@nucl-parquet/mcp 0.14.0 → 0.15.0

package/dist/index.d.ts

@@ -1,5 +1,3 @@
-import duckdb from 'duckdb';
-
 /**
  * nucl-parquet MCP server — wraps local data via DuckDB.
  *
@@ -7,8 +5,8 @@ import duckdb from 'duckdb';
  * DuckDB-backed Parquet views, not a re-implementation of parquet I/O.
  * All data is read from the local data directory — no HTTP fetching.
  */
-
-declare const PKG_VERSION: string;
+import duckdb from "duckdb";
+export declare const PKG_VERSION: string;
 interface Library {
     name: string;
     description: string;
@@ -41,7 +39,7 @@ interface Catalog {
     views?: Record<string, ViewDef>;
     [key: string]: unknown;
 }
-declare function ensureCatalog(): Catalog;
+export declare function ensureCatalog(): Catalog;
 /**
  * Parse and validate a catalog.
  *
@@ -49,7 +47,7 @@ declare function ensureCatalog(): Catalog;
  * singleton, which a test cannot re-enter — so the validation below would be
  * unreachable from a test and, in practice, unverified.
  */
-declare function parseCatalog(raw: string, dataDir: string): Catalog;
+export declare function parseCatalog(raw: string, dataDir: string): Catalog;
 /**
  * The `list_libraries` payload: the data release, then the libraries.
  *
@@ -57,11 +55,11 @@ declare function parseCatalog(raw: string, dataDir: string): Catalog;
  * the tool actually returns. Asserting only that the catalog *has* a
  * data_version would pass while the tool still returned a bare array.
  */
-declare function libraryListPayload(cat: Catalog): {
+export declare function libraryListPayload(cat: Catalog): {
     data_version: string;
     libraries: Array<Record<string, unknown>>;
 };
-declare function getDb(): duckdb.Database;
+export declare function getDb(): duckdb.Database;
 /**
  * Server instructions, naming the data release in the client's context.
  *
@@ -76,6 +74,7 @@ declare function getDb(): duckdb.Database;
  * Kept word-for-word in step with the Rust server's `instructions()`; a test
  * pins that the two do not drift.
  */
-declare function instructions(dataVersion: string): string;
-
-export { PKG_VERSION, ensureCatalog, getDb, instructions, libraryListPayload, parseCatalog };
+export declare function instructions(dataVersion: string): string;
+export declare const BLOCKED_FUNCTIONS: RegExp;
+export declare const ALLOWED_FIRST_WORDS: Set<string>;
+export {};

package/dist/index.js

@@ -109,11 +109,20 @@ function registerViews(db, dataDir) {
     db.run("CREATE VIEW fluorescence AS SELECT * FROM atomic_relaxation WHERE transition_type = 'radiative'");
   }
 }
+function harden(db, dataDir) {
+  const quoted = dataDir.replaceAll("'", "''");
+  db.run(`SET allowed_directories = ['${quoted}']`);
+  db.run("SET enable_external_access = false");
+  db.run("SET autoinstall_known_extensions = false");
+  db.run("SET autoload_known_extensions = false");
+  db.run("SET lock_configuration = true");
+}
 function getDb() {
   if (_db) return _db;
   const dataDir = resolveDataDir();
   const db = new duckdb.Database(":memory:");
   registerViews(db, dataDir);
+  harden(db, dataDir);
   _db = db;
   return db;
 }
@@ -484,7 +493,7 @@ server.tool(
   "get_compound_compositions",
   "Get elemental compositions (weight fractions) for NIST XCOM standard materials. Useful for Bragg-additive cross-section calculations.",
   {
-    material: z.string().optional().describe("Material name (e.g. 'Water, Liquid'). Omit to list all materials.")
+    material: z.string().optional().describe("Material key (e.g. 'water', 'air', 'concrete'). Omit to list all materials.")
   },
   async ({ material }) => {
     const db = getDb();
@@ -633,6 +642,8 @@ server.tool(
 var transport = new StdioServerTransport();
 await server.connect(transport);
 export {
+  ALLOWED_FIRST_WORDS,
+  BLOCKED_FUNCTIONS,
   PKG_VERSION,
   ensureCatalog,
   getDb,

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/index.ts"],"sourcesContent":["/**\n * nucl-parquet MCP server — wraps local data via DuckDB.\n *\n * SSoT refactor (epic #173, Sub-D #178): the MCP is a thin shell over\n * DuckDB-backed Parquet views, not a re-implementation of parquet I/O.\n * All data is read from the local data directory — no HTTP fetching.\n */\n\nimport { existsSync, readFileSync, readdirSync } from \"node:fs\";\nimport { createRequire } from \"node:module\";\nimport { join, resolve } from \"node:path\";\nimport { homedir } from \"node:os\";\n\nimport { McpServer } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport { StdioServerTransport } from \"@modelcontextprotocol/sdk/server/stdio.js\";\nimport duckdb from \"duckdb\";\nimport { z } from \"zod\";\n\nconst require = createRequire(import.meta.url);\nexport const { version: PKG_VERSION } = require(\"../package.json\") as { version: string };\n\n// ---------------------------------------------------------------------------\n// Data directory resolution\n// ---------------------------------------------------------------------------\n\nfunction resolveDataDir(): string {\n  // 1. Explicit env var\n  const envDir = process.env.NUCL_PARQUET_DATA;\n  if (envDir && existsSync(envDir)) return resolve(envDir);\n\n  // 2. Repo-local data/ (development)\n  const repoDir = resolve(import.meta.dirname ?? \".\", \"..\", \"..\", \"..\", \"..\", \"data\");\n  if (existsSync(join(repoDir, \"catalog.json\"))) return repoDir;\n\n  // 3. ~/.nucl-parquet/ (installed data)\n  const homeData = join(homedir(), \".nucl-parquet\");\n  if (existsSync(join(homeData, \"catalog.json\"))) return homeData;\n\n  throw new Error(\n    \"Cannot find nucl-parquet data directory. Set NUCL_PARQUET_DATA env var \" +\n    \"or place data at ~/.nucl-parquet/. Data releases: \" +\n    \"https://github.com/exoma-ch/nucl-parquet/releases\",\n  );\n}\n\n// ---------------------------------------------------------------------------\n// Catalog (loaded from disk, not hardcoded)\n// ---------------------------------------------------------------------------\n\ninterface Library {\n  name: string;\n  description: string;\n  source_url?: string;\n  projectiles?: string[];\n  data_type?: string;\n  version: string;\n  path?: string;\n}\n\ninterface ViewDef {\n  path: string;\n  type?: \"file\" | \"glob\";\n  optional?: boolean;\n  note?: string;\n}\n\ninterface Catalog {\n  /**\n   * The data release this server is serving, e.g. `2026.8.3`.\n   *\n   * Distinct from `Library.version`, which is the *evaluation's* version\n   * (\"2023-iso\"). They answer different questions, and conflating them would\n   * make a cross-server check silently wrong rather than merely absent (#348).\n   *\n   * Read from the catalog on disk, never compiled in — a build-time constant\n   * would be a second source of truth for the one fact whose whole job is to\n   * identify the data actually being read.\n   */\n  data_version: string;\n  libraries: Record<string, Library>;\n  views?: Record<string, ViewDef>;\n  [key: string]: unknown;\n}\n\nlet _catalog: Catalog | undefined;\n\nexport function ensureCatalog(): Catalog {\n  if (_catalog) return _catalog;\n  const dataDir = resolveDataDir();\n  _catalog = parseCatalog(readFileSync(join(dataDir, \"catalog.json\"), \"utf-8\"), dataDir);\n  return _catalog;\n}\n\n/**\n * Parse and validate a catalog.\n *\n * Separate from {@link ensureCatalog} because that one memoises a module-level\n * singleton, which a test cannot re-enter — so the validation below would be\n * unreachable from a test and, in practice, unverified.\n */\nexport function parseCatalog(raw: string, dataDir: string): Catalog {\n  const parsed = JSON.parse(raw) as Catalog;\n  // `as Catalog` is a claim, not a check. `data_version` is required by\n  // data/catalog.schema.json, and the whole point of reporting it is that it\n  // identifies the tree actually being read — so an absent one must fail here\n  // rather than surface as `undefined` in a referral an agent is trying to\n  // verify (#348). The Rust server refuses the same catalog, for the same\n  // reason.\n  if (typeof parsed.data_version !== \"string\" || parsed.data_version === \"\") {\n    throw new Error(\n      `catalog.json at ${dataDir} has no 'data_version'. It is required by ` +\n        `data/catalog.schema.json and identifies the data release this server serves; ` +\n        `refusing to start rather than report an unknown release as if it were known.`,\n    );\n  }\n  return parsed;\n}\n\n/**\n * The `list_libraries` payload: the data release, then the libraries.