npm - @nucl-parquet/mcp - Versions diffs - 0.13.2 → 0.15.0 - Mend

@nucl-parquet/mcp 0.13.2 → 0.15.0

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Files changed (4) hide show

package/dist/index.d.ts CHANGED Viewed

@@ -1,27 +1,80 @@
+/**
+ * nucl-parquet MCP server — wraps local data via DuckDB.
+ *
+ * SSoT refactor (epic #173, Sub-D #178): the MCP is a thin shell over
+ * DuckDB-backed Parquet views, not a re-implementation of parquet I/O.
+ * All data is read from the local data directory — no HTTP fetching.
+ */
+import duckdb from "duckdb";
+export declare const PKG_VERSION: string;
 interface Library {
     name: string;
     description: string;
-    source_url: string;
-    projectiles: string[];
-    data_type: string;
+    source_url?: string;
+    projectiles?: string[];
+    data_type?: string;
     version: string;
+    path?: string;
+}
+interface ViewDef {
     path: string;
+    type?: "file" | "glob";
+    optional?: boolean;
+    note?: string;
 }
 interface Catalog {
+    /**
+     * The data release this server is serving, e.g. `2026.8.3`.
+     *
+     * Distinct from `Library.version`, which is the *evaluation's* version
+     * ("2023-iso"). They answer different questions, and conflating them would
+     * make a cross-server check silently wrong rather than merely absent (#348).
+     *
+     * Read from the catalog on disk, never compiled in — a build-time constant
+     * would be a second source of truth for the one fact whose whole job is to
+     * identify the data actually being read.
+     */
+    data_version: string;
     libraries: Record<string, Library>;
-    shared: {
-        meta: {
-            path: string;
-            files: Record<string, string>;
-        };
-        stopping: {
-            path: string;
-            files: Record<string, string>;
-            sources: string[];
-        };
-    };
+    views?: Record<string, ViewDef>;
+    [key: string]: unknown;
 }
-declare function fetchParquetRows(relativePath: string, baseUrl?: string): Promise<Record<string, unknown>[]>;
-declare function getCatalog(): Catalog;
-export { fetchParquetRows, getCatalog };
+export declare function ensureCatalog(): Catalog;
+/**
+ * Parse and validate a catalog.
+ *
+ * Separate from {@link ensureCatalog} because that one memoises a module-level
+ * singleton, which a test cannot re-enter — so the validation below would be
+ * unreachable from a test and, in practice, unverified.
+ */
+export declare function parseCatalog(raw: string, dataDir: string): Catalog;
+/**
+ * The `list_libraries` payload: the data release, then the libraries.
+ *
+ * A named function rather than an inline object so a test can assert the shape
+ * the tool actually returns. Asserting only that the catalog *has* a
+ * data_version would pass while the tool still returned a bare array.
+ */
+export declare function libraryListPayload(cat: Catalog): {
+    data_version: string;
+    libraries: Array<Record<string, unknown>>;
+};
+export declare function getDb(): duckdb.Database;
+/**
+ * Server instructions, naming the data release in the client's context.
+ *
+ * The referral case #348 is about does not go through `list_libraries`:
+ * hyrr-mcp sends an agent straight to `get_cross_sections` for full σ(E)
+ * curves, having stated the release *it* computed against. Reporting the
+ * release only from a tool the agent has no reason to call would leave that
+ * claim as unverifiable as it was — so it is stated here too, where it reaches
+ * the model without a round trip, and in `list_libraries` where it can be read
+ * programmatically. Both read the same loaded catalog, so they cannot disagree.
+ *
+ * Kept word-for-word in step with the Rust server's `instructions()`; a test
+ * pins that the two do not drift.
+ */
+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 CHANGED Viewed

@@ -1,120 +1,214 @@
 #!/usr/bin/env node
 // src/index.ts
+import { existsSync, readFileSync, readdirSync } from "fs";
+import { createRequire } from "module";
+import { join, resolve } from "path";
+import { homedir } from "os";
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-import { parquetRead } from "hyparquet";
-import { compressors } from "hyparquet-compressors";
+import duckdb from "duckdb";
 import { z } from "zod";
-var BASE_URL = process.env.NUCL_PARQUET_BASE_URL ?? "https://raw.githubusercontent.com/exoma-ch/nucl-parquet/main/data/";
-var CATALOG = {
-  libraries: {
-    "tendl-2024": { name: "TENDL-2024", description: "TALYS Evaluated Nuclear Data Library 2024 (IAEA/PSI)", source_url: "https://tendl.web.psi.ch/tendl_2024/tendl2024.html", projectiles: ["p", "d", "t", "h", "a"], data_type: "cross_sections", version: "2024", path: "tendl-2024/xs/" },
-    "endfb-8.1": { name: "ENDF/B-VIII.1", description: "US Evaluated Nuclear Data File (NNDC/BNL)", source_url: "https://www.nndc.bnl.gov/endf-b8.1/", projectiles: ["n", "p", "d", "t", "h", "a"], data_type: "cross_sections", version: "VIII.1", path: "endfb-8.1/xs/" },
-    "jeff-4.0": { name: "JEFF-4.0", description: "Joint Evaluated Fission and Fusion File (NEA)", source_url: "https://www.oecd-nea.org/dbdata/jeff/", projectiles: ["n", "p"], data_type: "cross_sections", version: "4.0", path: "jeff-4.0/xs/" },
