bonecode 1.0.0

package/bone/output/rag/package.json

@@ -0,0 +1,36 @@
+{
+  "name": "ragdomain",
+  "version": "1.0.0",
+  "private": true,
+  "scripts": {
+    "build": "tsc",
+    "start": "node dist/index.js",
+    "dev": "ts-node src/index.ts",
+    "migrate": "ts-node src/migrate.ts"
+  },
+  "dependencies": {
+    "express": "4.18.2",
+    "pg": "8.11.3",
+    "ioredis": "5.3.2",
+    "ws": "8.16.0",
+    "uuid": "9.0.0",
+    "cors": "2.8.5",
+    "helmet": "7.1.0",
+    "express-rate-limit": "7.1.5",
+    "jsonwebtoken": "9.0.2",
+    "dotenv": "16.3.1",
+    "node-cron": "3.0.3"
+  },
+  "devDependencies": {
+    "@types/express": "4.17.21",
+    "@types/node": "18.19.0",
+    "@types/pg": "8.10.9",
+    "@types/ws": "8.5.10",
+    "@types/cors": "2.8.17",
+    "@types/jsonwebtoken": "9.0.5",
+    "@types/uuid": "9.0.7",
+    "@types/node-cron": "3.0.11",
+    "typescript": "5.3.3",
+    "ts-node": "10.9.2"
+  }
+}