\n *\n * A named function rather than an inline object so a test can assert the shape\n * the tool actually returns. Asserting only that the catalog *has* a\n * data_version would pass while the tool still returned a bare array.\n */\nexport function libraryListPayload(cat: Catalog): {\n  data_version: string;\n  libraries: Array<Record<string, unknown>>;\n} {\n  return {\n    // Beside the array rather than on each entry, so the release and a\n    // library's evaluation `version` cannot be read as the same kind of thing.\n    data_version: cat.data_version,\n    libraries: Object.entries(cat.libraries)\n      .filter(([, lib]) => lib.projectiles)\n      .map(([id, lib]) => ({\n        id,\n        name: lib.name,\n        description: lib.description,\n        projectiles: lib.projectiles,\n        version: lib.version,\n        data_type: lib.data_type,\n      })),\n  };\n}\n\n// ---------------------------------------------------------------------------\n// DuckDB connection (lazy init, thread-safe via singleton)\n// ---------------------------------------------------------------------------\n\nlet _db: duckdb.Database | undefined;\n\nfunction hasParquetFiles(dir: string): boolean {\n  if (!existsSync(dir)) return false;\n  try {\n    return readdirSync(dir).some((f) => f.endsWith(\".parquet\"));\n  } catch {\n    return false;\n  }\n}\n\nfunction registerParquet(db: duckdb.Database, filePath: string, viewName: string): void {\n  if (existsSync(filePath)) {\n    db.run(`CREATE VIEW ${viewName} AS SELECT * FROM read_parquet('${filePath}')`);\n  }\n}\n\nfunction registerGlob(db: duckdb.Database, dir: string, viewName: string): void {\n  if (hasParquetFiles(dir)) {\n    const glob = join(dir, \"*.parquet\");\n    db.run(`CREATE VIEW ${viewName} AS SELECT * FROM read_parquet('${glob}')`);\n  }\n}\n\nfunction registerViews(db: duckdb.Database, dataDir: string): void {\n  const catalog = ensureCatalog();\n\n  // --- Cross-section libraries ---\n  const libViews: string[] = [];\n  for (const [libKey, lib] of Object.entries(catalog.libraries)) {\n    if (!lib.path) continue;\n    const libDir = join(dataDir, lib.path);\n    if (!hasParquetFiles(libDir)) continue;\n\n    const viewName = libKey.replace(/-/g, \"_\").replace(/\\./g, \"_\");\n    const glob = join(libDir, \"*.parquet\");\n    db.run(\n      `CREATE VIEW ${viewName} AS SELECT *, '${libKey}' AS library FROM read_parquet('${glob}', filename=true)`,\n    );\n    if (lib.data_type === \"cross_sections\") libViews.push(viewName);\n  }\n  if (libViews.length > 0) {\n    const union = libViews.map((v) => `SELECT * FROM ${v}`).join(\" UNION ALL \");\n    db.run(`CREATE VIEW xs AS ${union}`);\n  }\n\n  // --- Catalog-driven view registration ---\n  // All views declared in catalog.json::views — single source of truth.\n  // New data tables become queryable by adding an entry to catalog.json,\n  // no code changes needed in any client (Python, TypeScript, Rust).\n  for (const [viewName, viewDef] of Object.entries(catalog.views ?? {})) {\n    const viewPath = join(dataDir, viewDef.path);\n    if (viewDef.type === \"glob\") {\n      registerGlob(db, viewPath, viewName);\n    } else {\n      registerParquet(db, viewPath, viewName);\n    }\n  }\n\n  // --- Special views that need logic beyond simple registration ---\n\n  // ground_states: when nuclides.parquet exists, override with filtered view\n  const nuclidesPath = join(dataDir, \"meta\", \"ensdf\", \"nuclides.parquet\");\n  if (existsSync(nuclidesPath)) {\n    // `'g'`, not `''`: #380 gave `state` one vocabulary and nuclides.parquet\n    // now reads g=3148 / m=739 / m2=82 / m3=7 / null=13, with no `''` at all.\n    // This view was silently empty against the rebuilt data.\n    db.run(\"CREATE OR REPLACE VIEW ground_states AS SELECT * FROM nuclides WHERE state = 'g'\");\n  }\n\n  // EADL aliases: eadl_transitions (v0.11 compat) + fluorescence (radiative subset)\n  const eadlDir = join(dataDir, \"meta\", \"eadl\");\n  if (hasParquetFiles(eadlDir)) {\n    db.run(\"CREATE VIEW eadl_transitions AS SELECT * FROM atomic_relaxation\");\n    db.run(\"CREATE VIEW fluorescence AS SELECT * FROM atomic_relaxation WHERE transition_type = 'radiative'\");\n  }\n}\n\nexport function getDb(): duckdb.Database {\n  if (_db) return _db;\n  const dataDir = resolveDataDir();\n  const db = new duckdb.Database(\":memory:\");\n  registerViews(db, dataDir);\n  _db = db;\n  return db;\n}\n\n// ---------------------------------------------------------------------------\n// DuckDB async helpers\n// ---------------------------------------------------------------------------\n\nfunction dbAll(db: duckdb.Database, sql: string, params?: unknown[]): Promise<Record<string, unknown>[]> {\n  return new Promise((resolve, reject) => {\n    const cb = (err: Error | null, rows: Record<string, unknown>[]) => {\n      if (err) reject(err);\n      else resolve(rows);\n    };\n    if (params && params.length > 0) {\n      db.all(sql, ...params, cb);\n    } else {\n      db.all(sql, cb);\n    }\n  });\n}\n\nfunction dbRun(db: duckdb.Database, sql: string): Promise<void> {\n  return new Promise((resolve, reject) => {\n    db.run(sql, (err: Error | null) => {\n      if (err) reject(err);\n      else resolve();\n    });\n  });\n}\n\n/** Serialize rows to JSON, converting BigInt values to Number. */\nfunction safeStringify(obj: unknown, indent?: number): string {\n  return JSON.stringify(\n    obj,\n    (_key, value) => (typeof value === \"bigint\" ? Number(value) : value),\n    indent,\n  );\n}\n\n// ---------------------------------------------------------------------------\n// Query helper\n// ---------------------------------------------------------------------------\n\nasync function query(\n  sql: string,\n  params?: unknown[],\n  maxRows: number = 500,\n): Promise<{ total: number; truncated: boolean; rows: Record<string, unknown>[] }> {\n  const db = getDb();\n  // Get total count via subquery\n  const countSql = `SELECT CAST(COUNT(*) AS INTEGER) AS n FROM (${sql})`;\n  const countRows = await dbAll(db, countSql, params);\n  const total = (countRows[0]?.n as number) ?? 0;\n\n  // Get limited rows\n  const limitSql = `${sql} LIMIT ${maxRows}`;\n  const rows = await dbAll(db, limitSql, params);\n  return { total, truncated: total > maxRows, rows };\n}\n\n// ---------------------------------------------------------------------------\n// MCP Server\n// ---------------------------------------------------------------------------\n\n/**\n * Server instructions, naming the data release in the client's context.\n *\n * The referral case #348 is about does not go through `list_libraries`:\n * hyrr-mcp sends an agent straight to `get_cross_sections` for full σ(E)\n * curves, having stated the release *it* computed against. Reporting the\n * release only from a tool the agent has no reason to call would leave that\n * claim as unverifiable as it was — so it is stated here too, where it reaches\n * the model without a round trip, and in `list_libraries` where it can be read\n * programmatically. Both read the same loaded catalog, so they cannot disagree.\n *\n * Kept word-for-word in step with the Rust server's `instructions()`; a test\n * pins that the two do not drift.\n */\nexport function instructions(dataVersion: string): string {\n  return (\n    `Serving nucl-parquet data release ${dataVersion}. This identifies the *data*, ` +\n    `not this server's version — report it whenever you compare results with another ` +\n    `server or tool. If another source states a different release, say so: agreement ` +\n    `or disagreement computed across two releases is an artefact of the mismatch, not ` +\n    `a physics result. Call list_libraries to read the same value programmatically.`\n  );\n}\n\nconst server = new McpServer(\n  {\n    name: \"nucl-parquet\",\n    // The package version — the software, not the data. Both are reported\n    // because they answer different questions, and only one of them changes\n    // when the data does.\n    version: PKG_VERSION,\n  },\n  { instructions: instructions(ensureCatalog().data_version) },\n);\n\n// ---------------------------------------------------------------------------\n// Library / cross-section tools\n// ---------------------------------------------------------------------------\n\nserver.tool(\n  \"list_libraries\",\n  \"List all available nuclear data libraries with projectiles and descriptions\",\n  {},\n  async () => {\n    // An envelope, not a bare array: `data_version` identifies the data\n    // *release* these libraries came out of, a different fact from any one\n    // library's evaluation `version`, and it has nowhere else to live (#348).