-    "jendl-5": { name: "JENDL-5", description: "Japanese Evaluated Nuclear Data Library (JAEA)", source_url: "https://wwwndc.jaea.go.jp/jendl/j5/j5.html", projectiles: ["n", "p", "d", "a"], data_type: "cross_sections", version: "5", path: "jendl-5/xs/" },
-    "tendl-2025": { name: "TENDL-2025", description: "TALYS Evaluated Nuclear Data Library 2025 (PSI)", source_url: "https://tendl.web.psi.ch/", projectiles: ["n", "p", "d", "t", "h", "a"], data_type: "cross_sections", version: "2025", path: "tendl-2025/xs/" },
-    "cendl-3.2": { name: "CENDL-3.2", description: "Chinese Evaluated Nuclear Data Library (CIAE)", source_url: "http://www.nuclear.csdb.cn/", projectiles: ["n"], data_type: "cross_sections", version: "3.2", path: "cendl-3.2/xs/" },
-    "brond-3.1": { name: "BROND-3.1", description: "Russian Evaluated Nuclear Data Library (IPPE)", source_url: "https://vant.ippe.ru/", projectiles: ["n"], data_type: "cross_sections", version: "3.1", path: "brond-3.1/xs/" },
-    "fendl-3.2": { name: "FENDL-3.2", description: "Fusion Evaluated Nuclear Data Library (IAEA)", source_url: "https://www-nds.iaea.org/fendl/", projectiles: ["n"], data_type: "cross_sections", version: "3.2", path: "fendl-3.2/xs/" },
-    "eaf-2010": { name: "EAF-2010", description: "European Activation File (CCFE)", source_url: "https://fispact.ukaea.uk/", projectiles: ["n"], data_type: "cross_sections", version: "2010", path: "eaf-2010/xs/" },
-    "irdff-2": { name: "IRDFF-II", description: "International Reactor Dosimetry and Fusion File (IAEA)", source_url: "https://www-nds.iaea.org/IRDFF/", projectiles: ["n"], data_type: "cross_sections", version: "II", path: "irdff-2/xs/" },
-    "iaea-medical": { name: "IAEA-Medical", description: "Medical isotope production cross-sections (IAEA)", source_url: "https://www-nds.iaea.org/medical/", projectiles: ["p", "d", "h", "a"], data_type: "cross_sections", version: "latest", path: "iaea-medical/xs/" },
-    "jendl-ad-2017": { name: "JENDL/AD-2017", description: "Activation/Dosimetry Library (JAEA)", source_url: "https://wwwndc.jaea.go.jp/jendl/jad/jad.html", projectiles: ["n", "p"], data_type: "cross_sections", version: "2017", path: "jendl-ad-2017/xs/" },
-    "jendl-deu-2020": { name: "JENDL-DEU-2020", description: "Dedicated deuteron-induced reaction library (JAEA)", source_url: "https://wwwndc.jaea.go.jp/jendl/deu/deu.html", projectiles: ["d"], data_type: "cross_sections", version: "2020", path: "jendl-deu-2020/xs/" },
-    "iaea-pd-2019": { name: "IAEA-PD-2019", description: "Photonuclear Data Library (IAEA)", source_url: "https://www-nds.iaea.org/photonuclear/", projectiles: ["g"], data_type: "cross_sections", version: "2019", path: "iaea-pd-2019/xs/" },
-    "exfor": { name: "EXFOR", description: "Experimental nuclear reaction data (IAEA NDS)", source_url: "https://www-nds.iaea.org/exfor/", projectiles: ["n", "p", "d", "t", "h", "a"], data_type: "experimental_cross_sections", version: "latest", path: "exfor/" }
-  },
-  shared: {
-    meta: { path: "meta/", files: { abundances: "abundances.parquet", decay: "decay.parquet", elements: "elements.parquet" } },
-    stopping: {
-      path: "stopping/",
-      files: {
-        PSTAR: "PSTAR.parquet",
-        ASTAR: "ASTAR.parquet",
-        ESTAR: "ESTAR.parquet",
-        dSTAR: "dSTAR.parquet",
-        tSTAR: "tSTAR.parquet",
-        catima: "catima/catima.parquet"
-      },
-      sources: ["PSTAR", "ASTAR", "ESTAR", "dSTAR", "tSTAR", "catima"]
+var require2 = createRequire(import.meta.url);
+var { version: PKG_VERSION } = require2("../package.json");
+function resolveDataDir() {
+  const envDir = process.env.NUCL_PARQUET_DATA;
+  if (envDir && existsSync(envDir)) return resolve(envDir);
+  const repoDir = resolve(import.meta.dirname ?? ".", "..", "..", "..", "..", "data");
+  if (existsSync(join(repoDir, "catalog.json"))) return repoDir;
+  const homeData = join(homedir(), ".nucl-parquet");
+  if (existsSync(join(homeData, "catalog.json"))) return homeData;
+  throw new Error(
+    "Cannot find nucl-parquet data directory. Set NUCL_PARQUET_DATA env var or place data at ~/.nucl-parquet/. Data releases: https://github.com/exoma-ch/nucl-parquet/releases"
+  );
+}
+var _catalog;
+function ensureCatalog() {
+  if (_catalog) return _catalog;
+  const dataDir = resolveDataDir();
+  _catalog = parseCatalog(readFileSync(join(dataDir, "catalog.json"), "utf-8"), dataDir);
+  return _catalog;
+}
+function parseCatalog(raw, dataDir) {
+  const parsed = JSON.parse(raw);
+  if (typeof parsed.data_version !== "string" || parsed.data_version === "") {
+    throw new Error(
+      `catalog.json at ${dataDir} has no 'data_version'. It is required by data/catalog.schema.json and identifies the data release this server serves; refusing to start rather than report an unknown release as if it were known.`
+    );
+  }
+  return parsed;
+}
+function libraryListPayload(cat) {
+  return {
+    // Beside the array rather than on each entry, so the release and a
+    // library's evaluation `version` cannot be read as the same kind of thing.