package/bone/output/rag/schema.graphql

@@ -0,0 +1,245 @@
+# Generated by BoneScript compiler. DO NOT EDIT.
+# System: RAGDomain v1.0.0
+
+type KnowledgeBase {
+  id: ID!
+  created_at: String!
+  updated_at: String!
+  project_id: ID!
+  name: String!
+  description: String
+  embedding_model: String!
+  embedding_dimensions: Int!
+  chunk_strategy: String!
+  chunk_size: Int!
+  chunk_overlap: Int!
+  total_files: Int!
+  total_chunks: Int!
+  last_indexed_at: String
+}
+
+type KnowledgeBasePage {
+  items: [KnowledgeBase!]!
+  total: Int!
+  page: Int!
+  pageSize: Int!
+}
+
+input KnowledgeBaseInput {
+  project_id: ID!
+  name: String!
+  description: String
+  embedding_model: String!
+  embedding_dimensions: Int!
+  chunk_strategy: String!
+  chunk_size: Int!
+  chunk_overlap: Int!
+  total_files: Int!
+  total_chunks: Int!
+  last_indexed_at: String
+}
+
+type CodeFile {
+  id: ID!
+  created_at: String!
+  updated_at: String!
+  knowledge_base_id: ID!
+  project_id: ID!
+  file_path: String!
+  language: String
+  file_hash: String!
+  file_size_bytes: Int!
+  total_chunks: Int!
+  last_modified_at: String!
+  metadata: String
+}
+
+type CodeFilePage {
+  items: [CodeFile!]!
+  total: Int!
+  page: Int!
+  pageSize: Int!
+}
+
+input CodeFileInput {
+  knowledge_base_id: ID!
+  project_id: ID!
+  file_path: String!
+  language: String
+  file_hash: String!
+  file_size_bytes: Int!
+  total_chunks: Int!
+  last_modified_at: String!
+  metadata: String
+}
+
+type CodeChunk {
+  id: ID!
+  created_at: String!
+  updated_at: String!
+  code_file_id: ID!
+  knowledge_base_id: ID!
+  project_id: ID!
+  content: String!
+  start_line: Int!
+  end_line: Int!
+  chunk_index: Int!
+  language: String
+  symbol_name: String
+  symbol_type: String
+  metadata: String
+}
+
+type CodeChunkPage {
+  items: [CodeChunk!]!
+  total: Int!
+  page: Int!
+  pageSize: Int!
+}
+
+input CodeChunkInput {
+  code_file_id: ID!
+  knowledge_base_id: ID!
+  project_id: ID!
+  content: String!
+  start_line: Int!
+  end_line: Int!
+  chunk_index: Int!
+  language: String
+  symbol_name: String
+  symbol_type: String
+  metadata: String
+}
+
+type MemoryEntry {
+  id: ID!
+  created_at: String!
+  updated_at: String!
+  session_id: ID!
+  project_id: ID!
+  agent_id: ID
+  memory_type: String!
+  content: String!
+  importance: Float!
+  access_count: Int!
+  last_accessed_at: String
+  expires_at: String
+  metadata: String
+}
+
+type MemoryEntryPage {
+  items: [MemoryEntry!]!
+  total: Int!
+  page: Int!
+  pageSize: Int!
+}
+
+input MemoryEntryInput {
+  session_id: ID!
+  project_id: ID!
+  agent_id: ID
+  memory_type: String!
+  content: String!
+  importance: Float!
+  access_count: Int!
+  last_accessed_at: String
+  expires_at: String
+  metadata: String
+}
+
+type IndexingJob {
+  id: ID!
+  created_at: String!
+  updated_at: String!
+  knowledge_base_id: ID!
+  project_id: ID!
+  job_type: String!
+  file_paths: String!
+  files_total: Int!
+  files_processed: Int!
+  chunks_total: Int!
+  chunks_embedded: Int!
+  error: String
+}
+
+type IndexingJobPage {
+  items: [IndexingJob!]!
+  total: Int!
+  page: Int!
+  pageSize: Int!
+}
+
+input IndexingJobInput {
+  knowledge_base_id: ID!
+  project_id: ID!
+  job_type: String!
+  file_paths: String!
+  files_total: Int!
+  files_processed: Int!
+  chunks_total: Int!
+  chunks_embedded: Int!
+  error: String
+}
+
+type CapabilityResult {
+  ok: Boolean!
+  action: String!
+}
+
+input KnowledgeBaseIngestCodebaseInput {
+  knowledge_base: String!
+  file_paths: String!
+}
+
+input KnowledgeBaseIndexFileInput {
+  knowledge_base: String!
+  file_path: String!
+}
+
+input KnowledgeBaseRetrieveContextInput {
+  knowledge_base: String!
+  query: String!
+  limit: Int!
+}
+
+input KnowledgeBaseSemanticSearchInput {
+  knowledge_base: String!
+  query: String!
+  filters: String!
+  limit: Int!
+}
+
+type Query {
+  knowledgeBase(id: ID!): KnowledgeBase
+  knowledgeBases(page: Int, pageSize: Int): KnowledgeBasePage
+  codeFile(id: ID!): CodeFile
+  codeFiles(page: Int, pageSize: Int): CodeFilePage
+  codeChunk(id: ID!): CodeChunk
+  codeChunks(page: Int, pageSize: Int): CodeChunkPage
+  memoryEntry(id: ID!): MemoryEntry
+  memoryEntrys(page: Int, pageSize: Int): MemoryEntryPage
+  indexingJob(id: ID!): IndexingJob
+  indexingJobs(page: Int, pageSize: Int): IndexingJobPage
+}
+
+type Mutation {
+  createKnowledgeBase(input: KnowledgeBaseInput!): KnowledgeBase!
+  updateKnowledgeBase(id: ID!, input: KnowledgeBaseInput!): KnowledgeBase!
+  deleteKnowledgeBase(id: ID!): Boolean!
+  ingestCodebase(input: KnowledgeBaseIngestCodebaseInput): CapabilityResult!
+  indexFile(input: KnowledgeBaseIndexFileInput): CapabilityResult!
+  retrieveContext(input: KnowledgeBaseRetrieveContextInput): CapabilityResult!
+  semanticSearch(input: KnowledgeBaseSemanticSearchInput): CapabilityResult!
+  createCodeFile(input: CodeFileInput!): CodeFile!
+  updateCodeFile(id: ID!, input: CodeFileInput!): CodeFile!
+  deleteCodeFile(id: ID!): Boolean!
+  createCodeChunk(input: CodeChunkInput!): CodeChunk!
+  updateCodeChunk(id: ID!, input: CodeChunkInput!): CodeChunk!
+  deleteCodeChunk(id: ID!): Boolean!
+  createMemoryEntry(input: MemoryEntryInput!): MemoryEntry!
+  updateMemoryEntry(id: ID!, input: MemoryEntryInput!): MemoryEntry!
+  deleteMemoryEntry(id: ID!): Boolean!
+  createIndexingJob(input: IndexingJobInput!): IndexingJob!
+  updateIndexingJob(id: ID!, input: IndexingJobInput!): IndexingJob!
+  deleteIndexingJob(id: ID!): Boolean!
+}