\n    return {\n      content: [\n        { type: \"text\" as const, text: safeStringify(libraryListPayload(ensureCatalog()), 2) },\n      ],\n    };\n  },\n);\n\nserver.tool(\n  \"list_isotopes\",\n  \"List available target elements for a given library and projectile. Returns element symbols.\",\n  {\n    library: z.string().describe(\"Library ID, e.g. 'tendl-2025', 'endfb-8.1'\"),\n    projectile: z.string().describe(\"Projectile: n, p, d, t, h, a, g\"),\n  },\n  async ({ library, projectile }) => {\n    const cat = ensureCatalog();\n    const lib = cat.libraries[library];\n    if (!lib) throw new Error(`Unknown library: ${library}. Use list_libraries to see available libraries.`);\n    if (!lib.projectiles?.includes(projectile)) {\n      throw new Error(`Projectile '${projectile}' not available for ${library}. Available: ${lib.projectiles?.join(\", \") ?? \"none\"}`);\n    }\n\n    const dataDir = resolveDataDir();\n    const libPath = lib.path;\n    if (!libPath?.endsWith(\"xs/\")) {\n      throw new Error(`Library ${library} path does not end with 'xs/' — cannot derive manifest path`);\n    }\n    const manifestPath = join(dataDir, libPath.replace(\"xs/\", \"manifest.json\"));\n    if (!existsSync(manifestPath)) {\n      throw new Error(`Manifest not found at ${manifestPath}`);\n    }\n    const manifest = JSON.parse(readFileSync(manifestPath, \"utf-8\")) as { elements?: string[] };\n    const elements = manifest.elements ?? [];\n\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ library, projectile, elements, count: elements.length }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_cross_sections\",\n  \"Get nuclear reaction cross-section data for a specific target element. Returns energy (MeV) and cross-section (mb) arrays with reaction product info.\",\n  {\n    library: z.string().describe(\"Library ID, e.g. 'tendl-2025'\"),\n    projectile: z.string().describe(\"Projectile: n, p, d, t, h, a, g\"),\n    element: z.string().describe(\"Target element symbol, e.g. 'Cu', 'Fe', 'Au'\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ library, projectile, element, max_rows }) => {\n    if (!/^[npdthag]$/.test(projectile)) {\n      throw new Error(`Invalid projectile: '${projectile}'. Must be one of: n, p, d, t, h, a, g`);\n    }\n    if (!/^[A-Z][a-z]?$/.test(element)) {\n      throw new Error(`Invalid element symbol: '${element}'. Must be 1-2 letters (e.g. 'Cu', 'Fe')`);\n    }\n\n    const cat = ensureCatalog();\n    const lib = cat.libraries[library];\n    if (!lib) throw new Error(`Unknown library: ${library}`);\n\n    const dataDir = resolveDataDir();\n    const parquetPath = join(dataDir, `${lib.path}${projectile}_${element}.parquet`);\n    if (!existsSync(parquetPath)) {\n      throw new Error(`No data for ${projectile}_${element} in ${library}`);\n    }\n\n    const db = getDb();\n    const result = await query(\n      `SELECT * FROM read_parquet('${parquetPath}')`,\n      [],\n      max_rows ?? 500,\n    );\n\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ library, projectile, element, ...result }, 2),\n      }],\n    };\n  },\n);\n\n// ---------------------------------------------------------------------------\n// Nuclear structure tools (DuckDB views)\n// ---------------------------------------------------------------------------\n\nserver.tool(\n  \"get_decay_data\",\n  \"Get radioactive decay data (half-lives, decay modes, daughters) for a nuclide or element. Filter by Z and/or A.\",\n  {\n    z: z.number().optional().describe(\"Atomic number (e.g. 92 for U)\"),\n    a: z.number().optional().describe(\"Mass number (e.g. 238)\"),\n  },\n  async ({ z: zNum, a: aNum }) => {\n    if (zNum === undefined && aNum === undefined) {\n      throw new Error(\"Provide at least z or a to filter decay data.\");\n    }\n    const conditions: string[] = [];\n    const params: unknown[] = [];\n    if (zNum !== undefined) { conditions.push(\"Z = ?\"); params.push(zNum); }\n    if (aNum !== undefined) { conditions.push(\"A = ?\"); params.push(aNum); }\n\n    const result = await query(\n      `SELECT * FROM decay WHERE ${conditions.join(\" AND \")}`,\n      params,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, count: result.total, rows: result.rows }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_abundances\",\n  \"Get natural isotope abundances and atomic masses for an element.\",\n  {\n    z: z.number().describe(\"Atomic number (e.g. 29 for Cu)\"),\n  },\n  async ({ z: zNum }) => {\n    const result = await query(\"SELECT * FROM abundances WHERE Z = ?\", [zNum]);\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, count: result.total, isotopes: result.rows }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_stopping_power\",\n  \"Get mass stopping power (dE/dx) data for a projectile in a target element.\",\n  {\n    source: z.string().describe(\n      \"Data source: PSTAR (protons), ASTAR (α, NIST ICRU-49), ESTAR (electrons), dSTAR, tSTAR (velocity-scaled from PSTAR), or catima (full Z×Z table)\",\n    ),\n    target_z: z.number().describe(\"Target element atomic number\"),\n  },\n  async ({ source, target_z }) => {\n    const viewMap: Record<string, string> = {\n      PSTAR: \"stopping\", ASTAR: \"stopping\", ESTAR: \"stopping\",\n      dSTAR: \"stopping\", tSTAR: \"stopping\", catima: \"catima_stopping\",\n    };\n    if (!(source in viewMap)) {\n      throw new Error(`Unknown source '${source}'. Valid: PSTAR, ASTAR, ESTAR, dSTAR, tSTAR, catima`);\n    }\n    const view = viewMap[source];\n    const sql = source === \"catima\"\n      ? `SELECT * FROM ${view} WHERE target_Z = ?`\n      : `SELECT * FROM ${view} WHERE source = ? AND target_Z = ?`;\n    const params = source === \"catima\" ? [target_z] : [source, target_z];\n\n    const result = await query(sql, params);\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ source, target_z, count: result.total, rows: result.rows }, 2),\n      }],\n    };\n  },\n);\n\n// ---------------------------------------------------------------------------\n// Radiation / coincidence / spectra tools\n// ---------------------------------------------------------------------------\n\nserver.tool(\n  \"get_radiation\",\n  \"Get radiation emissions (gammas, X-rays, Auger electrons, conversion electrons) for a nuclide.\",\n  {\n    z: z.number().describe(\"Atomic number of the parent nuclide\"),\n    a: z.number().optional().describe(\"Mass number (omit for all isotopes of element Z)\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, max_rows }) => {\n    const conditions = [\"Z = ?\"];\n    const params: unknown[] = [zNum];\n    if (aNum !== undefined) { conditions.push(\"A = ?\"); params.push(aNum); }\n\n    const result = await query(\n      `SELECT * FROM radiation WHERE ${conditions.join(\" AND \")}`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_coincidences\",\n  \"Get gamma-gamma and mixed-emission coincidence pairs for a nuclide. Includes beta/EC/X-ray/Auger/511 keV annihilation paired with gammas.\",\n  {\n    z: z.number().describe(\"Atomic number of the parent nuclide\"),\n    a: z.number().optional().describe(\"Mass number (omit for all isotopes of element Z)\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, max_rows }) => {\n    const conditions = [\"Z = ?\"];\n    const params: unknown[] = [zNum];\n    if (aNum !== undefined) { conditions.push(\"A = ?\"); params.push(aNum); }\n\n    const result = await query(\n      `SELECT * FROM coincidences WHERE ${conditions.join(\" AND \")}`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_summing_partners\",\n  \"Get ICC-corrected summing partners for HPGe true-coincidence-summing (TCS) corrections. Returns emission pairs with pre-computed icc_correction_factor and pure_emission_joint_intensity.\",\n  {\n    z: z.number().describe(\"Atomic number of the daughter nuclide (filing convention)\"),\n    a: z.number().describe(\"Mass number\"),\n    primary_energy_keV: z.number().optional().describe(\"Filter to pairs matching this energy on either side\"),\n    tolerance_keV: z.number().optional().describe(\"Energy match tolerance in keV (default 0.5)\"),\n    emission1_rad_type: z.string().optional().describe(\"Filter side 1: 'gamma', 'xray', 'auger'\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, primary_energy_keV, tolerance_keV, emission1_rad_type, max_rows }) => {\n    const conditions = [\"Z = ?