+    data_version: cat.data_version,
+    libraries: Object.entries(cat.libraries).filter(([, lib]) => lib.projectiles).map(([id, lib]) => ({
+      id,
+      name: lib.name,
+      description: lib.description,
+      projectiles: lib.projectiles,
+      version: lib.version,
+      data_type: lib.data_type
+    }))
+  };
+}
+var _db;
+function hasParquetFiles(dir) {
+  if (!existsSync(dir)) return false;
+  try {
+    return readdirSync(dir).some((f) => f.endsWith(".parquet"));
+  } catch {
+    return false;
+  }
+}
+function registerParquet(db, filePath, viewName) {
+  if (existsSync(filePath)) {
+    db.run(`CREATE VIEW ${viewName} AS SELECT * FROM read_parquet('${filePath}')`);
+  }
+}
+function registerGlob(db, dir, viewName) {
+  if (hasParquetFiles(dir)) {
+    const glob = join(dir, "*.parquet");
+    db.run(`CREATE VIEW ${viewName} AS SELECT * FROM read_parquet('${glob}')`);
+  }
+}
+function registerViews(db, dataDir) {
+  const catalog = ensureCatalog();
+  const libViews = [];
+  for (const [libKey, lib] of Object.entries(catalog.libraries)) {
+    if (!lib.path) continue;
+    const libDir = join(dataDir, lib.path);
+    if (!hasParquetFiles(libDir)) continue;
+    const viewName = libKey.replace(/-/g, "_").replace(/\./g, "_");
+    const glob = join(libDir, "*.parquet");
+    db.run(
+      `CREATE VIEW ${viewName} AS SELECT *, '${libKey}' AS library FROM read_parquet('${glob}', filename=true)`
+    );
+    if (lib.data_type === "cross_sections") libViews.push(viewName);
+  }
+  if (libViews.length > 0) {
+    const union = libViews.map((v) => `SELECT * FROM ${v}`).join(" UNION ALL ");
+    db.run(`CREATE VIEW xs AS ${union}`);
+  }
+  for (const [viewName, viewDef] of Object.entries(catalog.views ?? {})) {
+    const viewPath = join(dataDir, viewDef.path);
+    if (viewDef.type === "glob") {
+      registerGlob(db, viewPath, viewName);
+    } else {
+      registerParquet(db, viewPath, viewName);
     }
   }
-};
-var parquetCache = /* @__PURE__ */ new Map();
-async function fetchParquetRows(relativePath, baseUrl = BASE_URL) {
-  if (parquetCache.has(relativePath)) return parquetCache.get(relativePath);
-  const url = new URL(relativePath, baseUrl).href;
-  const resp = await fetch(url);
-  if (!resp.ok) throw new Error(`HTTP ${resp.status} fetching ${url}`);
-  const buffer = await resp.arrayBuffer();
-  const rows = [];
-  await parquetRead({
-    file: buffer,
-    compressors,
-    rowFormat: "object",
-    onComplete: (data) => {
-      rows.push(...data);
+  const nuclidesPath = join(dataDir, "meta", "ensdf", "nuclides.parquet");
+  if (existsSync(nuclidesPath)) {
+    db.run("CREATE OR REPLACE VIEW ground_states AS SELECT * FROM nuclides WHERE state = 'g'");
+  }
+  const eadlDir = join(dataDir, "meta", "eadl");
+  if (hasParquetFiles(eadlDir)) {
+    db.run("CREATE VIEW eadl_transitions AS SELECT * FROM atomic_relaxation");
+    db.run("CREATE VIEW fluorescence AS SELECT * FROM atomic_relaxation WHERE transition_type = 'radiative'");
+  }
+}
+function harden(db, dataDir) {
+  const quoted = dataDir.replaceAll("'", "''");
+  db.run(`SET allowed_directories = ['${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;
+}
+function dbAll(db, sql, params) {
+  return new Promise((resolve2, reject) => {
+    const cb = (err, rows) => {
+      if (err) reject(err);
+      else resolve2(rows);
+    };
+    if (params && params.length > 0) {
+      db.all(sql, ...params, cb);
+    } else {
+      db.all(sql, cb);
     }
   });
-  parquetCache.set(relativePath, rows);
-  return rows;
 }
-async function fetchManifest(libraryId) {
-  const lib = CATALOG.libraries[libraryId];
-  if (!lib) throw new Error(`Unknown library: ${libraryId}`);
-  const manifestPath = lib.path.replace(/xs\/$/, "manifest.json");
-  const url = new URL(manifestPath, BASE_URL).href;
-  const resp = await fetch(url);
-  if (!resp.ok) throw new Error(`HTTP ${resp.status} fetching manifest for ${libraryId}`);
-  return await resp.json();
+function safeStringify(obj, indent) {
+  return JSON.stringify(
+    obj,
+    (_key, value) => typeof value === "bigint" ? Number(value) : value,
+    indent
+  );
 }
-function getCatalog() {
-  return CATALOG;
+async function query(sql, params, maxRows = 500) {
+  const db = getDb();
+  const countSql = `SELECT CAST(COUNT(*) AS INTEGER) AS n FROM (${sql})`;
+  const countRows = await dbAll(db, countSql, params);
+  const total = countRows[0]?.n ?? 0;
+  const limitSql = `${sql} LIMIT ${maxRows}`;
+  const rows = await dbAll(db, limitSql, params);
+  return { total, truncated: total > maxRows, rows };
 }
-function truncateRows(rows, limit) {
-  if (rows.length <= limit) return { rows, truncated: false, total: rows.length };
-  return { rows: rows.slice(0, limit), truncated: true, total: rows.length };
+function instructions(dataVersion) {
+  return `Serving nucl-parquet data release ${dataVersion}. This identifies the *data*, not this server's version \u2014 report it whenever you compare results with another server or tool. If another source states a different release, say so: agreement or disagreement computed across two releases is an artefact of the mismatch, not a physics result. Call list_libraries to read the same value programmatically.`;
 }
-var server = new McpServer({
-  name: "nucl-parquet",
-  version: "0.3.7"
-});
+var server = new McpServer(
+  {
+    name: "nucl-parquet",
+    // The package version — the software, not the data. Both are reported
+    // because they answer different questions, and only one of them changes
+    // when the data does.