package/bone/output/rag/sdk/client.ts

@@ -0,0 +1,234 @@
+// Generated by BoneScript compiler. Import this file into your frontend.
+// System: RAGDomain v1.0.0
+
+export interface KnowledgeBase {
+  id: string;
+  created_at: string;
+  updated_at: string;
+  project_id: string;
+  name: string;
+  description: string | null | null;
+  embedding_model: string;
+  embedding_dimensions: number;
+  chunk_strategy: string;
+  chunk_size: number;
+  chunk_overlap: number;
+  total_files: number;
+  total_chunks: number;
+  last_indexed_at: string | null | null;
+}
+
+export interface CodeFile {
+  id: string;
+  created_at: string;
+  updated_at: string;
+  knowledge_base_id: string;
+  project_id: string;
+  file_path: string;
+  language: string | null | null;
+  file_hash: string;
+  file_size_bytes: number;
+  total_chunks: number;
+  last_modified_at: string;
+  metadata: unknown | null | null;
+}
+
+export interface CodeChunk {
+  id: string;
+  created_at: string;
+  updated_at: string;
+  code_file_id: string;
+  knowledge_base_id: string;
+  project_id: string;
+  content: string;
+  start_line: number;
+  end_line: number;
+  chunk_index: number;
+  language: string | null | null;
+  symbol_name: string | null | null;
+  symbol_type: string | null | null;
+  metadata: unknown | null | null;
+}
+
+export interface MemoryEntry {
+  id: string;
+  created_at: string;
+  updated_at: string;
+  session_id: string;
+  project_id: string;
+  agent_id: string | null | null;
+  memory_type: string;
+  content: string;
+  importance: number;
+  access_count: number;
+  last_accessed_at: string | null | null;
+  expires_at: string | null | null;
+  metadata: unknown | null | null;
+}
+
+export interface IndexingJob {
+  id: string;
+  created_at: string;
+  updated_at: string;
+  knowledge_base_id: string;
+  project_id: string;
+  job_type: string;
+  file_paths: unknown;
+  files_total: number;
+  files_processed: number;
+  chunks_total: number;
+  chunks_embedded: number;
+  error: string | null | null;
+}
+
+export class RAGDomainClient {
+  constructor(private baseUrl: string, private getToken?: () => string | null) {}
+
+  private async request<T>(method: string, path: string, body?: unknown): Promise<T> {
+    const headers: Record<string, string> = {
+      "Content-Type": "application/json",
+    };
+    if (this.getToken) {
+      const token = this.getToken();
+      if (token) headers["Authorization"] = "Bearer " + token;
+    }
+    const res = await fetch(this.baseUrl + path, {
+      method,
+      headers,
+      body: body !== undefined ? JSON.stringify(body) : undefined,
+    });
+    if (!res.ok) {
+      const text = await res.text().catch(() => res.statusText);
+      throw new Error(`HTTP ${res.status}: ${text}`);
+    }
+    if (res.status === 204) return undefined as unknown as T;
+    return res.json() as Promise<T>;
+  }
+
+  // ─── KnowledgeBase ───
+
+  listKnowledgeBase(page = 1, pageSize = 50): Promise<{ items: KnowledgeBase[]; total: number; page: number; page_size: number }> {
+    return this.request("GET", `/knowledge_bases?page=${page}&page_size=${pageSize}`);
+  }
+
+  getKnowledgeBase(id: string): Promise<KnowledgeBase> {
+    return this.request("GET", `/knowledge_bases/${id}`);
+  }
+
+  createKnowledgeBase(data: Partial<KnowledgeBase>): Promise<KnowledgeBase> {
+    return this.request("POST", "/knowledge_bases", data);
+  }
+
+  updateKnowledgeBase(id: string, data: Partial<KnowledgeBase>): Promise<KnowledgeBase> {
+    return this.request("PUT", `/knowledge_bases/${id}`, data);
+  }
+
+  deleteKnowledgeBase(id: string): Promise<void> {
+    return this.request("DELETE", `/knowledge_bases/${id}`);
+  }
+