\", \"A = ?\"];\n    const params: unknown[] = [zNum, aNum];\n    const tol = tolerance_keV ?? 0.5;\n\n    if (primary_energy_keV !== undefined) {\n      conditions.push(\"(ABS(emission1_energy_keV - ?) < ? OR ABS(emission2_energy_keV - ?) < ?)\");\n      params.push(primary_energy_keV, tol, primary_energy_keV, tol);\n    }\n    if (emission1_rad_type !== undefined) {\n      conditions.push(\"emission1_rad_type = ?\");\n      params.push(emission1_rad_type);\n    }\n\n    const result = await query(\n      `SELECT * FROM summing_partners WHERE ${conditions.join(\" AND \")} ORDER BY pure_emission_joint_intensity DESC`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, primary_energy_keV, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_emissions\",\n  \"Get absolute per-decay photon emission intensities (NuDat-equivalent). Returns gamma emissions for a parent nuclide with absolute intensities (photon emission probability per decay, 0-100%). Filed by parent, not daughter.\",\n  {\n    parent_z: z.number().describe(\"Atomic number of the decaying parent (e.g. 27 for Co-60)\"),\n    parent_a: z.number().describe(\"Mass number of the parent (e.g. 60 for Co-60)\"),\n    parent_state: z.string().optional().describe(\"Nuclear state: '' (ground), 'm', 'm2'\"),\n    decay_mode: z.string().optional().describe(\"Filter by decay mode: 'beta-', 'KshellEC', 'IT', etc.\"),\n    energy_keV: z.number().optional().describe(\"Filter to gammas near this energy\"),\n    tolerance_keV: z.number().optional().describe(\"Energy tolerance (default 0.5 keV)\"),\n    min_intensity_pct: z.number().optional().describe(\"Minimum absolute intensity (%) to include\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ parent_z, parent_a, parent_state, decay_mode, energy_keV, tolerance_keV, min_intensity_pct, max_rows }) => {\n    const conditions = [\"parent_Z = ?\", \"parent_A = ?\", \"parent_state = ?\"];\n    const params: unknown[] = [parent_z, parent_a, parent_state ?? \"\"];\n    const tol = tolerance_keV ?? 0.5;\n\n    if (decay_mode !== undefined) {\n      conditions.push(\"decay_mode = ?\");\n      params.push(decay_mode);\n    }\n    if (energy_keV !== undefined) {\n      conditions.push(\"ABS(energy_keV - ?) < ?\");\n      params.push(energy_keV, tol);\n    }\n    if (min_intensity_pct !== undefined && min_intensity_pct > 0) {\n      conditions.push(\"intensity_pct >= ?\");\n      params.push(min_intensity_pct);\n    }\n\n    const result = await query(\n      `SELECT * FROM emissions WHERE ${conditions.join(\" AND \")} ORDER BY intensity_pct DESC`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ parent_z, parent_a, parent_state: parent_state ?? \"\", ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_beta_spectrum\",\n  \"Get the continuous beta-decay kinetic-energy spectrum for a nuclide. Returns pre-tabulated Fermi-function spectra (dN/dE normalized to 1).\",\n  {\n    z: z.number().describe(\"Atomic number of the parent nuclide\"),\n    a: z.number().describe(\"Mass number of the parent nuclide\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, max_rows }) => {\n    const result = await query(\n      \"SELECT * FROM beta_spectra WHERE Z = ? AND A = ?\",\n      [zNum, aNum],\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_compound_compositions\",\n  \"Get elemental compositions (weight fractions) for NIST XCOM standard materials. Useful for Bragg-additive cross-section calculations.\",\n  {\n    material: z.string().optional().describe(\"Material name (e.g. 'Water, Liquid'). Omit to list all materials.\"),\n  },\n  async ({ material }) => {\n    const db = getDb();\n    if (material === undefined) {\n      const rows = await dbAll(db, \"SELECT DISTINCT material FROM compound_compositions ORDER BY material\");\n      const materials = rows.map((r) => r.material as string);\n      return {\n        content: [{\n          type: \"text\" as const,\n          text: safeStringify({ count: materials.length, materials }, 2),\n        }],\n      };\n    }\n    const result = await query(\n      \"SELECT * FROM compound_compositions WHERE material = ?\",\n      [material],\n    );\n    if (result.total === 0) {\n      const allRows = await dbAll(db, \"SELECT DISTINCT material FROM compound_compositions ORDER BY material\");\n      const all = allRows.map((r) => r.material as string);\n      throw new Error(`Unknown material: '${material}'. Available: ${all.join(\", \")}`);\n    }\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ material, count: result.total, composition: result.rows }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_electron_stopping\",\n  \"Get electron stopping power with collision/radiative split. Richer than ESTAR — includes ~183 compounds plus all elements Z=1..98.\",\n  {\n    target: z.string().optional().describe(\"Compound name (e.g. 'G4_WATER'). For elements use target_z instead.\"),\n    target_z: z.number().optional().describe(\"Atomic number for elemental targets\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ target, target_z, max_rows }) => {\n    if (target === undefined && target_z === undefined) {\n      throw new Error(\"Provide target (compound name) or target_z (atomic number).\");\n    }\n    let result;\n    if (target_z !== undefined) {\n      result = await query(\n        \"SELECT * FROM electron_stopping WHERE target_Z = ?\",\n        [target_z],\n        max_rows ?? 500,\n      );\n    } else {\n      result = await query(\n        \"SELECT * FROM electron_stopping WHERE name = ? OR g4_name = ?\",\n        [target, target],\n        max_rows ?? 500,\n      );\n    }\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ target, target_z, ...result }, 2),\n      }],\n    };\n  },\n);\n\n// ---------------------------------------------------------------------------\n// SQL escape hatch (Sub-E #179)\n// ---------------------------------------------------------------------------\n\n// Patterns that indicate file-access functions — blocked in user SQL to prevent\n// read_parquet('/etc/passwd') style attacks. The pre-registered DuckDB views\n// already expose all nuclear data; there's no legitimate need for raw file access.\nconst BLOCKED_FUNCTIONS = /\\b(read_parquet|parquet_scan|parquet_metadata|parquet_schema|read_csv|read_csv_auto|read_json|read_json_auto|read_text|read_blob|glob|copy|export|attach|load|install|create|drop|alter|insert|update|delete|truncate|query_table|pragma)\\b/i;\n\nconst ALLOWED_FIRST_WORDS = new Set([\"SELECT\", \"WITH\", \"EXPLAIN\", \"DESCRIBE\", \"SHOW\", \"SUMMARIZE\"]);\n\nserver.tool(\n  \"sql_query\",\n  \"Execute read-only SQL against all 70+ nuclear data tables. Supports JOINs, aggregations, window functions. Use describe_schema() to discover available tables and columns.\",\n  {\n    sql: z.string().describe(\"Read-only SQL query. DDL/DML will be rejected.\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 10000)\"),\n  },\n  async ({ sql: userSql, max_rows }) => {\n    const stripped = userSql.trim();\n    if (!stripped) throw new Error(\"Empty SQL query\");\n\n    const firstWord = stripped.split(/\\s/)[0].toUpperCase();\n    if (!ALLOWED_FIRST_WORDS.has(firstWord)) {\n      throw new Error(`Only read queries are allowed (SELECT, WITH, EXPLAIN, DESCRIBE). Got: ${firstWord}`);\n    }\n    if (BLOCKED_FUNCTIONS.test(stripped)) {\n      throw new Error(\"Only read queries are allowed (SELECT, WITH, EXPLAIN, DESCRIBE). File-access and DDL functions are blocked.\");\n    }\n\n    const db = getDb();\n    const limit = max_rows ?? 10000;\n    let total: number;\n    let rows: Record<string, unknown>[];\n    try {\n      // Get total count first, then fetch limited rows\n      const countRows = await dbAll(db, `SELECT CAST(COUNT(*) AS INTEGER) AS n FROM (${stripped})`);\n      total = (countRows[0]?.n as number) ?? 0;\n      rows = await dbAll(db, `SELECT * FROM (${stripped}) LIMIT ${limit}`);\n    } catch (e) {\n      throw new Error(`SQL error: ${(e as Error).message}`);\n    }\n\n    const truncated = total > limit;\n    const display = rows;\n\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ total, truncated, rows: display }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"describe_schema\",\n  \"List all available tables/views with their column names and types. Use this to discover what data is available before writing SQL queries.