database = database;
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// Add API key header if configured
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if (apiKey) {
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clientOptions.headers = {
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'Authorization': `Bearer ${apiKey}`
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};
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}
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logger.info('CHROMA_SYNC', 'Connecting with tenant isolation', {
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tenant,
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database,
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hasApiKey: !!apiKey
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});
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}
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this.chromaClient = new ChromaClient(clientOptions);
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// Verify connection with heartbeat
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await this.chromaClient.heartbeat();
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logger.info('CHROMA_SYNC', 'Connected to Chroma HTTP server', {
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project: this.project,
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host,
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port,
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ssl,
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mode,
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tenant: mode === 'remote' ? tenant : 'default_tenant'
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await chromaMcp.callTool('chroma_create_collection', {
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collection_name: this.collectionName
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});
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} catch (error) {
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logger.error('CHROMA_SYNC', 'Failed to connect to Chroma HTTP server', { project: this.project }, error as Error);
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this.chromaClient = null;
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throw new Error(`Chroma connection failed: ${error instanceof Error ? error.message : String(error)}`);
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}
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}
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/**
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* Ensure collection exists, create if needed
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* Throws error if collection creation fails
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*/
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private async ensureCollection(): Promise<void> {
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await this.ensureConnection();
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if (this.collection) {
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return;
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}
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if (!this.chromaClient) {
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throw new Error(
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'Chroma client not initialized. Call ensureConnection() before using client methods.' +
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` Project: ${this.project}`
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);
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}
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try {
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// Store model cache outside node_modules so reinstalls don't corrupt it
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const { env } = await import('@huggingface/transformers');
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env.cacheDir = path.join(os.homedir(), '.claude-mem', 'models');
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// Use WASM backend to avoid native ONNX binary issues (#1104, #1105, #1110).
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// Same model (all-MiniLM-L6-v2), same embeddings, but runs in WASM —
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// no native binary loading, no segfaults, no ENOENT errors.
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const { DefaultEmbeddingFunction } = await import('@chroma-core/default-embed');
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const embeddingFunction = new DefaultEmbeddingFunction({ wasm: true });
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this.collection = await this.chromaClient.getOrCreateCollection({
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name: this.collectionName,
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embeddingFunction
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});
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logger.debug('CHROMA_SYNC', 'Collection ready', {
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collection: this.collectionName
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});
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} catch (error) {
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const errorMessage = error instanceof Error ? error.message : String(error);
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// Self-heal: corrupted model cache → clear and retry once
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if (errorMessage.includes('Protobuf parsing failed') && !this.modelCacheCorruptionRetried) {
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this.modelCacheCorruptionRetried = true;
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logger.warn('CHROMA_SYNC', 'Corrupted model cache detected, clearing and retrying...');
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const modelCacheDir = path.join(os.homedir(), '.claude-mem', 'models');
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const fs = await import('fs');
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if (fs.existsSync(modelCacheDir)) {
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fs.rmSync(modelCacheDir, { recursive: true, force: true });
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}
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return this.ensureCollection(); // retry once
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const message = error instanceof Error ? error.message : String(error);
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if (!message.includes('already exists')) {
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throw error;
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}
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logger.error('CHROMA_SYNC', 'Failed to get/create collection', { collection: this.collectionName }, error as Error);
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throw new Error(`Collection setup failed: ${errorMessage}`);
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// Collection already exists - this is the expected path after first creation
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}
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this.collectionCreated = true;
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logger.debug('CHROMA_SYNC', 'Collection ready', {
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collection: this.collectionName