+  ingestCodebase(data: Record<string, unknown>): Promise<{ ok: boolean; action: string }> {
+    return this.request("POST", "/knowledge_bases/ingest-codebase", data);
+  }
+
+  indexFile(data: Record<string, unknown>): Promise<{ ok: boolean; action: string }> {
+    return this.request("POST", "/knowledge_bases/index-file", data);
+  }
+
+  retrieveContext(data: Record<string, unknown>): Promise<{ ok: boolean; action: string }> {
+    return this.request("POST", "/knowledge_bases/retrieve-context", data);
+  }
+
+  semanticSearch(data: Record<string, unknown>): Promise<{ ok: boolean; action: string }> {
+    return this.request("POST", "/knowledge_bases/semantic-search", data);
+  }
+
+  // ─── CodeFile ───
+
+  listCodeFile(page = 1, pageSize = 50): Promise<{ items: CodeFile[]; total: number; page: number; page_size: number }> {
+    return this.request("GET", `/code_files?page=${page}&page_size=${pageSize}`);
+  }
+
+  getCodeFile(id: string): Promise<CodeFile> {
+    return this.request("GET", `/code_files/${id}`);
+  }
+
+  createCodeFile(data: Partial<CodeFile>): Promise<CodeFile> {
+    return this.request("POST", "/code_files", data);
+  }
+
+  updateCodeFile(id: string, data: Partial<CodeFile>): Promise<CodeFile> {
+    return this.request("PUT", `/code_files/${id}`, data);
+  }
+
+  deleteCodeFile(id: string): Promise<void> {
+    return this.request("DELETE", `/code_files/${id}`);
+  }
+
+  // ─── CodeChunk ───
+
+  listCodeChunk(page = 1, pageSize = 50): Promise<{ items: CodeChunk[]; total: number; page: number; page_size: number }> {
+    return this.request("GET", `/code_chunks?page=${page}&page_size=${pageSize}`);
+  }
+
+  getCodeChunk(id: string): Promise<CodeChunk> {
+    return this.request("GET", `/code_chunks/${id}`);
+  }
+
+  createCodeChunk(data: Partial<CodeChunk>): Promise<CodeChunk> {
+    return this.request("POST", "/code_chunks", data);
+  }
+
+  updateCodeChunk(id: string, data: Partial<CodeChunk>): Promise<CodeChunk> {
+    return this.request("PUT", `/code_chunks/${id}`, data);
+  }
+
+  deleteCodeChunk(id: string): Promise<void> {
+    return this.request("DELETE", `/code_chunks/${id}`);
+  }
+
+  // ─── MemoryEntry ───
+
+  listMemoryEntry(page = 1, pageSize = 50): Promise<{ items: MemoryEntry[]; total: number; page: number; page_size: number }> {
+    return this.request("GET", `/memory_entrys?page=${page}&page_size=${pageSize}`);
+  }
+
+  getMemoryEntry(id: string): Promise<MemoryEntry> {
+    return this.request("GET", `/memory_entrys/${id}`);
+  }
+
+  createMemoryEntry(data: Partial<MemoryEntry>): Promise<MemoryEntry> {
+    return this.request("POST", "/memory_entrys", data);
+  }
+
+  updateMemoryEntry(id: string, data: Partial<MemoryEntry>): Promise<MemoryEntry> {
+    return this.request("PUT", `/memory_entrys/${id}`, data);
+  }
+
+  deleteMemoryEntry(id: string): Promise<void> {
+    return this.request("DELETE", `/memory_entrys/${id}`);
+  }
+
+  // ─── IndexingJob ───
+
+  listIndexingJob(page = 1, pageSize = 50): Promise<{ items: IndexingJob[]; total: number; page: number; page_size: number }> {
+    return this.request("GET", `/indexing_jobs?page=${page}&page_size=${pageSize}`);
+  }
+
+  getIndexingJob(id: string): Promise<IndexingJob> {
+    return this.request("GET", `/indexing_jobs/${id}`);
+  }
+
+  createIndexingJob(data: Partial<IndexingJob>): Promise<IndexingJob> {
+    return this.request("POST", "/indexing_jobs", data);
+  }
+
+  updateIndexingJob(id: string, data: Partial<IndexingJob>): Promise<IndexingJob> {
+    return this.request("PUT", `/indexing_jobs/${id}`, data);
+  }
+
+  deleteIndexingJob(id: string): Promise<void> {
+    return this.request("DELETE", `/indexing_jobs/${id}`);
+  }
+
+}