\",\n  {},\n  async () => {\n    const db = getDb();\n    const tables = await dbAll(db, \"SHOW TABLES\");\n    const tableNames = tables.map((r) => r.name as string).sort();\n\n    const schema: Record<string, { name: string; type: string }[]> = {};\n    for (const tbl of tableNames) {\n      try {\n        const cols = await dbAll(db, `DESCRIBE ${tbl}`);\n        schema[tbl] = cols.map((c) => ({ name: c.column_name as string, type: c.column_type as string }));\n      } catch {\n        schema[tbl] = [];\n      }\n    }\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ tables: tableNames.length, schema }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"list_tables\",\n  \"List all available table/view names (short form of describe_schema).\",\n  {},\n  async () => {\n    const db = getDb();\n    const tables = await dbAll(db, \"SHOW TABLES\");\n    const tableNames = tables.map((r) => r.name as string).sort();\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ count: tableNames.length, tables: tableNames }, 2),\n      }],\n    };\n  },\n);\n\n// ---------------------------------------------------------------------------\n// Main\n// ---------------------------------------------------------------------------\n\nconst transport = new StdioServerTransport();\nawait 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Explicit env var\n  const envDir = process.env.NUCL_PARQUET_DATA;\n  if (envDir && existsSync(envDir)) return resolve(envDir);\n\n  // 2. Repo-local data/ (development)\n  const repoDir = resolve(import.meta.dirname ?? \".\", \"..\", \"..\", \"..\", \"..\", \"data\");\n  if (existsSync(join(repoDir, \"catalog.json\"))) return repoDir;\n\n  // 3. ~/.nucl-parquet/ (installed data)\n  const homeData = join(homedir(), \".nucl-parquet\");\n  if (existsSync(join(homeData, \"catalog.json\"))) return homeData;\n\n  throw new Error(\n    \"Cannot find nucl-parquet data directory. Set NUCL_PARQUET_DATA env var \" +\n    \"or place data at ~/.nucl-parquet/. Data releases: \" +\n    \"https://github.com/exoma-ch/nucl-parquet/releases\",\n  );\n}\n\n// ---------------------------------------------------------------------------\n// Catalog (loaded from disk, not hardcoded)\n// ---------------------------------------------------------------------------\n\ninterface Library {\n  name: string;\n  description: string;\n  source_url?: string;\n  projectiles?: string[];\n  data_type?: string;\n  version: string;\n  path?: string;\n}\n\ninterface ViewDef {\n  path: string;\n  type?: \"file\" | \"glob\";\n  optional?: boolean;\n  note?: string;\n}\n\ninterface Catalog {\n  /**\n   * The data release this server is serving, e.g. `2026.8.3`.\n   *\n   * Distinct from `Library.version`, which is the *evaluation's* version\n   * (\"2023-iso\"). They answer different questions, and conflating them would\n   * make a cross-server check silently wrong rather than merely absent (#348).\n   *\n   * Read from the catalog on disk, never compiled in — a build-time constant\n   * would be a second source of truth for the one fact whose whole job is to\n   * identify the data actually being read.\n   */\n  data_version: string;\n  libraries: Record<string, Library>;\n  views?: Record<string, ViewDef>;\n  [key: string]: unknown;\n}\n\nlet _catalog: Catalog | undefined;\n\nexport function ensureCatalog(): Catalog {\n  if (_catalog) return _catalog;\n  const dataDir = resolveDataDir();\n  _catalog = parseCatalog(readFileSync(join(dataDir, \"catalog.json\"), \"utf-8\"), dataDir);\n  return _catalog;\n}\n\n/**\n * Parse and validate a catalog.\n *\n * Separate from {@link ensureCatalog} because that one memoises a module-level\n * singleton, which a test cannot re-enter — so the validation below would be\n * unreachable from a test and, in practice, unverified.\n */\nexport function parseCatalog(raw: string, dataDir: string): Catalog {\n  const parsed = JSON.parse(raw) as Catalog;\n  // `as Catalog` is a claim, not a check. `data_version` is required by\n  // data/catalog.schema.json, and the whole point of reporting it is that it\n  // identifies the tree actually being read — so an absent one must fail here\n  // rather than surface as `undefined` in a referral an agent is trying to\n  // verify (#348). The Rust server refuses the same catalog, for the same\n  // reason.\n  if (typeof parsed.data_version !== \"string\" || parsed.data_version === \"\") {\n    throw new Error(\n      `catalog.json at ${dataDir} has no 'data_version'. It is required by ` +\n        `data/catalog.schema.json and identifies the data release this server serves; ` +\n        `refusing to start rather than report an unknown release as if it were known.`,\n    );\n  }\n  return parsed;\n}\n\n/**\n * The `list_libraries` payload: the data release, then the libraries.\n *\n * A named function rather than an inline object so a test can assert the shape\n * the tool actually returns. Asserting only that the catalog *has* a\n * data_version would pass while the tool still returned a bare array.\n */\nexport function libraryListPayload(cat: Catalog): {\n  data_version: string;\n  libraries: Array<Record<string, unknown>>;\n} {\n  return {\n    // Beside the array rather than on each entry, so the release and a\n    // library's evaluation `version` cannot be read as the same kind of thing.\n    data_version: cat.data_version,\n    libraries: Object.entries(cat.libraries)\n      .filter(([, lib]) => lib.projectiles)\n      .map(([id, lib]) => ({\n        id,\n        name: lib.name,\n        description: lib.description,\n        projectiles: lib.projectiles,\n        version: lib.version,\n        data_type: lib.data_type,\n      })),\n  };\n}\n\n// ---------------------------------------------------------------------------\n// DuckDB connection (lazy init, thread-safe via singleton)\n// ---------------------------------------------------------------------------\n\nlet _db: duckdb.Database | undefined;\n\nfunction hasParquetFiles(dir: string): boolean {\n  if (!existsSync(dir)) return false;\n  try {\n    return readdirSync(dir).some((f) => f.endsWith(\".parquet\"));\n  } catch {\n    return false;\n  }\n}\n\nfunction registerParquet(db: duckdb.Database, filePath: string, viewName: string): void {\n  if (existsSync(filePath)) {\n    db.run(`CREATE VIEW ${viewName} AS SELECT * FROM read_parquet('${filePath}')`);\n  }\n}\n\nfunction registerGlob(db: duckdb.Database, dir: string, viewName: string): void {\n  if (hasParquetFiles(dir)) {\n    const glob = join(dir, \"*.parquet\");\n    db.run(`CREATE VIEW ${viewName} AS SELECT * FROM read_parquet('${glob}')`);\n  }\n}\n\nfunction registerViews(db: duckdb.Database, dataDir: string): void {\n  const catalog = ensureCatalog();\n\n  // --- Cross-section libraries ---\n  const libViews: string[] = [];\n  for (const [libKey, lib] of Object.entries(catalog.libraries)) {\n    if (!lib.path) continue;\n    const libDir = join(dataDir, lib.path);\n    if (!hasParquetFiles(libDir)) continue;\n\n    const viewName = libKey.replace(/-/g, \"_\").replace(/\\./g, \"_\");\n    const glob = join(libDir, \"*.parquet\");\n    db.run(\n      `CREATE VIEW ${viewName} AS SELECT *, '${libKey}' AS library FROM read_parquet('${glob}', filename=true)`,\n    );\n    if (lib.data_type === \"cross_sections\") libViews.push(viewName);\n  }\n  if (libViews.length > 0) {\n    const union = libViews.map((v) => `SELECT * FROM ${v}`).join(\" UNION ALL \");\n    db.run(`CREATE VIEW xs AS ${union}`);\n  }\n\n  // --- Catalog-driven view registration ---\n  // All views declared in catalog.json::views — single source of truth.\n  // New data tables become queryable by adding an entry to catalog.json,\n  // no code changes needed in any client (Python, TypeScript, Rust).\n  for (const [viewName, viewDef] of Object.entries(catalog.views ?? {})) {\n    const viewPath = join(dataDir, viewDef.path);\n    if (viewDef.type === \"glob\") {\n      registerGlob(db, viewPath, viewName);\n    } else {\n      registerParquet(db, viewPath, viewName);\n    }\n  }\n\n  // --- Special views that need logic beyond simple registration ---\n\n  // ground_states: when nuclides.parquet exists, override with filtered view\n  const nuclidesPath = join(dataDir, \"meta\", \"ensdf\", \"nuclides.parquet\");\n  if (existsSync(nuclidesPath)) {\n    // `'g'`, not `''`: #380 gave `state` one vocabulary and nuclides.parquet\n    // now reads g=3148 / m=739 / m2=82 / m3=7 / null=13, with no `''` at all.