+    version: PKG_VERSION
+  },
+  { instructions: instructions(ensureCatalog().data_version) }
+);
 server.tool(
   "list_libraries",
   "List all available nuclear data libraries with projectiles and descriptions",
   {},
   async () => {
-    const libs = Object.entries(CATALOG.libraries).map(([id, lib]) => ({
-      id,
-      name: lib.name,
-      description: lib.description,
-      projectiles: lib.projectiles,
-      version: lib.version,
-      data_type: lib.data_type
-    }));
-    return { content: [{ type: "text", text: JSON.stringify(libs, null, 2) }] };
+    return {
+      content: [
+        { type: "text", text: safeStringify(libraryListPayload(ensureCatalog()), 2) }
+      ]
+    };
   }
 );
 server.tool(
   "list_isotopes",
   "List available target elements for a given library and projectile. Returns element symbols.",
   {
-    library: z.string().describe("Library ID, e.g. 'tendl-2024', 'endfb-8.1'"),
+    library: z.string().describe("Library ID, e.g. 'tendl-2025', 'endfb-8.1'"),
     projectile: z.string().describe("Projectile: n, p, d, t, h, a, g")
   },
   async ({ library, projectile }) => {
-    const lib = CATALOG.libraries[library];
+    const cat = ensureCatalog();
+    const lib = cat.libraries[library];
     if (!lib) throw new Error(`Unknown library: ${library}. Use list_libraries to see available libraries.`);
-    if (!lib.projectiles.includes(projectile)) {
-      throw new Error(`Projectile '${projectile}' not available for ${library}. Available: ${lib.projectiles.join(", ")}`);
+    if (!lib.projectiles?.includes(projectile)) {
+      throw new Error(`Projectile '${projectile}' not available for ${library}. Available: ${lib.projectiles?.join(", ") ?? "none"}`);
+    }
+    const dataDir = resolveDataDir();
+    const libPath = lib.path;
+    if (!libPath?.endsWith("xs/")) {
+      throw new Error(`Library ${library} path does not end with 'xs/' \u2014 cannot derive manifest path`);
+    }
+    const manifestPath = join(dataDir, libPath.replace("xs/", "manifest.json"));
+    if (!existsSync(manifestPath)) {
+      throw new Error(`Manifest not found at ${manifestPath}`);
     }
-    const manifest = await fetchManifest(library);
+    const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
     const elements = manifest.elements ?? [];
     return {
       content: [{
         type: "text",
-        text: JSON.stringify({ library, projectile, elements, count: elements.length }, null, 2)
+        text: safeStringify({ library, projectile, elements, count: elements.length }, 2)
       }]
     };
   }
@@ -123,26 +217,36 @@ server.tool(
   "get_cross_sections",
   "Get nuclear reaction cross-section data for a specific target element. Returns energy (MeV) and cross-section (mb) arrays with reaction product info.",
   {
-    library: z.string().describe("Library ID, e.g. 'tendl-2024'"),
+    library: z.string().describe("Library ID, e.g. 'tendl-2025'"),
     projectile: z.string().describe("Projectile: n, p, d, t, h, a, g"),
     element: z.string().describe("Target element symbol, e.g. 'Cu', 'Fe', 'Au'"),
     max_rows: z.number().optional().describe("Max rows to return (default 500)")
   },
   async ({ library, projectile, element, max_rows }) => {
-    const lib = CATALOG.libraries[library];
+    if (!/^[npdthag]$/.test(projectile)) {
+      throw new Error(`Invalid projectile: '${projectile}'. Must be one of: n, p, d, t, h, a, g`);
+    }
+    if (!/^[A-Z][a-z]?$/.test(element)) {
+      throw new Error(`Invalid element symbol: '${element}'. Must be 1-2 letters (e.g. 'Cu', 'Fe')`);
+    }
+    const cat = ensureCatalog();
+    const lib = cat.libraries[library];
     if (!lib) throw new Error(`Unknown library: ${library}`);
-    const parquetPath = `${lib.path}${projectile}_${element}.parquet`;
-    const rows = await fetchParquetRows(parquetPath);
-    const result = truncateRows(rows, max_rows ?? 500);
+    const dataDir = resolveDataDir();
+    const parquetPath = join(dataDir, `${lib.path}${projectile}_${element}.parquet`);
+    if (!existsSync(parquetPath)) {
+      throw new Error(`No data for ${projectile}_${element} in ${library}`);
+    }
+    const db = getDb();
+    const result = await query(
+      `SELECT * FROM read_parquet('${parquetPath}')`,
+      [],
+      max_rows ?? 500
+    );
     return {
       content: [{
         type: "text",
-        text: JSON.stringify({
-          library,
-          projectile,
-          element,
-          ...result
-        }, null, 2)
+        text: safeStringify({ library, projectile, element, ...result }, 2)
       }]
     };
   }
@@ -158,17 +262,24 @@ server.tool(
     if (zNum === void 0 && aNum === void 0) {
       throw new Error("Provide at least z or a to filter decay data.");
     }
-    const metaPath = CATALOG.shared.meta.path + CATALOG.shared.meta.files.decay;
-    const rows = await fetchParquetRows(metaPath);
-    const filtered = rows.filter((row) => {
-      if (zNum !== void 0 && row["Z"] !== zNum) return false;
-      if (aNum !== void 0 && row["A"] !== aNum) return false;
-      return true;
-    });
+    const conditions = [];
+    const params = [];
+    if (zNum !== void 0) {
+      conditions.push("Z = ?");
+      params.push(zNum);
+    }
+    if (aNum !== void 0) {
+      conditions.push("A = ?");
+      params.push(aNum);
+    }
+    const result = await query(
+      `SELECT * FROM decay WHERE ${conditions.join(" AND ")}`,
+      params
+    );
     return {
       content: [{
         type: "text",
-        text: JSON.stringify({ z: zNum, a: aNum, count: filtered.length, rows: filtered }, null, 2)
+        text: safeStringify({ z: zNum, a: aNum, count: result.total, rows: result.rows }, 2)
       }]
     };
   }
@@ -180,13 +291,11 @@ server.tool(
     z: z.number().describe("Atomic number (e.g. 29 for Cu)")
   },
   async ({ z: zNum }) => {
-    const metaPath = CATALOG.shared.meta.path + CATALOG.shared.meta.files.abundances;
-    const rows = await fetchParquetRows(metaPath);
-    const filtered = rows.filter((row) => row["Z"] === zNum);
+    const result = await query("SELECT * FROM abundances WHERE Z = ?", [zNum]);
     return {
       content: [{
         type: "text",
-        text: JSON.stringify({ z: zNum, count: filtered.length, isotopes: filtered }, null, 2)
+        text: safeStringify({ z: zNum, count: result.total, isotopes: result.rows }, 2)
       }]
     };
   }
@@ -196,34 +305,336 @@ server.tool(
   "Get mass stopping power (dE/dx) data for a projectile in a target element.",
   {
     source: z.string().describe(
-      "Data source: PSTAR (protons), ASTAR (\u03B1, NIST ICRU-49), ESTAR (electrons), dSTAR, tSTAR (velocity-scaled from PSTAR), or catima (full Z\xD7Z table; \u03B1/\xB3He fallback for non-NIST elements)"
+      "Data source: PSTAR (protons), ASTAR (\u03B1, NIST ICRU-49), ESTAR (electrons), dSTAR, tSTAR (velocity-scaled from PSTAR), or catima (full Z\xD7Z table)"
     ),
