nds-mcp 0.1.0

package/dist/tools/registry.js

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+import { z } from 'zod';
+import { zodToMcpInputSchema } from './mcpSchema.js';
+import { requireNdsDbPathFromEnv, getFileMetadata } from '../db/ndsDb.js';
+import { getMass } from '../db/masses.js';
+import { getSeparationEnergy, getQValue } from '../db/reactions.js';
+import { getDecay, findNuclidesByElement, findNuclideByZA, findNuclidesByA, searchNuclides } from '../db/nubase.js';
+import { getChargeRadius } from '../db/chargeRadii.js';
+import { queryAllLevels } from '../db/levels.js';
+import { queryGammas } from '../db/gammas.js';
+import { queryDecayFeedings } from '../db/decayFeedings.js';
+import { lookupReference } from '../db/references.js';
+import { invalidParams, notFound, sqlite3JsonQuery } from '../shared/index.js';
+import { NDS_FIND_NUCLIDE, NDS_GET_MASS, NDS_GET_SEPARATION_ENERGY, NDS_GET_Q_VALUE, NDS_GET_DECAY, NDS_GET_CHARGE_RADIUS, NDS_SEARCH, NDS_INFO, NDS_QUERY_LEVELS, NDS_QUERY_GAMMAS, NDS_QUERY_DECAY_FEEDINGS, NDS_LOOKUP_REFERENCE, } from '../constants.js';
+export function isToolExposed(spec, mode) {
+    return mode === 'full' ? true : spec.exposure === 'standard';
+}
+// ── Element symbol lookup (for resolving element names to Z) ──────────────
+const ELEMENT_SYMBOLS = {
+    n: 0, H: 1, He: 2, Li: 3, Be: 4, B: 5, C: 6, N: 7, O: 8, F: 9,
+    Ne: 10, Na: 11, Mg: 12, Al: 13, Si: 14, P: 15, S: 16, Cl: 17, Ar: 18, K: 19,
+    Ca: 20, Sc: 21, Ti: 22, V: 23, Cr: 24, Mn: 25, Fe: 26, Co: 27, Ni: 28, Cu: 29,
+    Zn: 30, Ga: 31, Ge: 32, As: 33, Se: 34, Br: 35, Kr: 36, Rb: 37, Sr: 38, Y: 39,
+    Zr: 40, Nb: 41, Mo: 42, Tc: 43, Ru: 44, Rh: 45, Pd: 46, Ag: 47, Cd: 48, In: 49,
+    Sn: 50, Sb: 51, Te: 52, I: 53, Xe: 54, Cs: 55, Ba: 56, La: 57, Ce: 58, Pr: 59,
+    Nd: 60, Pm: 61, Sm: 62, Eu: 63, Gd: 64, Tb: 65, Dy: 66, Ho: 67, Er: 68, Tm: 69,
+    Yb: 70, Lu: 71, Hf: 72, Ta: 73, W: 74, Re: 75, Os: 76, Ir: 77, Pt: 78, Au: 79,
+    Hg: 80, Tl: 81, Pb: 82, Bi: 83, Po: 84, At: 85, Rn: 86, Fr: 87, Ra: 88, Ac: 89,
+    Th: 90, Pa: 91, U: 92, Np: 93, Pu: 94, Am: 95, Cm: 96, Bk: 97, Cf: 98, Es: 99,
+    Fm: 100, Md: 101, No: 102, Lr: 103, Rf: 104, Db: 105, Sg: 106, Bh: 107, Hs: 108, Mt: 109,
+    Ds: 110, Rg: 111, Cn: 112, Nh: 113, Fl: 114, Mc: 115, Lv: 116, Ts: 117, Og: 118,
+};
+function resolveElement(element) {
+    // Try exact match first, then case-insensitive
+    if (ELEMENT_SYMBOLS[element] !== undefined)
+        return ELEMENT_SYMBOLS[element];
+    const titleCase = element.charAt(0).toUpperCase() + element.slice(1).toLowerCase();
+    return ELEMENT_SYMBOLS[titleCase];
+}
+// ── Tool Schemas ──────────────────────────────────────────────────────────
+const NdsInfoSchema = z.object({});
+const NdsFindNuclideSchema = z.object({
+    element: z.string().min(1).optional().describe('Element symbol (e.g. "He", "U", "Pb")'),
+    Z: z.number().int().min(0).optional().describe('Atomic number'),
+    A: z.number().int().min(1).optional().describe('Mass number'),
+}).refine(v => v.element !== undefined || v.Z !== undefined || v.A !== undefined, { message: 'At least one of element, Z, or A must be provided' });
+const NdsGetMassSchema = z.object({
+    Z: z.number().int().min(0).describe('Atomic number'),
+    A: z.number().int().min(1).describe('Mass number'),
+});
+const NdsGetSeparationEnergySchema = z.object({
+    Z: z.number().int().min(0).describe('Atomic number'),
+    A: z.number().int().min(1).describe('Mass number'),
+    type: z.enum(['Sn', 'Sp', 'S2n', 'S2p']).optional().describe('Separation energy type (omit for all)'),
+});
+const NdsGetQValueSchema = z.object({
+    Z: z.number().int().min(0).describe('Atomic number'),
+    A: z.number().int().min(1).describe('Mass number'),
+    type: z.enum(['Qa', 'Q2bm', 'Qep', 'Qbn', 'Q4bm', 'Qda', 'Qpa', 'Qna']).optional().describe('Q-value type (omit for all)'),
+});
+const NdsGetDecaySchema = z.object({
+    Z: z.number().int().min(0).describe('Atomic number'),