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});
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}
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/**
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@@ -369,7 +251,7 @@ export class ChromaSync {
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}
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/**
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* Add documents to Chroma in batch
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* Add documents to Chroma in batch via MCP
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* Throws error if batch add fails
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*/
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private async addDocuments(documents: ChromaDocument[]): Promise<void> {
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@@ -377,33 +259,26 @@ export class ChromaSync {
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return;
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}
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await this.ensureCollection();
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await this.ensureCollectionExists();
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if (!this.collection) {
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throw new Error(
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'Chroma collection not initialized. Call ensureCollection() before using collection methods.' +
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` Project: ${this.project}`
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);
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const chromaMcp = ChromaMcpManager.getInstance();
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// Add in batches
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for (let i = 0; i < documents.length; i += this.BATCH_SIZE) {
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const batch = documents.slice(i, i + this.BATCH_SIZE);
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await chromaMcp.callTool('chroma_add_documents', {
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collection_name: this.collectionName,
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ids: batch.map(d => d.id),
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documents: batch.map(d => d.document),
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metadatas: batch.map(d => d.metadata)
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});
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}
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try {
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await this.collection.add({
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ids: documents.map(d => d.id),
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documents: documents.map(d => d.document),
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metadatas: documents.map(d => d.metadata)
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});
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logger.debug('CHROMA_SYNC', 'Documents added', {
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collection: this.collectionName,
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count: documents.length
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});
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} catch (error) {
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logger.error('CHROMA_SYNC', 'Failed to add documents', {
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collection: this.collectionName,
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count: documents.length
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}, error as Error);
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throw new Error(`Document add failed: ${error instanceof Error ? error.message : String(error)}`);
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}
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logger.debug('CHROMA_SYNC', 'Documents added', {
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collection: this.collectionName,
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count: documents.length
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});
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}
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/**
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@@ -545,7 +420,7 @@ export class ChromaSync {
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}
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/**
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* Fetch all existing document IDs from Chroma collection
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* Fetch all existing document IDs from Chroma collection via MCP
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* Returns Sets of SQLite IDs for observations, summaries, and prompts
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*/
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private async getExistingChromaIds(projectOverride?: string): Promise<{
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@@ -554,14 +429,9 @@ export class ChromaSync {
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prompts: Set<number>;
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}> {
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const targetProject = projectOverride ?? this.project;
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await this.ensureCollection();
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await this.ensureCollectionExists();
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if (!this.collection) {
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throw new Error(
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'Chroma collection not initialized. Call ensureCollection() before using collection methods.' +
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` Project: ${targetProject}`
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);
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}
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const chromaMcp = ChromaMcpManager.getInstance();
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const observationIds = new Set<number>();
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const summaryIds = new Set<number>();
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@@ -573,45 +443,42 @@ export class ChromaSync {
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logger.info('CHROMA_SYNC', 'Fetching existing Chroma document IDs...', { project: targetProject });
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while (true) {
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try {
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const result = await this.collection.get({
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limit,
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offset,
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where: { project: targetProject },
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include: ['metadatas']
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});
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const result = await chromaMcp.callTool('chroma_get_documents', {
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collection_name: this.collectionName,
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limit: limit,