package/bone/output/rag/src/algorithms.ts

@@ -0,0 +1,2 @@
+// No algorithms used in this system.
+export {};

package/bone/output/rag/src/audit.ts

@@ -0,0 +1,37 @@
+// Generated by BoneScript compiler.
+// Audit middleware for: RAGDomain v1.0.0
+
+import { Request, Response, NextFunction } from "express";
+import { query } from "./db";
+
+export function auditLog(action: string, entityType?: string) {
+  return async (req: Request, _res: Response, next: NextFunction): Promise<void> => {
+    try {
+      const auth = (req as any).auth as { actor_id?: string | null } | undefined;
+      const actorId = auth?.actor_id ?? null;
+      const entityId = req.params.id ?? (req.body as Record<string, unknown>)?.id ?? null;
+      const payload = req.body ?? null;
+      const ipAddress = req.ip ?? null;
+      const userAgent = req.headers["user-agent"] ?? null;
+
+      await query(
+        `INSERT INTO audit_log
+          (actor_id, action, entity_type, entity_id, payload, ip_address, user_agent)
+          VALUES ($1, $2, $3, $4, $5, $6, $7)`,
+        [actorId, action, entityType ?? null, entityId, JSON.stringify(payload), ipAddress, userAgent]
+      );
+    } catch (err) {
+      // Audit failures must not block the request — log and continue
+      console.error("[audit] Failed to write audit log:", err);
+    }
+    next();
+  };
+}
+
+export async function getAuditLog(entityType: string, entityId: string): Promise<any[]> {
+  const result = await query(
+    "SELECT * FROM audit_log WHERE entity_type = $1 AND entity_id = $2 ORDER BY created_at DESC LIMIT 100",
+    [entityType, entityId]
+  );
+  return result.rows;
+}