     target_z: z.number().describe("Target element atomic number")
   },
   async ({ source, target_z }) => {
-    const fileMap = CATALOG.shared.stopping.files;
-    if (!(source in fileMap)) {
+    const viewMap = {
+      PSTAR: "stopping",
+      ASTAR: "stopping",
+      ESTAR: "stopping",
+      dSTAR: "stopping",
+      tSTAR: "stopping",
+      catima: "catima_stopping"
+    };
+    if (!(source in viewMap)) {
+      throw new Error(`Unknown source '${source}'. Valid: PSTAR, ASTAR, ESTAR, dSTAR, tSTAR, catima`);
+    }
+    const view = viewMap[source];
+    const sql = source === "catima" ? `SELECT * FROM ${view} WHERE target_Z = ?` : `SELECT * FROM ${view} WHERE source = ? AND target_Z = ?`;
+    const params = source === "catima" ? [target_z] : [source, target_z];
+    const result = await query(sql, params);
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ source, target_z, count: result.total, rows: result.rows }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "get_radiation",
+  "Get radiation emissions (gammas, X-rays, Auger electrons, conversion electrons) for a nuclide.",
+  {
+    z: z.number().describe("Atomic number of the parent nuclide"),
+    a: z.number().optional().describe("Mass number (omit for all isotopes of element Z)"),
+    max_rows: z.number().optional().describe("Max rows to return (default 500)")
+  },
+  async ({ z: zNum, a: aNum, max_rows }) => {
+    const conditions = ["Z = ?"];
+    const params = [zNum];
+    if (aNum !== void 0) {
+      conditions.push("A = ?");
+      params.push(aNum);
+    }
+    const result = await query(
+      `SELECT * FROM radiation WHERE ${conditions.join(" AND ")}`,
+      params,
+      max_rows ?? 500
+    );
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ z: zNum, a: aNum, ...result }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "get_coincidences",
+  "Get gamma-gamma and mixed-emission coincidence pairs for a nuclide. Includes beta/EC/X-ray/Auger/511 keV annihilation paired with gammas.",
+  {
+    z: z.number().describe("Atomic number of the parent nuclide"),
+    a: z.number().optional().describe("Mass number (omit for all isotopes of element Z)"),
+    max_rows: z.number().optional().describe("Max rows to return (default 500)")
+  },
+  async ({ z: zNum, a: aNum, max_rows }) => {
+    const conditions = ["Z = ?"];
+    const params = [zNum];
+    if (aNum !== void 0) {
+      conditions.push("A = ?");
+      params.push(aNum);
+    }
+    const result = await query(
+      `SELECT * FROM coincidences WHERE ${conditions.join(" AND ")}`,
+      params,
+      max_rows ?? 500
+    );
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ z: zNum, a: aNum, ...result }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "get_summing_partners",
+  "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.",
+  {
+    z: z.number().describe("Atomic number of the daughter nuclide (filing convention)"),
+    a: z.number().describe("Mass number"),
+    primary_energy_keV: z.number().optional().describe("Filter to pairs matching this energy on either side"),
+    tolerance_keV: z.number().optional().describe("Energy match tolerance in keV (default 0.5)"),
+    emission1_rad_type: z.string().optional().describe("Filter side 1: 'gamma', 'xray', 'auger'"),
+    max_rows: z.number().optional().describe("Max rows to return (default 500)")
+  },
+  async ({ z: zNum, a: aNum, primary_energy_keV, tolerance_keV, emission1_rad_type, max_rows }) => {
+    const conditions = ["Z = ?", "A = ?"];
+    const params = [zNum, aNum];
+    const tol = tolerance_keV ?? 0.5;
+    if (primary_energy_keV !== void 0) {
+      conditions.push("(ABS(emission1_energy_keV - ?) < ? OR ABS(emission2_energy_keV - ?) < ?)");
+      params.push(primary_energy_keV, tol, primary_energy_keV, tol);
+    }
+    if (emission1_rad_type !== void 0) {
+      conditions.push("emission1_rad_type = ?");
+      params.push(emission1_rad_type);
+    }
+    const result = await query(
+      `SELECT * FROM summing_partners WHERE ${conditions.join(" AND ")} ORDER BY pure_emission_joint_intensity DESC`,
+      params,
+      max_rows ?? 500
+    );
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ z: zNum, a: aNum, primary_energy_keV, ...result }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "get_emissions",
+  "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.",
+  {
+    parent_z: z.number().describe("Atomic number of the decaying parent (e.g. 27 for Co-60)"),
+    parent_a: z.number().describe("Mass number of the parent (e.g. 60 for Co-60)"),
+    parent_state: z.string().optional().describe("Nuclear state: '' (ground), 'm', 'm2'"),
+    decay_mode: z.string().optional().describe("Filter by decay mode: 'beta-', 'KshellEC', 'IT', etc."),
+    energy_keV: z.number().optional().describe("Filter to gammas near this energy"),
+    tolerance_keV: z.number().optional().describe("Energy tolerance (default 0.5 keV)"),
+    min_intensity_pct: z.number().optional().describe("Minimum absolute intensity (%) to include"),
+    max_rows: z.number().optional().describe("Max rows to return (default 500)")
+  },
+  async ({ parent_z, parent_a, parent_state, decay_mode, energy_keV, tolerance_keV, min_intensity_pct, max_rows }) => {
+    const conditions = ["parent_Z = ?", "parent_A = ?", "parent_state = ?"];
+    const params = [parent_z, parent_a, parent_state ?? ""];
+    const tol = tolerance_keV ?? 0.5;
+    if (decay_mode !== void 0) {
+      conditions.push("decay_mode = ?");
+      params.push(decay_mode);
+    }
+    if (energy_keV !== void 0) {
+      conditions.push("ABS(energy_keV - ?) < ?");
+      params.push(energy_keV, tol);
+    }
+    if (min_intensity_pct !== void 0 && min_intensity_pct > 0) {
+      conditions.push("intensity_pct >= ?");
+      params.push(min_intensity_pct);
+    }
+    const result = await query(
+      `SELECT * FROM emissions WHERE ${conditions.join(" AND ")} ORDER BY intensity_pct DESC`,
+      params,
+      max_rows ?? 500
+    );
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ parent_z, parent_a, parent_state: parent_state ?? "", ...result }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "get_beta_spectrum",
+  "Get the continuous beta-decay kinetic-energy spectrum for a nuclide. Returns pre-tabulated Fermi-function spectra (dN/dE normalized to 1).",
+  {
+    z: z.number().describe("Atomic number of the parent nuclide"),
+    a: z.number().describe("Mass number of the parent nuclide"),
+    max_rows: z.number().optional().describe("Max rows to return (default 500)")
+  },
+  async ({ z: zNum, a: aNum, max_rows }) => {
+    const result = await query(
+      "SELECT * FROM beta_spectra WHERE Z = ? AND A = ?",
+      [zNum, aNum],
+      max_rows ?? 500
+    );
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ z: zNum, a: aNum, ...result }, 2)
+      }]
+    };
+  }
+);
+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 key (e.g. 'water', 'air', 'concrete'). Omit to list all materials.")
