NCBI Entrez MCP Server

// src/lib/ChunkingEngine.ts export interface ChunkMetadata { contentId: string; totalChunks: number; originalSize: number; } export class ChunkingEngine { private readonly CHUNK_SIZE_THRESHOLD = 32 * 1024; // 32KB private readonly CHUNK_SIZE = 16 * 1024; // 16KB public shouldChunk(content: string): boolean { return content.length > this.CHUNK_SIZE_THRESHOLD; } public async storeChunkedContent( content: string, sql: any, ): Promise<ChunkMetadata> { const contentId = "chunk_" + crypto.randomUUID(); await this.ensureChunksTable(sql); const chunks = []; for (let i = 0; i < content.length; i += this.CHUNK_SIZE) { chunks.push(content.slice(i, i + this.CHUNK_SIZE)); } for (let i = 0; i < chunks.length; i++) { sql.exec( `INSERT INTO content_chunks (content_id, chunk_index, chunk_data) VALUES (?, ?, ?)`, contentId, i, chunks[i], ); } const metadata = { contentId, totalChunks: chunks.length, originalSize: content.length, }; sql.exec( `INSERT INTO chunk_metadata (content_id, total_chunks, original_size) VALUES (?, ?, ?)`, metadata.contentId, metadata.totalChunks, metadata.originalSize, ); return metadata; } public async retrieveChunkedContent( contentId: string, sql: any, ): Promise<string | null> { const result = sql .exec( `SELECT chunk_data FROM content_chunks WHERE content_id = ? ORDER BY chunk_index ASC`, contentId, ) .toArray(); return result.length > 0 ? result.map((row: any) => row.chunk_data).join("") : null; } public createContentReference(metadata: ChunkMetadata): string { return `__CHUNKED__:${metadata.contentId}`; } public isContentReference(value: any): boolean { return typeof value === "string" && value.startsWith("__CHUNKED__:"); } public extractContentId(reference: string): string { return reference.substring(12); } public async smartJsonStringify(obj: any, sql: any): Promise<string> { const jsonString = JSON.stringify(obj); if (!this.shouldChunk(jsonString)) { return jsonString; } const metadata = await this.storeChunkedContent(jsonString, sql); return this.createContentReference(metadata); } private async ensureChunksTable(sql: any): Promise<void> { sql.exec(` CREATE TABLE IF NOT EXISTS content_chunks ( id INTEGER PRIMARY KEY, content_id TEXT NOT NULL, chunk_index INTEGER NOT NULL, chunk_data TEXT NOT NULL, UNIQUE(content_id, chunk_index) ) `); sql.exec( `CREATE TABLE IF NOT EXISTS chunk_metadata (content_id TEXT PRIMARY KEY, total_chunks INTEGER, original_size INTEGER)`, ); } }