+    A: z.number().int().min(1).describe('Mass number'),
+});
+const NdsGetChargeRadiusSchema = z.object({
+    Z: z.number().int().min(0).describe('Atomic number'),
+    A: z.number().int().min(1).optional().describe('Mass number (omit for all isotopes of element)'),
+});
+const NdsSearchSchema = z.object({
+    property: z.enum(['half_life', 'mass_excess', 'half_life_seconds', 'mass_excess_keV']).describe('Property to search by. Note: stable nuclides have null half_life_seconds and are excluded from half-life range searches.'),
+    min: z.number().finite().optional().describe('Minimum value'),
+    max: z.number().finite().optional().describe('Maximum value'),
+    Z_min: z.number().int().min(0).optional().describe('Minimum atomic number'),
+    Z_max: z.number().int().min(0).optional().describe('Maximum atomic number'),
+    limit: z.number().int().min(1).max(200).optional().default(50).describe('Maximum results'),
+}).refine(v => v.min !== undefined || v.max !== undefined, { message: 'At least one of min or max must be provided' }).refine(v => (v.min === undefined || v.max === undefined || v.min <= v.max), { message: 'min must be <= max when both are provided' }).refine(v => (v.Z_min === undefined || v.Z_max === undefined || v.Z_min <= v.Z_max), { message: 'Z_min must be <= Z_max when both are provided' });
+const NdsQueryLevelsSchema = z.object({
+    Z: z.number().int().min(0).describe('Atomic number'),
+    A: z.number().int().min(1).describe('Mass number'),
+    energy_min: z.number().optional().describe('Minimum level energy (keV)'),
+    energy_max: z.number().optional().describe('Maximum level energy (keV)'),
+    include_decay_datasets: z.boolean().optional().default(false)
+        .describe('Include levels from decay datasets (default: ADOPTED only)'),
+    include_tunl: z.boolean().optional()
+        .describe('Include TUNL resonance data (default: true for A ≤ 20, false otherwise)'),
+    limit: z.number().int().min(1).max(500).optional().default(100),
+});
+const NdsQueryGammasSchema = z.object({
+    Z: z.number().int().min(0).describe('Atomic number'),
+    A: z.number().int().min(1).describe('Mass number'),
+    level_energy: z.number().optional().describe('Filter gammas from specific level (keV)'),
+    gamma_energy_min: z.number().optional().describe('Minimum gamma energy (keV)'),
+    gamma_energy_max: z.number().optional().describe('Maximum gamma energy (keV)'),
+    limit: z.number().int().min(1).max(500).optional().default(100),
+});
+const NdsQueryDecayFeedingsSchema = z.object({
+    Z: z.number().int().min(0).describe('Parent atomic number'),
+    A: z.number().int().min(1).describe('Parent mass number'),
+    decay_mode: z.enum(['B-', 'EC', 'EC+B+', 'IT']).optional().describe('Filter by decay mode'),
+});
+const NdsLookupReferenceSchema = z.object({
+    keynumber: z.string().optional().describe('NSR keynumber (e.g. "2012WA38")'),
+    A: z.number().int().min(1).optional().describe('Mass number (list all references for this A)'),
+}).refine(v => v.keynumber !== undefined || v.A !== undefined, { message: 'At least one of keynumber or A must be provided' });
+// ── Tool Specs ────────────────────────────────────────────────────────────
+export const TOOL_SPECS = [
+    {
+        name: NDS_INFO,
+        description: 'Return NDS database metadata: data versions, nuclide counts, DB file hash.',
+        exposure: 'standard',
+        zodSchema: NdsInfoSchema,
+        handler: async () => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const meta = await sqlite3JsonQuery(dbPath, 'SELECT key, value FROM nds_meta');
+            const metaMap = {};
+            for (const row of meta) {
+                const r = row;
+                metaMap[r.key] = r.value;
+            }
+            const fileMeta = await getFileMetadata(dbPath);
+            return { ...metaMap, db_path: dbPath, ...fileMeta };
+        },
+    },
+    {
+        name: NDS_FIND_NUCLIDE,