package/bone/output/rag/src/auth.ts

@@ -0,0 +1,57 @@
+// Generated by BoneScript compiler. DO NOT EDIT.
+import { Request, Response, NextFunction } from "express";
+import jwt from "jsonwebtoken";
+
+// JWT_SECRET must be set in production. The server will refuse to start without it
+// when NODE_ENV is "production" to prevent accidental use of a weak fallback.
+const JWT_SECRET = (() => {
+  const secret = process.env.JWT_SECRET;
+  if (!secret) {
+    if (process.env.NODE_ENV === "production") {
+      console.error("[FATAL] JWT_SECRET environment variable is not set. Refusing to start in production.");
+      process.exit(1);
+    }
+    console.warn("[WARN] JWT_SECRET is not set. Using insecure default — do not use in production.");
+    return "bonescript-dev-secret-do-not-use-in-production";
+  }
+  if (secret.length < 32) {
+    console.warn("[WARN] JWT_SECRET is shorter than 32 characters. Use a longer secret in production.");
+  }
+  return secret;
+})();
+
+export interface AuthContext {
+  authenticated: boolean;
+  actor_id: string | null;
+  trace_id: string;
+}
+
+export function authMiddleware(req: Request, res: Response, next: NextFunction): void {
+  const header = req.headers.authorization;
+  if (!header || !header.startsWith("Bearer ")) {
+    (req as any).auth = { authenticated: false, actor_id: null, trace_id: req.headers["x-trace-id"] as string || "" };
+    next();
+    return;
+  }
+  try {
+    const token = header.slice(7);
+    const decoded = jwt.verify(token, JWT_SECRET) as { sub: string };
+    (req as any).auth = {
+      authenticated: true,
+      actor_id: decoded.sub,
+      trace_id: req.headers["x-trace-id"] as string || "",
+    };
+  } catch {
+    (req as any).auth = { authenticated: false, actor_id: null, trace_id: req.headers["x-trace-id"] as string || "" };
+  }
+  next();
+}
+
+export function requireAuth(req: Request, res: Response, next: NextFunction): void {
+  const auth: AuthContext = (req as any).auth;
+  if (!auth || !auth.authenticated) {
+    res.status(401).json({ error: { code: "UNAUTHORIZED", message: "Authentication required" } });
+    return;
+  }
+  next();
+}

package/bone/output/rag/src/cron.ts

@@ -0,0 +1,12 @@
+// Generated by BoneScript compiler.
+// Cron jobs — scheduled background tasks.
+// Uncomment and configure as needed.
+
+import cron from "node-cron";
+import { logger } from "./logger";
+
+export function startCronJobs(): void {
+  logger.info("cron_started", { event: "startup" });
+
+  // No batch capabilities declared — add cron jobs here.
+}

package/bone/output/rag/src/db.ts

@@ -0,0 +1,32 @@
+// Generated by BoneScript compiler. DO NOT EDIT.
+import { Pool, PoolClient } from "pg";
+
+// Lazy pool — created on first use so DATABASE_URL is read after dotenv loads
+let _pool: Pool | null = null;
+function getPool(): Pool {
+  if (!_pool) {
+  _pool = new Pool({ connectionString: process.env.DATABASE_URL || "postgresql://localhost:5432/ragdomain", max: 20 });
+  _pool.on("error", (err: Error) => console.error("[DB] Pool error (non-fatal):", err.message));
+  }
+  return _pool;
+}
+export const pool = new Proxy({} as Pool, { get(_t: any, p: any) { return (getPool() as any)[p]; } });
+
+export async function query<T = any>(text: string, params?: any[]): Promise<T[]> {
+  try { const result = await pool.query(text, params); return result.rows as T[]; }
+  catch (e: any) { throw new Error(`DB query failed: ${e.message}`); }
+}
+export async function queryOne<T = any>(text: string, params?: any[]): Promise<T | null> {
+  try { const rows = await query<T>(text, params); return rows[0] || null; }
+  catch (e: any) { throw new Error(`DB query failed: ${e.message}`); }
+}
+export async function execute(text: string, params?: any[]): Promise<number> {
+  try { const result = await pool.query(text, params); return result.rowCount || 0; }
+  catch (e: any) { throw new Error(`DB execute failed: ${e.message}`); }
+}
+export async function transaction<T>(fn: (client: PoolClient) => Promise<T>): Promise<T> {
+  const client = await pool.connect();
+  try { await client.query("BEGIN"); const result = await fn(client); await client.query("COMMIT"); return result; }
+  catch (e) { await client.query("ROLLBACK"); throw e; }
+  finally { client.release(); }
+}