+  },
+  async ({ material }) => {
+    const db = getDb();
+    if (material === void 0) {
+      const rows = await dbAll(db, "SELECT DISTINCT material FROM compound_compositions ORDER BY material");
+      const materials = rows.map((r) => r.material);
       return {
         content: [{
           type: "text",
-          text: JSON.stringify({
-            error: `unknown source ${source}; valid: ${CATALOG.shared.stopping.sources.join(", ")}`
-          }, null, 2)
+          text: safeStringify({ count: materials.length, materials }, 2)
         }]
       };
     }
-    const stoppingPath = CATALOG.shared.stopping.path + fileMap[source];
-    const rows = await fetchParquetRows(stoppingPath);
-    const filtered = rows.filter((row) => row["target_Z"] === target_z);
+    const result = await query(
+      "SELECT * FROM compound_compositions WHERE material = ?",
+      [material]
+    );
+    if (result.total === 0) {
+      const allRows = await dbAll(db, "SELECT DISTINCT material FROM compound_compositions ORDER BY material");
+      const all = allRows.map((r) => r.material);
+      throw new Error(`Unknown material: '${material}'. Available: ${all.join(", ")}`);
+    }
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ material, count: result.total, composition: result.rows }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "get_electron_stopping",
+  "Get electron stopping power with collision/radiative split. Richer than ESTAR \u2014 includes ~183 compounds plus all elements Z=1..98.",
+  {
+    target: z.string().optional().describe("Compound name (e.g. 'G4_WATER'). For elements use target_z instead."),
+    target_z: z.number().optional().describe("Atomic number for elemental targets"),
+    max_rows: z.number().optional().describe("Max rows to return (default 500)")
+  },
+  async ({ target, target_z, max_rows }) => {
+    if (target === void 0 && target_z === void 0) {
+      throw new Error("Provide target (compound name) or target_z (atomic number).");
+    }
+    let result;
+    if (target_z !== void 0) {
+      result = await query(
+        "SELECT * FROM electron_stopping WHERE target_Z = ?",
+        [target_z],
+        max_rows ?? 500
+      );
+    } else {
+      result = await query(
+        "SELECT * FROM electron_stopping WHERE name = ? OR g4_name = ?",
+        [target, target],
+        max_rows ?? 500
+      );
+    }
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ target, target_z, ...result }, 2)
+      }]
+    };
+  }
+);
+var 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;
+var ALLOWED_FIRST_WORDS = /* @__PURE__ */ new Set(["SELECT", "WITH", "EXPLAIN", "DESCRIBE", "SHOW", "SUMMARIZE"]);
+server.tool(
+  "sql_query",
+  "Execute read-only SQL against all 70+ nuclear data tables. Supports JOINs, aggregations, window functions. Use describe_schema() to discover available tables and columns.",
+  {
+    sql: z.string().describe("Read-only SQL query. DDL/DML will be rejected."),
+    max_rows: z.number().optional().describe("Max rows to return (default 10000)")
+  },
+  async ({ sql: userSql, max_rows }) => {
+    const stripped = userSql.trim();
+    if (!stripped) throw new Error("Empty SQL query");
+    const firstWord = stripped.split(/\s/)[0].toUpperCase();
+    if (!ALLOWED_FIRST_WORDS.has(firstWord)) {
+      throw new Error(`Only read queries are allowed (SELECT, WITH, EXPLAIN, DESCRIBE). Got: ${firstWord}`);
+    }
+    if (BLOCKED_FUNCTIONS.test(stripped)) {
+      throw new Error("Only read queries are allowed (SELECT, WITH, EXPLAIN, DESCRIBE). File-access and DDL functions are blocked.");
+    }
+    const db = getDb();
+    const limit = max_rows ?? 1e4;
+    let total;
+    let rows;
+    try {
+      const countRows = await dbAll(db, `SELECT CAST(COUNT(*) AS INTEGER) AS n FROM (${stripped})`);
+      total = countRows[0]?.n ?? 0;
+      rows = await dbAll(db, `SELECT * FROM (${stripped}) LIMIT ${limit}`);
+    } catch (e) {
+      throw new Error(`SQL error: ${e.message}`);
+    }
+    const truncated = total > limit;
+    const display = rows;
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ total, truncated, rows: display }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "describe_schema",
+  "List all available tables/views with their column names and types. Use this to discover what data is available before writing SQL queries.",
+  {},
+  async () => {
+    const db = getDb();
+    const tables = await dbAll(db, "SHOW TABLES");
+    const tableNames = tables.map((r) => r.name).sort();
+    const schema = {};
+    for (const tbl of tableNames) {
+      try {
+        const cols = await dbAll(db, `DESCRIBE ${tbl}`);
+        schema[tbl] = cols.map((c) => ({ name: c.column_name, type: c.column_type }));
+      } catch {
+        schema[tbl] = [];
+      }
+    }
+    return {
+      content: [{
+        type: "text",
+        text: safeStringify({ tables: tableNames.length, schema }, 2)
+      }]
+    };
+  }
+);
+server.tool(
+  "list_tables",
+  "List all available table/view names (short form of describe_schema).",
+  {},
+  async () => {
+    const db = getDb();
+    const tables = await dbAll(db, "SHOW TABLES");