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offset: offset,
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where: { project: targetProject },
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include: ['metadatas']
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}) as any;
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const metadatas = result.metadatas || [];
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// chroma_get_documents returns flat arrays: { ids, metadatas, documents }
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const metadatas = result?.metadatas || [];
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if (metadatas.length === 0) {
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break; // No more documents
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}
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if (metadatas.length === 0) {
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break; // No more documents
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}
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// Extract SQLite IDs from metadata
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for (const meta of metadatas) {
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if (meta && meta.sqlite_id) {
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const sqliteId = meta.sqlite_id as number;
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if (meta.doc_type === 'observation') {
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observationIds.add(sqliteId);
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} else if (meta.doc_type === 'session_summary') {
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summaryIds.add(sqliteId);
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} else if (meta.doc_type === 'user_prompt') {
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promptIds.add(sqliteId);
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}
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// Extract SQLite IDs from metadata
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for (const meta of metadatas) {
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if (meta && meta.sqlite_id) {
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const sqliteId = meta.sqlite_id as number;
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if (meta.doc_type === 'observation') {
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observationIds.add(sqliteId);
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} else if (meta.doc_type === 'session_summary') {
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summaryIds.add(sqliteId);
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} else if (meta.doc_type === 'user_prompt') {
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promptIds.add(sqliteId);
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}
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}
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offset += limit;
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logger.debug('CHROMA_SYNC', 'Fetched batch of existing IDs', {
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project: targetProject,
|
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offset,
|
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batchSize: metadatas.length
|
||||
});
|
||||
} catch (error) {
|
||||
logger.error('CHROMA_SYNC', 'Failed to fetch existing IDs', { project: targetProject }, error as Error);
|
||||
throw error;
|
||||
}
|
||||
|
||||
offset += limit;
|
||||
|
||||
logger.debug('CHROMA_SYNC', 'Fetched batch of existing IDs', {
|
||||
project: targetProject,
|
||||
offset,
|
||||
batchSize: metadatas.length
|
||||
});
|
||||
}
|
||||
|
||||
logger.info('CHROMA_SYNC', 'Existing IDs fetched', {
|
||||
@@ -635,7 +502,7 @@ export class ChromaSync {
|
||||
const backfillProject = projectOverride ?? this.project;
|
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logger.info('CHROMA_SYNC', 'Starting smart backfill', { project: backfillProject });
|
||||
|
||||
await this.ensureCollection();
|
||||
await this.ensureCollectionExists();
|
||||
|
||||
// Fetch existing IDs from Chroma (fast, metadata only)
|
||||
const existing = await this.getExistingChromaIds(backfillProject);
|
||||
@@ -644,7 +511,8 @@ export class ChromaSync {
|
||||
|
||||
try {
|
||||
// Build exclusion list for observations
|
||||
const existingObsIds = Array.from(existing.observations);
|
||||
// Filter to validated positive integers before interpolating into SQL
|
||||
const existingObsIds = Array.from(existing.observations).filter(id => Number.isInteger(id) && id > 0);
|
||||
const obsExclusionClause = existingObsIds.length > 0
|
||||
? `AND id NOT IN (${existingObsIds.join(',')})`
|
||||
: '';
|
||||
@@ -685,7 +553,7 @@ export class ChromaSync {
|
||||
}
|
||||
|
||||
// Build exclusion list for summaries
|
||||
const existingSummaryIds = Array.from(existing.summaries);
|
||||
const existingSummaryIds = Array.from(existing.summaries).filter(id => Number.isInteger(id) && id > 0);
|
||||
const summaryExclusionClause = existingSummaryIds.length > 0
|
||||
? `AND id NOT IN (${existingSummaryIds.join(',')})`
|
||||
: '';
|
||||
@@ -726,7 +594,7 @@ export class ChromaSync {
|
||||
}
|
||||
|
||||
// Build exclusion list for prompts
|
||||
const existingPromptIds = Array.from(existing.prompts);
|
||||
const existingPromptIds = Array.from(existing.prompts).filter(id => Number.isInteger(id) && id > 0);
|
||||
const promptExclusionClause = existingPromptIds.length > 0
|
||||
? `AND up.id NOT IN (${existingPromptIds.join(',')})`
|
||||
: '';
|
||||
@@ -797,7 +665,7 @@ export class ChromaSync {
|
||||
}
|
||||
|
||||
/**
|
||||
* Query Chroma collection for semantic search
|
||||
* Query Chroma collection for semantic search via MCP
|
||||
* Used by SearchManager for vector-based search
|
||||
*/
|
||||
async queryChroma(
|
||||
@@ -805,27 +673,34 @@ export class ChromaSync {
|
||||
limit: number,
|
||||
whereFilter?: Record<string, any>
|
||||
): Promise<{ ids: number[]; distances: number[]; metadatas: any[] }> {
|
||||
await this.ensureCollection();
|
||||
|
||||
if (!this.collection) {
|
||||
throw new Error(
|
||||
'Chroma collection not initialized. Call ensureCollection() before using collection methods.' +
|
||||
` Project: ${this.project}`
|
||||
);
|
||||
}
|
||||
await this.ensureCollectionExists();
|
||||
|
||||
try {
|
||||
const results = await this.collection.query({
|
||||
queryTexts: [query],
|
||||
nResults: limit,
|
||||
where: whereFilter,
|
||||
const chromaMcp = ChromaMcpManager.getInstance();
|
||||
const results = await chromaMcp.callTool('chroma_query_documents', {
|
||||
collection_name: this.collectionName,
|
||||
query_texts: [query],
|
||||
n_results: limit,
|
||||
...(whereFilter && { where: whereFilter }),
|
||||
include: ['documents', 'metadatas', 'distances']
|
||||
});
|
||||
}) as any;
|
||||
|
||||
// Extract unique SQLite IDs from document IDs
|
||||
// chroma_query_documents returns nested arrays (one per query text)
|
||||
// We always pass a single query text, so we access [0]
|
||||
const ids: number[] = [];
|
||||
const docIds = results.ids?.[0] || [];
|
||||
for (const docId of docIds) {
|
||||
const seen = new Set<number>();
|
||||
const docIds = results?.ids?.[0] || [];
|
||||
const rawMetadatas = results?.metadatas?.[0] || [];
|
||||
const rawDistances = results?.distances?.[0] || [];
|
||||
|
||||
// Build deduplicated arrays that stay index-aligned:
|
||||
// Multiple Chroma docs map to the same SQLite ID (one per field).