+        description: 'Find nuclides by element symbol, Z (atomic number), and/or A (mass number). Returns basic properties from NUBASE2020.',
+        exposure: 'standard',
+        zodSchema: NdsFindNuclideSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const { element, Z, A } = params;
+            // Resolve element to Z if provided
+            let resolvedZ;
+            if (element !== undefined) {
+                resolvedZ = resolveElement(element);
+                if (resolvedZ === undefined) {
+                    throw invalidParams(`Unknown element symbol: ${element}`);
+                }
+                // Check for conflicting Z
+                if (Z !== undefined && Z !== resolvedZ) {
+                    throw invalidParams(`Conflicting parameters: element ${element} is Z=${resolvedZ}, but Z=${Z} was provided.`);
+                }
+            }
+            const effectiveZ = resolvedZ ?? Z;
+            if (effectiveZ !== undefined && A !== undefined) {
+                return findNuclideByZA(dbPath, effectiveZ, A);
+            }
+            if (effectiveZ !== undefined) {
+                // Find element symbol from DB for querying by canonical name
+                const rows = await sqlite3JsonQuery(dbPath, `SELECT DISTINCT element FROM nubase WHERE Z=${effectiveZ} LIMIT 1`);
+                if (rows.length === 0)
+                    throw notFound(`No nuclides found for Z=${effectiveZ}`);
+                const el = rows[0].element;
+                return findNuclidesByElement(dbPath, el);
+            }
+            if (A !== undefined) {
+                return findNuclidesByA(dbPath, A);
+            }
+            return [];
+        },
+    },
+    {
+        name: NDS_GET_MASS,
+        description: 'Get atomic mass data for a nuclide (Z, A) from AME2020: mass excess, binding energy/A, beta-decay energy, atomic mass.',
+        exposure: 'standard',
+        zodSchema: NdsGetMassSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const result = await getMass(dbPath, params.Z, params.A);
+            if (!result)
+                throw notFound(`No mass data for Z=${params.Z}, A=${params.A}`);
+            return result;
+        },
+    },
+    {
+        name: NDS_GET_SEPARATION_ENERGY,
+        description: 'Get nucleon separation energies from AME2020: Sn, Sp, S2n, S2p.',
+        exposure: 'standard',
+        zodSchema: NdsGetSeparationEnergySchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const result = await getSeparationEnergy(dbPath, params.Z, params.A, params.type);
+            if (!result)
+                throw notFound(`No separation energy data for Z=${params.Z}, A=${params.A}`);
+            return result;
+        },
+    },
+    {
+        name: NDS_GET_Q_VALUE,
+        description: 'Get Q-values from AME2020: Qα, Q(2β⁻), Q(εp), Q(β⁻n), Q(4β⁻), Q(d,α), Q(p,α), Q(n,α).',
+        exposure: 'standard',
+        zodSchema: NdsGetQValueSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const result = await getQValue(dbPath, params.Z, params.A, params.type);
+            if (!result)
+                throw notFound(`No Q-value data for Z=${params.Z}, A=${params.A}`);
+            return result;
+        },
+    },
+    {
+        name: NDS_GET_DECAY,
+        description: 'Get decay information from NUBASE2020: half-life, spin/parity, decay modes with branching ratios, isomers.',
+        exposure: 'standard',
+        zodSchema: NdsGetDecaySchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const results = await getDecay(dbPath, params.Z, params.A);
+            if (results.length === 0)
+                throw notFound(`No decay data for Z=${params.Z}, A=${params.A}`);
+            return results;
+        },
+    },
+    {
+        name: NDS_GET_CHARGE_RADIUS,
+        description: 'Get nuclear charge radius (rms) from IAEA data, enriched with laser spectroscopy provenance from Li et al. 2021 where available. If A is omitted, returns all isotopes of the element.',