\n    // This view was silently empty against the rebuilt data.\n    db.run(\"CREATE OR REPLACE VIEW ground_states AS SELECT * FROM nuclides WHERE state = 'g'\");\n  }\n\n  // EADL aliases: eadl_transitions (v0.11 compat) + fluorescence (radiative subset)\n  const eadlDir = join(dataDir, \"meta\", \"eadl\");\n  if (hasParquetFiles(eadlDir)) {\n    db.run(\"CREATE VIEW eadl_transitions AS SELECT * FROM atomic_relaxation\");\n    db.run(\"CREATE VIEW fluorescence AS SELECT * FROM atomic_relaxation WHERE transition_type = 'radiative'\");\n  }\n}\n\n/**\n * Confine the connection to reading the data tree, then freeze its settings.\n *\n * `sql_query` hands callers a SQL prompt, and its keyword blocklist cannot list\n * every DuckDB function that opens a file: `sniff_csv('/etc/passwd')` and\n * `read_json_objects(...)` both got past it and read outside the data tree. The\n * connection itself must not be able to, whatever the SQL says:\n *\n * - `allowed_directories` first, because the views read Parquet files, which is\n *   itself external access; without the exception every tool fails.\n * - `enable_external_access = false`: no other files, no network, no INSTALL.\n * - extension auto-install and auto-load off.\n * - `lock_configuration` last, so a caller cannot `SET` any of it back.\n *\n * Queued on the same connection after `registerViews`, so it takes effect\n * before the first caller query.\n */\nfunction harden(db: duckdb.Database, dataDir: string): void {\n  const quoted = dataDir.replaceAll(\"'\", \"''\");\n  db.run(`SET allowed_directories = ['${quoted}']`);\n  db.run(\"SET enable_external_access = false\");\n  db.run(\"SET autoinstall_known_extensions = false\");\n  db.run(\"SET autoload_known_extensions = false\");\n  db.run(\"SET lock_configuration = true\");\n}\n\nexport function getDb(): duckdb.Database {\n  if (_db) return _db;\n  const dataDir = resolveDataDir();\n  const db = new duckdb.Database(\":memory:\");\n  registerViews(db, dataDir);\n  harden(db, dataDir);\n  _db = db;\n  return db;\n}\n\n// ---------------------------------------------------------------------------\n// DuckDB async helpers\n// ---------------------------------------------------------------------------\n\nfunction dbAll(db: duckdb.Database, sql: string, params?: unknown[]): Promise<Record<string, unknown>[]> {\n  return new Promise((resolve, reject) => {\n    const cb = (err: Error | null, rows: Record<string, unknown>[]) => {\n      if (err) reject(err);\n      else resolve(rows);\n    };\n    if (params && params.length > 0) {\n      db.all(sql, ...params, cb);\n    } else {\n      db.all(sql, cb);\n    }\n  });\n}\n\nfunction dbRun(db: duckdb.Database, sql: string): Promise<void> {\n  return new Promise((resolve, reject) => {\n    db.run(sql, (err: Error | null) => {\n      if (err) reject(err);\n      else resolve();\n    });\n  });\n}\n\n/** Serialize rows to JSON, converting BigInt values to Number. */\nfunction safeStringify(obj: unknown, indent?: number): string {\n  return JSON.stringify(\n    obj,\n    (_key, value) => (typeof value === \"bigint\" ? Number(value) : value),\n    indent,\n  );\n}\n\n// ---------------------------------------------------------------------------\n// Query helper\n// ---------------------------------------------------------------------------\n\nasync function query(\n  sql: string,\n  params?: unknown[],\n  maxRows: number = 500,\n): Promise<{ total: number; truncated: boolean; rows: Record<string, unknown>[] }> {\n  const db = getDb();\n  // Get total count via subquery\n  const countSql = `SELECT CAST(COUNT(*) AS INTEGER) AS n FROM (${sql})`;\n  const countRows = await dbAll(db, countSql, params);\n  const total = (countRows[0]?.n as number) ?? 0;\n\n  // Get limited rows\n  const limitSql = `${sql} LIMIT ${maxRows}`;\n  const rows = await dbAll(db, limitSql, params);\n  return { total, truncated: total > maxRows, rows };\n}\n\n// ---------------------------------------------------------------------------\n// MCP Server\n// ---------------------------------------------------------------------------\n\n/**\n * Server instructions, naming the data release in the client's context.\n *\n * The referral case #348 is about does not go through `list_libraries`:\n * hyrr-mcp sends an agent straight to `get_cross_sections` for full σ(E)\n * curves, having stated the release *it* computed against. Reporting the\n * release only from a tool the agent has no reason to call would leave that\n * claim as unverifiable as it was — so it is stated here too, where it reaches\n * the model without a round trip, and in `list_libraries` where it can be read\n * programmatically. Both read the same loaded catalog, so they cannot disagree.\n *\n * Kept word-for-word in step with the Rust server's `instructions()`; a test\n * pins that the two do not drift.\n */\nexport function instructions(dataVersion: string): string {\n  return (\n    `Serving nucl-parquet data release ${dataVersion}. This identifies the *data*, ` +\n    `not this server's version — report it whenever you compare results with another ` +\n    `server or tool. If another source states a different release, say so: agreement ` +\n    `or disagreement computed across two releases is an artefact of the mismatch, not ` +\n    `a physics result. Call list_libraries to read the same value programmatically.`\n  );\n}\n\nconst server = new McpServer(\n  {\n    name: \"nucl-parquet\",\n    // The package version — the software, not the data. Both are reported\n    // because they answer different questions, and only one of them changes\n    // when the data does.\n    version: PKG_VERSION,\n  },\n  { instructions: instructions(ensureCatalog().data_version) },\n);\n\n// ---------------------------------------------------------------------------\n// Library / cross-section tools\n// ---------------------------------------------------------------------------\n\nserver.tool(\n  \"list_libraries\",\n  \"List all available nuclear data libraries with projectiles and descriptions\",\n  {},\n  async () => {\n    // An envelope, not a bare array: `data_version` identifies the data\n    // *release* these libraries came out of, a different fact from any one\n    // library's evaluation `version`, and it has nowhere else to live (#348).\n    return {\n      content: [\n        { type: \"text\" as const, text: safeStringify(libraryListPayload(ensureCatalog()), 2) },\n      ],\n    };\n  },\n);\n\nserver.tool(\n  \"list_isotopes\",\n  \"List available target elements for a given library and projectile. Returns element symbols.\",\n  {\n    library: z.string().describe(\"Library ID, e.g. 'tendl-2025', 'endfb-8.1'\"),\n    projectile: z.string().describe(\"Projectile: n, p, d, t, h, a, g\"),\n  },\n  async ({ library, projectile }) => {\n    const cat = ensureCatalog();\n    const lib = cat.libraries[library];\n    if (!lib) throw new Error(`Unknown library: ${library}. Use list_libraries to see available libraries.`);\n    if (!lib.projectiles?.includes(projectile)) {\n      throw new Error(`Projectile '${projectile}' not available for ${library}. Available: ${lib.projectiles?.join(\", \") ?? \"none\"}`);\n    }\n\n    const dataDir = resolveDataDir();\n    const libPath = lib.path;\n    if (!libPath?.endsWith(\"xs/\")) {\n      throw new Error(`Library ${library} path does not end with 'xs/' — cannot derive manifest path`);\n    }\n    const manifestPath = join(dataDir, libPath.replace(\"xs/\", \"manifest.json\"));\n    if (!existsSync(manifestPath)) {\n      throw new Error(`Manifest not found at ${manifestPath}`);\n    }\n    const manifest = JSON.parse(readFileSync(manifestPath, \"utf-8\")) as { elements?: string[] };\n    const elements = manifest.elements ?? [];\n\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ library, projectile, elements, count: elements.length }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_cross_sections\",\n  \"Get nuclear reaction cross-section data for a specific target element. Returns energy (MeV) and cross-section (mb) arrays with reaction product info.\",\n  {\n    library: z.string().describe(\"Library ID, e.g. 