+    const tableNames = tables.map((r) => r.name).sort();
     return {
       content: [{
         type: "text",
-        text: JSON.stringify({
-          source,
-          target_z,
-          count: filtered.length,
-          rows: filtered
-        }, null, 2)
+        text: safeStringify({ count: tableNames.length, tables: tableNames }, 2)
       }]
     };
   }
@@ -231,7 +642,13 @@ server.tool(
 var transport = new StdioServerTransport();
 await server.connect(transport);
 export {
-  fetchParquetRows,
-  getCatalog
+  ALLOWED_FIRST_WORDS,
+  BLOCKED_FUNCTIONS,
+  PKG_VERSION,
+  ensureCatalog,
+  getDb,
+  instructions,
+  libraryListPayload,
+  parseCatalog
 };
 //# sourceMappingURL=index.js.map

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"sources":["../src/index.ts"],"sourcesContent":["import { McpServer } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport { StdioServerTransport } from \"@modelcontextprotocol/sdk/server/stdio.js\";\nimport { parquetRead } from \"hyparquet\";\nimport { compressors } from \"hyparquet-compressors\";\nimport { z } from \"zod\";\n\n// ---------------------------------------------------------------------------\n// Configuration\n// ---------------------------------------------------------------------------\n\nconst BASE_URL =\n process.env.NUCL_PARQUET_BASE_URL ??\n \"https://raw.githubusercontent.com/exoma-ch/nucl-parquet/main/data/\";\n\n// ---------------------------------------------------------------------------\n// Embedded catalog (from catalog.json)\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 Catalog {\n libraries: Record<string, Library>;\n shared: {\n meta: { path: string; files: Record<string, string> };\n stopping: { path: string; files: Record<string, string>; sources: string[] };\n };\n}\n\nconst CATALOG: Catalog = {\n libraries: {\n \"tendl-2024\": { name: \"TENDL-2024\", description: \"TALYS Evaluated Nuclear Data Library 2024 (IAEA/PSI)\", source_url: \"https://tendl.web.psi.ch/tendl_2024/tendl2024.html\", projectiles: [\"p\", \"d\", \"t\", \"h\", \"a\"], data_type: \"cross_sections\", version: \"2024\", path: \"tendl-2024/xs/\" },\n \"endfb-8.1\": { name: \"ENDF/B-VIII.1\", description: \"US Evaluated Nuclear Data File (NNDC/BNL)\", source_url: \"https://www.nndc.bnl.gov/endf-b8.1/\", projectiles: [\"n\", \"p\", \"d\", \"t\", \"h\", \"a\"], data_type: \"cross_sections\", version: \"VIII.1\", path: \"endfb-8.1/xs/\" },\n \"jeff-4.0\": { name: \"JEFF-4.0\", description: \"Joint Evaluated Fission and Fusion File (NEA)\", source_url: \"https://www.oecd-nea.org/dbdata/jeff/\", projectiles: [\"n\", \"p\"], data_type: \"cross_sections\", version: \"4.0\", path: \"jeff-4.0/xs/\" },\n \"jendl-5\": { name: \"JENDL-5\", description: \"Japanese Evaluated Nuclear Data Library (JAEA)\", source_url: \"https://wwwndc.jaea.go.jp/jendl/j5/j5.html\", projectiles: [\"n\", \"p\", \"d\", \"a\"], data_type: \"cross_sections\", version: \"5\", path: \"jendl-5/xs/\" },\n \"tendl-2025\": { name: \"TENDL-2025\", description: \"TALYS Evaluated Nuclear Data Library 2025 (PSI)\", source_url: \"https://tendl.web.psi.ch/\", projectiles: [\"n\", \"p\", \"d\", \"t\", \"h\", \"a\"], data_type: \"cross_sections\", version: \"2025\", path: \"tendl-2025/xs/\" },\n \"cendl-3.2\": { name: \"CENDL-3.2\", description: \"Chinese Evaluated Nuclear Data Library (CIAE)\", source_url: \"http://www.nuclear.csdb.cn/\", projectiles: [\"n\"], data_type: \"cross_sections\", version: \"3.2\", path: \"cendl-3.2/xs/\" },\n \"brond-3.1\": { name: \"BROND-3.1\", description: \"Russian Evaluated Nuclear Data Library (IPPE)\", source_url: \"https://vant.ippe.ru/\", projectiles: [\"n\"], data_type: \"cross_sections\", version: \"3.1\", path: \"brond-3.1/xs/\" },\n \"fendl-3.2\": { name: \"FENDL-3.2\", description: \"Fusion Evaluated Nuclear Data Library (IAEA)\", source_url: \"https://www-nds.iaea.org/fendl/\", projectiles: [\"n\"], data_type: \"cross_sections\", version: \"3.2\", path: \"fendl-3.2/xs/\" },\n \"eaf-2010\": { name: \"EAF-2010\", description: \"European Activation File (CCFE)\", source_url: \"https://fispact.ukaea.uk/\", projectiles: [\"n\"], data_type: \"cross_sections\", version: \"2010\", path: \"eaf-2010/xs/\" },\n \"irdff-2\": { name: \"IRDFF-II\", description: \"International Reactor Dosimetry and Fusion File (IAEA)\", source_url: \"https://www-nds.iaea.org/IRDFF/\", projectiles: [\"n\"], data_type: \"cross_sections\", version: \"II\", path: \"irdff-2/xs/\" },\n \"iaea-medical\": { name: \"IAEA-Medical\", description: \"Medical isotope production cross-sections (IAEA)\", source_url: \"https://www-nds.iaea.org/medical/\", projectiles: [\"p\", \"d\", \"h\", \"a\"], data_type: \"cross_sections\", version: \"latest\", path: \"iaea-medical/xs/\" },\n \"jendl-ad-2017\": { name: \"JENDL/AD-2017\", description: \"Activation/Dosimetry Library (JAEA)\", source_url: \"https://wwwndc.jaea.go.jp/jendl/jad/jad.html\", projectiles: [\"n\", \"p\"], data_type: \"cross_sections\", version: \"2017\", path: \"jendl-ad-2017/xs/\" },\n \"jendl-deu-2020\": { name: \"JENDL-DEU-2020\", description: \"Dedicated deuteron-induced reaction library (JAEA)\", source_url: \"https://wwwndc.jaea.go.jp/jendl/deu/deu.html\", projectiles: [\"d\"], data_type: \"cross_sections\", version: \"2020\", path: \"jendl-deu-2020/xs/\" },\n \"iaea-pd-2019\": { name: \"IAEA-PD-2019\", description: \"Photonuclear Data Library (IAEA)\", source_url: \"https://www-nds.iaea.org/photonuclear/\", projectiles: [\"g\"], data_type: \"cross_sections\", version: \"2019\", path: \"iaea-pd-2019/xs/\" },\n \"exfor\": { name: \"EXFOR\", description: \"Experimental nuclear reaction data (IAEA NDS)\", source_url: \"https://www-nds.iaea.org/exfor/\", projectiles: [\"n\", \"p\", \"d\", \"t\", \"h\", \"a\"], data_type: \"experimental_cross_sections\", version: \"latest\", path: \"exfor/\" },\n },\n shared: {\n meta: { path: \"meta/\", files: { abundances: \"abundances.parquet\", decay: \"decay.parquet\", elements: \"elements.parquet\" } },\n stopping: {\n path: \"stopping/\",\n files: {\n PSTAR: \"PSTAR.parquet\",\n ASTAR: \"ASTAR.parquet\",\n ESTAR: \"ESTAR.parquet\",\n dSTAR: \"dSTAR.parquet\",\n tSTAR: \"tSTAR.parquet\",\n catima: \"catima/catima.parquet\",\n } as Record<string, string>,\n sources: [\"PSTAR\", \"ASTAR\", \"ESTAR\", \"dSTAR\", \"tSTAR\", \"catima\"],\n },\n },\n};\n\n// ---------------------------------------------------------------------------\n// Parquet fetch + cache\n// ---------------------------------------------------------------------------\n\nconst parquetCache = new Map<string, Record<string, unknown>[]>();\n\nexport async function fetchParquetRows(\n relativePath: string,\n baseUrl: string = BASE_URL,\n): Promise<Record<string, unknown>[]> {\n if (parquetCache.has(relativePath)) return parquetCache.get(relativePath)!;\n\n const url = new URL(relativePath, baseUrl).href;\n const resp = await fetch(url);\n if (!resp.ok) throw new Error(`HTTP ${resp.status} fetching ${url}`);\n const buffer = await resp.arrayBuffer();\n\n const rows: Record<string, unknown>[] = [];\n await parquetRead({\n file: buffer,\n compressors,\n rowFormat: \"object\",\n onComplete: (data: Record<string, unknown>[]) => {\n rows.push(...data);\n },\n });\n\n parquetCache.set(relativePath, rows);\n return rows;\n}\n\nasync function fetchManifest(libraryId: string): Promise<Record<string, unknown>> {\n const lib = CATALOG.libraries[libraryId];\n if (!lib) throw new Error(`Unknown library: ${libraryId}`);\n const manifestPath = lib.path.replace(/xs\\/$/, \"manifest.json\");\n const url = new URL(manifestPath, BASE_URL).href;\n const resp = await fetch(url);\n if (!resp.ok) throw new Error(`HTTP ${resp.status} fetching manifest for ${libraryId}`);\n return (await resp.json()) as Record<string, unknown>;\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\nexport function getCatalog(): Catalog {\n return CATALOG;\n}\n\nfunction truncateRows(rows: Record<string, unknown>[], limit: number): { rows: Record<string, unknown>[]; truncated: boolean; total: number } {\n if (rows.length <= limit) return { rows, truncated: false, total: rows.length };\n return { rows: rows.slice(0, limit), truncated: true, total: rows.length };\n}\n\n// ---------------------------------------------------------------------------\n// MCP Server\n// ---------------------------------------------------------------------------\n\nconst server = new McpServer({\n name: \"nucl-parquet\",\n version: \"0.3.7\",\n});\n\nserver.tool(\n \"list_libraries\",\n \"List all available nuclear data libraries with projectiles and descriptions\",\n {},\n async () => {\n const libs = Object.entries(CATALOG.libraries).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 return { content: [{ type: \"text\" as const, text: JSON.stringify(libs, null, 2) }] };\n },\n);\n\nserver.tool(\n \"list_isotopes\",\n \"List available target elements for a given library and projectile. 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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. 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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 = ? 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.\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). 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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 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package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "@nucl-parquet/mcp",
-  "version": "0.13.2",
-  "description": "MCP server for nuclear data — lazy-loads Parquet from GitHub",
+  "version": "0.15.0",
+  "description": "MCP server for nuclear data — wraps local Parquet via DuckDB",
   "type": "module",
   "bin": {
     "nucl-parquet-mcp": "./dist/index.js"
@@ -12,7 +12,7 @@
     "dist"
   ],
   "scripts": {
-    "build": "tsup",
+    "build": "tsup && tsc --emitDeclarationOnly",
     "test": "vitest run",
     "test:watch": "vitest",
     "start": "node dist/index.js"
@@ -20,15 +20,14 @@
   "repository": "https://github.com/exoma-ch/nucl-parquet",
   "license": "MIT",
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.12.0",
-    "hyparquet": "^1.7.0",
-    "hyparquet-compressors": "^1.1.0",
-    "zod": "^3.23.0"
+    "@modelcontextprotocol/sdk": "^1.30.1",
+    "duckdb": "^1.4.4",
+    "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"
   }
 }