+        exposure: 'standard',
+        zodSchema: NdsGetChargeRadiusSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const results = await getChargeRadius(dbPath, params.Z, params.A);
+            if (results.length === 0) {
+                const msg = params.A !== undefined
+                    ? `No charge radius data for Z=${params.Z}, A=${params.A}`
+                    : `No charge radius data for Z=${params.Z}`;
+                throw notFound(msg);
+            }
+            return results;
+        },
+    },
+    {
+        name: NDS_SEARCH,
+        description: 'Search nuclides by property range (half_life_seconds, mass_excess_keV). Returns ground-state nuclides matching criteria.',
+        exposure: 'standard',
+        zodSchema: NdsSearchSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            return searchNuclides(dbPath, params.property, params.min, params.max, params.Z_min, params.Z_max, params.limit);
+        },
+    },
+    {
+        name: NDS_QUERY_LEVELS,
+        description: 'Query nuclear energy levels from ENSDF and TUNL. Returns level energies, spin-parity, half-lives. For A ≤ 20, automatically includes TUNL resonance data (widths, isospin, decay modes, table_label for TUNL publication provenance). Each result has a "source" field ("ENSDF" or "TUNL").',
+        exposure: 'standard',
+        zodSchema: NdsQueryLevelsSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const results = await queryAllLevels(dbPath, params);
+            if (results.length === 0)
+                throw notFound(`No levels for Z=${params.Z}, A=${params.A}`);
+            return results;
+        },
+    },
+    {
+        name: NDS_QUERY_GAMMAS,
+        description: 'Query gamma-ray transitions from ENSDF. Returns energies, intensities, multipolarities, conversion coefficients for a nuclide.',
+        exposure: 'standard',
+        zodSchema: NdsQueryGammasSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const results = await queryGammas(dbPath, params);
+            if (results.length === 0)
+                throw notFound(`No ENSDF gammas for Z=${params.Z}, A=${params.A}`);
+            return results;
+        },
+    },
+    {
+        name: NDS_QUERY_DECAY_FEEDINGS,
+        description: 'Query beta/EC decay feeding patterns from ENSDF. Returns branching ratios, log(ft) values, endpoint energies for parent nuclide decays.',
+        exposure: 'standard',
+        zodSchema: NdsQueryDecayFeedingsSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const results = await queryDecayFeedings(dbPath, params);
+            if (results.length === 0)
+                throw notFound(`No ENSDF decay feedings for Z=${params.Z}, A=${params.A}`);
+            return results;
+        },
+    },
+    {
+        name: NDS_LOOKUP_REFERENCE,
+        description: 'Look up ENSDF/NSR bibliographic references by keynumber or mass number.',
+        exposure: 'standard',
+        zodSchema: NdsLookupReferenceSchema,
+        handler: async (params) => {
+            const dbPath = requireNdsDbPathFromEnv();
+            const results = await lookupReference(dbPath, params);
+            if (results.length === 0) {
+                const msg = params.keynumber ? `No reference for keynumber ${params.keynumber}` : `No references for A=${params.A}`;
+                throw notFound(msg);
+            }
+            return results;
+        },
+    },
+];
+// ── Exports ───────────────────────────────────────────────────────────────
+export function getToolSpec(name) {
+    return TOOL_SPECS.find(s => s.name === name);
+}
+export function getToolSpecs(mode = 'standard') {
+    return mode === 'full' ? TOOL_SPECS : TOOL_SPECS.filter(s => s.exposure === 'standard');
+}
+export function getTools(mode = 'standard') {
+    return getToolSpecs(mode).map(s => ({
+        name: s.name,
+        description: s.description,
+        inputSchema: zodToMcpInputSchema(s.zodSchema),
+    }));
+}
+//# sourceMappingURL=registry.js.map