'tendl-2025'\"),\n    projectile: z.string().describe(\"Projectile: n, p, d, t, h, a, g\"),\n    element: z.string().describe(\"Target element symbol, e.g. 'Cu', 'Fe', 'Au'\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ library, projectile, element, max_rows }) => {\n    if (!/^[npdthag]$/.test(projectile)) {\n      throw new Error(`Invalid projectile: '${projectile}'. Must be one of: n, p, d, t, h, a, g`);\n    }\n    if (!/^[A-Z][a-z]?$/.test(element)) {\n      throw new Error(`Invalid element symbol: '${element}'. Must be 1-2 letters (e.g. 'Cu', 'Fe')`);\n    }\n\n    const cat = ensureCatalog();\n    const lib = cat.libraries[library];\n    if (!lib) throw new Error(`Unknown library: ${library}`);\n\n    const dataDir = resolveDataDir();\n    const parquetPath = join(dataDir, `${lib.path}${projectile}_${element}.parquet`);\n    if (!existsSync(parquetPath)) {\n      throw new Error(`No data for ${projectile}_${element} in ${library}`);\n    }\n\n    const db = getDb();\n    const result = await query(\n      `SELECT * FROM read_parquet('${parquetPath}')`,\n      [],\n      max_rows ?? 500,\n    );\n\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ library, projectile, element, ...result }, 2),\n      }],\n    };\n  },\n);\n\n// ---------------------------------------------------------------------------\n// Nuclear structure tools (DuckDB views)\n// ---------------------------------------------------------------------------\n\nserver.tool(\n  \"get_decay_data\",\n  \"Get radioactive decay data (half-lives, decay modes, daughters) for a nuclide or element. Filter by Z and/or A.\",\n  {\n    z: z.number().optional().describe(\"Atomic number (e.g. 92 for U)\"),\n    a: z.number().optional().describe(\"Mass number (e.g. 238)\"),\n  },\n  async ({ z: zNum, a: aNum }) => {\n    if (zNum === undefined && aNum === undefined) {\n      throw new Error(\"Provide at least z or a to filter decay data.\");\n    }\n    const conditions: string[] = [];\n    const params: unknown[] = [];\n    if (zNum !== undefined) { conditions.push(\"Z = ?\"); params.push(zNum); }\n    if (aNum !== undefined) { conditions.push(\"A = ?\"); params.push(aNum); }\n\n    const result = await query(\n      `SELECT * FROM decay WHERE ${conditions.join(\" AND \")}`,\n      params,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, count: result.total, rows: result.rows }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_abundances\",\n  \"Get natural isotope abundances and atomic masses for an element.\",\n  {\n    z: z.number().describe(\"Atomic number (e.g. 29 for Cu)\"),\n  },\n  async ({ z: zNum }) => {\n    const result = await query(\"SELECT * FROM abundances WHERE Z = ?\", [zNum]);\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, count: result.total, isotopes: result.rows }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_stopping_power\",\n  \"Get mass stopping power (dE/dx) data for a projectile in a target element.\",\n  {\n    source: z.string().describe(\n      \"Data source: PSTAR (protons), ASTAR (α, NIST ICRU-49), ESTAR (electrons), dSTAR, tSTAR (velocity-scaled from PSTAR), or catima (full Z×Z table)\",\n    ),\n    target_z: z.number().describe(\"Target element atomic number\"),\n  },\n  async ({ source, target_z }) => {\n    const viewMap: Record<string, string> = {\n      PSTAR: \"stopping\", ASTAR: \"stopping\", ESTAR: \"stopping\",\n      dSTAR: \"stopping\", tSTAR: \"stopping\", catima: \"catima_stopping\",\n    };\n    if (!(source in viewMap)) {\n      throw new Error(`Unknown source '${source}'. Valid: PSTAR, ASTAR, ESTAR, dSTAR, tSTAR, catima`);\n    }\n    const view = viewMap[source];\n    const sql = source === \"catima\"\n      ? `SELECT * FROM ${view} WHERE target_Z = ?`\n      : `SELECT * FROM ${view} WHERE source = ? AND target_Z = ?`;\n    const params = source === \"catima\" ? [target_z] : [source, target_z];\n\n    const result = await query(sql, params);\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ source, target_z, count: result.total, rows: result.rows }, 2),\n      }],\n    };\n  },\n);\n\n// ---------------------------------------------------------------------------\n// Radiation / coincidence / spectra tools\n// ---------------------------------------------------------------------------\n\nserver.tool(\n  \"get_radiation\",\n  \"Get radiation emissions (gammas, X-rays, Auger electrons, conversion electrons) for a nuclide.\",\n  {\n    z: z.number().describe(\"Atomic number of the parent nuclide\"),\n    a: z.number().optional().describe(\"Mass number (omit for all isotopes of element Z)\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, max_rows }) => {\n    const conditions = [\"Z = ?\"];\n    const params: unknown[] = [zNum];\n    if (aNum !== undefined) { conditions.push(\"A = ?\"); params.push(aNum); }\n\n    const result = await query(\n      `SELECT * FROM radiation WHERE ${conditions.join(\" AND \")}`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_coincidences\",\n  \"Get gamma-gamma and mixed-emission coincidence pairs for a nuclide. Includes beta/EC/X-ray/Auger/511 keV annihilation paired with gammas.\",\n  {\n    z: z.number().describe(\"Atomic number of the parent nuclide\"),\n    a: z.number().optional().describe(\"Mass number (omit for all isotopes of element Z)\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, max_rows }) => {\n    const conditions = [\"Z = ?\"];\n    const params: unknown[] = [zNum];\n    if (aNum !== undefined) { conditions.push(\"A = ?\"); params.push(aNum); }\n\n    const result = await query(\n      `SELECT * FROM coincidences WHERE ${conditions.join(\" AND \")}`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_summing_partners\",\n  \"Get ICC-corrected summing partners for HPGe true-coincidence-summing (TCS) corrections. Returns emission pairs with pre-computed icc_correction_factor and pure_emission_joint_intensity.\",\n  {\n    z: z.number().describe(\"Atomic number of the daughter nuclide (filing convention)\"),\n    a: z.number().describe(\"Mass number\"),\n    primary_energy_keV: z.number().optional().describe(\"Filter to pairs matching this energy on either side\"),\n    tolerance_keV: z.number().optional().describe(\"Energy match tolerance in keV (default 0.5)\"),\n    emission1_rad_type: z.string().optional().describe(\"Filter side 1: 'gamma', 'xray', 'auger'\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, primary_energy_keV, tolerance_keV, emission1_rad_type, max_rows }) => {\n    const conditions = [\"Z = ?\", \"A = ?\"];\n    const params: unknown[] = [zNum, aNum];\n    const tol = tolerance_keV ?? 0.5;\n\n    if (primary_energy_keV !== undefined) {\n      conditions.push(\"(ABS(emission1_energy_keV - ?) < ? OR ABS(emission2_energy_keV - ?) < ?)\");\n      params.push(primary_energy_keV, tol, primary_energy_keV, tol);\n    }\n    if (emission1_rad_type !== undefined) {\n      conditions.push(\"emission1_rad_type = ?\");\n      params.push(emission1_rad_type);\n    }\n\n    const result = await query(\n      `SELECT * FROM summing_partners WHERE ${conditions.join(\" AND \")} ORDER BY pure_emission_joint_intensity DESC`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, primary_energy_keV, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_emissions\",\n  \"Get absolute per-decay photon emission intensities (NuDat-equivalent). Returns gamma emissions for a parent nuclide with absolute intensities (photon emission probability per decay, 0-100%). Filed by parent, not daughter.\",\n  {\n    parent_z: z.number().describe(\"Atomic number of the decaying parent (e.g. 27 for Co-60)\"),\n    parent_a: z.number().describe(\"Mass number of the parent (e.g. 60 for Co-60)\"),\n    parent_state: z.string().optional().describe(\"Nuclear state: '' (ground), 'm', 'm2'\"),\n    decay_mode: z.string().optional().describe(\"Filter by decay mode: 'beta-', 'KshellEC', 'IT', etc.\"),\n    energy_keV: z.number().optional().describe(\"Filter to gammas near this energy\"),\n    tolerance_keV: z.number().optional().describe(\"Energy tolerance (default 0.5 keV)\"),\n    min_intensity_pct: z.number().optional().describe(\"Minimum absolute intensity (%) to include\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ parent_z, parent_a, parent_state, decay_mode, energy_keV, tolerance_keV, min_intensity_pct, max_rows }) => {\n    const conditions = [\"parent_Z = ?\", \"parent_A = ?\", \"parent_state = ?\"];\n    const params: unknown[] = [parent_z, parent_a, parent_state ?? \"\"];\n    const tol = tolerance_keV ?? 