|
||||
// Keep the first (best-ranked) distance and metadata per SQLite ID.
|
||||
const metadatas: any[] = [];
|
||||
const distances: number[] = [];
|
||||
|
||||
for (let i = 0; i < docIds.length; i++) {
|
||||
const docId = docIds[i];
|
||||
// Extract sqlite_id from document ID (supports three formats):
|
||||
// - obs_{id}_narrative, obs_{id}_fact_0, etc (observations)
|
||||
// - summary_{id}_request, summary_{id}_learned, etc (session summaries)
|
||||
@@ -843,16 +718,15 @@ export class ChromaSync {
|
||||
sqliteId = parseInt(promptMatch[1], 10);
|
||||
}
|
||||
|
||||
if (sqliteId !== null && !ids.includes(sqliteId)) {
|
||||
if (sqliteId !== null && !seen.has(sqliteId)) {
|
||||
seen.add(sqliteId);
|
||||
ids.push(sqliteId);
|
||||
metadatas.push(rawMetadatas[i] ?? null);
|
||||
distances.push(rawDistances[i] ?? 0);
|
||||
}
|
||||
}
|
||||
|
||||
return {
|
||||
ids,
|
||||
distances: results.distances?.[0] || [],
|
||||
metadatas: results.metadatas?.[0] || []
|
||||
};
|
||||
return { ids, distances, metadatas };
|
||||
} catch (error) {
|
||||
const errorMessage = error instanceof Error ? error.message : String(error);
|
||||
|
||||
@@ -860,12 +734,13 @@ export class ChromaSync {
|
||||
const isConnectionError =
|
||||
errorMessage.includes('ECONNREFUSED') ||
|
||||
errorMessage.includes('ENOTFOUND') ||
|
||||
errorMessage.includes('fetch failed');
|
||||
errorMessage.includes('fetch failed') ||
|
||||
errorMessage.includes('subprocess closed') ||
|
||||
errorMessage.includes('timed out');
|
||||
|
||||
if (isConnectionError) {
|
||||
// Reset connection state so next call attempts reconnect
|
||||
this.chromaClient = null;
|
||||
this.collection = null;
|
||||
// Reset collection state so next call attempts reconnect
|
||||
this.collectionCreated = false;
|
||||
logger.error('CHROMA_SYNC', 'Connection lost during query',
|
||||
{ project: this.project, query }, error as Error);
|
||||
throw new Error(`Chroma query failed - connection lost: ${errorMessage}`);
|
||||
@@ -909,13 +784,13 @@ export class ChromaSync {
|
||||
}
|
||||
|
||||
/**
|
||||
* Close the Chroma client connection
|
||||
* Server lifecycle is managed by ChromaServerManager, not here
|
||||
* Close the ChromaSync instance
|
||||
* ChromaMcpManager is a singleton and manages its own lifecycle
|
||||
* We don't close it here - it's closed during graceful shutdown
|
||||
*/
|
||||
async close(): Promise<void> {
|
||||
// Just clear references - server lifecycle managed by ChromaServerManager
|
||||
this.chromaClient = null;
|
||||
this.collection = null;
|
||||
logger.info('CHROMA_SYNC', 'Chroma client closed', { project: this.project });
|
||||
// ChromaMcpManager is a singleton and manages its own lifecycle
|
||||
// We don't close it here - it's closed during graceful shutdown
|
||||
logger.info('CHROMA_SYNC', 'ChromaSync closed', { project: this.project });
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user