package/dist/tools/registry.js.map

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package/dist/utils/stdioHygiene.d.ts

@@ -0,0 +1,7 @@
+/**
+ * stdout hygiene:
+ * MCP uses stdout for JSON-RPC. Any logs to stdout will corrupt the protocol.
+ * Route console log-like methods to stderr to keep stdout pure.
+ */
+export {};
+//# sourceMappingURL=stdioHygiene.d.ts.map

package/dist/utils/stdioHygiene.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"stdioHygiene.d.ts","sourceRoot":"","sources":["../../src/utils/stdioHygiene.ts"],"names":[],"mappings":"AAAA;;;;GAIG"}

package/dist/utils/stdioHygiene.js

@@ -0,0 +1,16 @@
+/**
+ * stdout hygiene:
+ * MCP uses stdout for JSON-RPC. Any logs to stdout will corrupt the protocol.
+ * Route console log-like methods to stderr to keep stdout pure.
+ */
+function routeToStderr(...args) {
+    console.error(...args);
+}
+if (console.log !== routeToStderr)
+    console.log = routeToStderr;
+if (console.debug !== routeToStderr)
+    console.debug = routeToStderr;
+if (console.info !== routeToStderr)
+    console.info = routeToStderr;
+export {};
+//# sourceMappingURL=stdioHygiene.js.map

package/dist/utils/stdioHygiene.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,64 @@
+{
+  "name": "nds-mcp",
+  "version": "0.1.0",
+  "description": "Nuclear Data Services MCP server — offline SQLite-backed nuclear physics data queries",
+  "author": "Feng-Kun Guo",
+  "license": "MIT",
+  "type": "module",
+  "main": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "types": "./dist/index.d.ts"
+    },
+    "./tooling": {
+      "import": "./dist/tooling.js",
+      "types": "./dist/tooling.d.ts"
+    }
+  },
+  "bin": {
+    "nds-mcp": "./dist/index.js"
+  },
+  "files": [
+    "dist",
+    "bin"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "clean": "rm -rf dist",
+    "lint": "tsc --noEmit",
+    "dev": "tsx watch src/index.ts",
+    "start": "node dist/index.js",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "ingest": "tsx src/ingest/buildDb.ts"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.25.2",
+    "zod": "^4.3.5"
+  },
+  "devDependencies": {
+    "@types/node": "^25.0.3",
+    "tsx": "^4.21.0",
+    "typescript": "^5.4.0",
+    "vitest": "^4.0.16"
+  },
+  "engines": {
+    "node": ">=18"
+  },
+  "keywords": [
+    "mcp",
+    "nuclear-data",
+    "nuclear-physics",
+    "sqlite",
+    "ensdf",
+    "tunl",
+    "ame2020",
+    "nubase"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/fkguo/nds-mcp.git"
+  }
+}