0.5;\n\n    if (decay_mode !== undefined) {\n      conditions.push(\"decay_mode = ?\");\n      params.push(decay_mode);\n    }\n    if (energy_keV !== undefined) {\n      conditions.push(\"ABS(energy_keV - ?) < ?\");\n      params.push(energy_keV, tol);\n    }\n    if (min_intensity_pct !== undefined && min_intensity_pct > 0) {\n      conditions.push(\"intensity_pct >= ?\");\n      params.push(min_intensity_pct);\n    }\n\n    const result = await query(\n      `SELECT * FROM emissions WHERE ${conditions.join(\" AND \")} ORDER BY intensity_pct DESC`,\n      params,\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ parent_z, parent_a, parent_state: parent_state ?? \"\", ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_beta_spectrum\",\n  \"Get the continuous beta-decay kinetic-energy spectrum for a nuclide. Returns pre-tabulated Fermi-function spectra (dN/dE normalized to 1).\",\n  {\n    z: z.number().describe(\"Atomic number of the parent nuclide\"),\n    a: z.number().describe(\"Mass number of the parent nuclide\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ z: zNum, a: aNum, max_rows }) => {\n    const result = await query(\n      \"SELECT * FROM beta_spectra WHERE Z = ? AND A = ?\",\n      [zNum, aNum],\n      max_rows ?? 500,\n    );\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ z: zNum, a: aNum, ...result }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_compound_compositions\",\n  \"Get elemental compositions (weight fractions) for NIST XCOM standard materials. Useful for Bragg-additive cross-section calculations.\",\n  {\n    material: z.string().optional().describe(\"Material key (e.g. 'water', 'air', 'concrete'). Omit to list all materials.\"),\n  },\n  async ({ material }) => {\n    const db = getDb();\n    if (material === undefined) {\n      const rows = await dbAll(db, \"SELECT DISTINCT material FROM compound_compositions ORDER BY material\");\n      const materials = rows.map((r) => r.material as string);\n      return {\n        content: [{\n          type: \"text\" as const,\n          text: safeStringify({ count: materials.length, materials }, 2),\n        }],\n      };\n    }\n    const result = await query(\n      \"SELECT * FROM compound_compositions WHERE material = ?\",\n      [material],\n    );\n    if (result.total === 0) {\n      const allRows = await dbAll(db, \"SELECT DISTINCT material FROM compound_compositions ORDER BY material\");\n      const all = allRows.map((r) => r.material as string);\n      throw new Error(`Unknown material: '${material}'. Available: ${all.join(\", \")}`);\n    }\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ material, count: result.total, composition: result.rows }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"get_electron_stopping\",\n  \"Get electron stopping power with collision/radiative split. Richer than ESTAR — includes ~183 compounds plus all elements Z=1..98.\",\n  {\n    target: z.string().optional().describe(\"Compound name (e.g. 'G4_WATER'). For elements use target_z instead.\"),\n    target_z: z.number().optional().describe(\"Atomic number for elemental targets\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 500)\"),\n  },\n  async ({ target, target_z, max_rows }) => {\n    if (target === undefined && target_z === undefined) {\n      throw new Error(\"Provide target (compound name) or target_z (atomic number).\");\n    }\n    let result;\n    if (target_z !== undefined) {\n      result = await query(\n        \"SELECT * FROM electron_stopping WHERE target_Z = ?\",\n        [target_z],\n        max_rows ?? 500,\n      );\n    } else {\n      result = await query(\n        \"SELECT * FROM electron_stopping WHERE name = ? 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The pre-registered DuckDB views\n// already expose all nuclear data; there's no legitimate need for raw file access.\nexport const BLOCKED_FUNCTIONS = /\\b(read_parquet|parquet_scan|parquet_metadata|parquet_schema|read_csv|read_csv_auto|read_json|read_json_auto|read_text|read_blob|glob|copy|export|attach|load|install|create|drop|alter|insert|update|delete|truncate|query_table|pragma)\\b/i;\n\nexport const ALLOWED_FIRST_WORDS = new Set([\"SELECT\", \"WITH\", \"EXPLAIN\", \"DESCRIBE\", \"SHOW\", \"SUMMARIZE\"]);\n\nserver.tool(\n  \"sql_query\",\n  \"Execute read-only SQL against all 70+ nuclear data tables. Supports JOINs, aggregations, window functions. Use describe_schema() to discover available tables and columns.\",\n  {\n    sql: z.string().describe(\"Read-only SQL query. DDL/DML will be rejected.\"),\n    max_rows: z.number().optional().describe(\"Max rows to return (default 10000)\"),\n  },\n  async ({ sql: userSql, max_rows }) => {\n    const stripped = userSql.trim();\n    if (!stripped) throw new Error(\"Empty SQL query\");\n\n    const firstWord = stripped.split(/\\s/)[0].toUpperCase();\n    if (!ALLOWED_FIRST_WORDS.has(firstWord)) {\n      throw new Error(`Only read queries are allowed (SELECT, WITH, EXPLAIN, DESCRIBE). Got: ${firstWord}`);\n    }\n    if (BLOCKED_FUNCTIONS.test(stripped)) {\n      throw new Error(\"Only read queries are allowed (SELECT, WITH, EXPLAIN, DESCRIBE). File-access and DDL functions are blocked.\");\n    }\n\n    const db = getDb();\n    const limit = max_rows ?? 10000;\n    let total: number;\n    let rows: Record<string, unknown>[];\n    try {\n      // Get total count first, then fetch limited rows\n      const countRows = await dbAll(db, `SELECT CAST(COUNT(*) AS INTEGER) AS n FROM (${stripped})`);\n      total = (countRows[0]?.n as number) ?? 0;\n      rows = await dbAll(db, `SELECT * FROM (${stripped}) LIMIT ${limit}`);\n    } catch (e) {\n      throw new Error(`SQL error: ${(e as Error).message}`);\n    }\n\n    const truncated = total > limit;\n    const display = rows;\n\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ total, truncated, rows: display }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"describe_schema\",\n  \"List all available tables/views with their column names and types. Use this to discover what data is available before writing SQL queries.\",\n  {},\n  async () => {\n    const db = getDb();\n    const tables = await dbAll(db, \"SHOW TABLES\");\n    const tableNames = tables.map((r) => r.name as string).sort();\n\n    const schema: Record<string, { name: string; type: string }[]> = {};\n    for (const tbl of tableNames) {\n      try {\n        const cols = await dbAll(db, `DESCRIBE ${tbl}`);\n        schema[tbl] = cols.map((c) => ({ name: c.column_name as string, type: c.column_type as string }));\n      } catch {\n        schema[tbl] = [];\n      }\n    }\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ tables: tableNames.length, schema }, 2),\n      }],\n    };\n  },\n);\n\nserver.tool(\n  \"list_tables\",\n  \"List all available table/view names (short form of describe_schema).\",\n  {},\n  async () => {\n    const db = getDb();\n    const tables = await dbAll(db, \"SHOW TABLES\");\n    const tableNames = tables.map((r) => r.name as string).sort();\n    return {\n      content: [{\n        type: \"text\" as const,\n        text: safeStringify({ count: tableNames.length, tables: tableNames }, 2),\n      }],\n    };\n  },\n);\n\n// ---------------------------------------------------------------------------\n// Main\n// ---------------------------------------------------------------------------\n\nconst transport = new StdioServerTransport();\nawait 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nucl-parquet/mcp",
-  "version": "0.14.0",
+  "version": "0.15.0",
   "description": "MCP server for nuclear data — wraps local Parquet via DuckDB",
   "type": "module",
   "bin": {
@@ -12,7 +12,7 @@
     "dist"
   ],
   "scripts": {
-    "build": "tsup",
+    "build": "tsup && tsc --emitDeclarationOnly",
     "test": "vitest run",
     "test:watch": "vitest",
     "start": "node dist/index.js"
@@ -20,14 +20,14 @@
   "repository": "https://github.com/exoma-ch/nucl-parquet",
   "license": "MIT",
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.12.0",
+    "@modelcontextprotocol/sdk": "^1.30.1",
     "duckdb": "^1.4.4",
-    "zod": "^3.23.0"
+    "zod": "^4.6.5"
   },
   "devDependencies": {
-    "@types/node": "^22.0.0",
+    "@types/node": "^26.6.3",
     "tsup": "^8.0.0",
-    "typescript": "^5.4.0",
-    "vitest": "^2.0.0"
+    "typescript": "^7.0.2",
+    "vitest": "^5.0.2"
   }
 }