labgate 0.5.2 → 0.5.4

package/dist/lib/slurm-db.js

@@ -0,0 +1,179 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SlurmJobDB = exports.TERMINAL_STATES = void 0;
+const fs_1 = require("fs");
+const path_1 = require("path");
+exports.TERMINAL_STATES = new Set([
+    'COMPLETED',
+    'FAILED',
+    'CANCELLED',
+    'TIMEOUT',
+    'NODE_FAIL',
+    'PREEMPTED',
+    'OUT_OF_MEMORY',
+]);
+// ── Database abstraction ──────────────────────────────────
+let Database;
+try {
+    Database = require('better-sqlite3');
+}
+catch {
+    Database = null;
+}
+const SCHEMA = `
+CREATE TABLE IF NOT EXISTS slurm_jobs (
+  job_id        TEXT PRIMARY KEY,
+  name          TEXT,
+  state         TEXT NOT NULL,
+  submit_time   TEXT NOT NULL,
+  start_time    TEXT,
+  end_time      TEXT,
+  partition     TEXT,
+  nodes         TEXT,
+  num_nodes     INTEGER,
+  num_tasks     INTEGER,
+  cpus_per_task INTEGER,
+  mem           TEXT,
+  stdout_path   TEXT,
+  stderr_path   TEXT,
+  stdout_size   INTEGER,
+  stderr_size   INTEGER,
+  command       TEXT,
+  script_path   TEXT,
+  session_id    TEXT,
+  workdir       TEXT,
+  exit_code     INTEGER,
+  account       TEXT,
+  qos           TEXT,
+  time_limit    TEXT,
+  discovered_at TEXT NOT NULL,
+  updated_at    TEXT NOT NULL,
+  notes         TEXT
+);
+CREATE INDEX IF NOT EXISTS idx_slurm_jobs_state ON slurm_jobs(state);
+CREATE INDEX IF NOT EXISTS idx_slurm_jobs_session ON slurm_jobs(session_id);
+CREATE INDEX IF NOT EXISTS idx_slurm_jobs_submit_time ON slurm_jobs(submit_time);
+`;
+class SlurmJobDB {
+    db;
+    constructor(dbPath) {
+        if (!Database) {
+            throw new Error('SLURM tracking requires the "better-sqlite3" package. ' +
+                'Install it with: npm install better-sqlite3');
+        }
+        const dir = (0, path_1.dirname)(dbPath);
+        if (!(0, fs_1.existsSync)(dir)) {
+            (0, fs_1.mkdirSync)(dir, { recursive: true });
+        }
+        this.db = new Database(dbPath);
+        try {
+            (0, fs_1.chmodSync)(dbPath, 0o600);
+        }
+        catch {
+            // Best effort for filesystems without POSIX chmod semantics.
+        }
+        this.db.pragma('journal_mode = WAL');
+        this.db.pragma('busy_timeout = 5000');
+        this.db.exec(SCHEMA);
+        // Migration: add notes column for databases created before this feature
+        try {
+            this.db.exec('ALTER TABLE slurm_jobs ADD COLUMN notes TEXT');
+        }
+        catch { /* column already exists */ }
+    }
+    upsertJob(job) {
+        const now = new Date().toISOString();
+        const existing = this.getJob(job.job_id);
+        if (existing) {
+            // Don't overwrite with less information — only update fields that have values
+            const updates = [];
+            const values = [];
+            const fields = [
+                'name', 'state', 'submit_time', 'start_time', 'end_time',
+                'partition', 'nodes', 'num_nodes', 'num_tasks', 'cpus_per_task',
+                'mem', 'stdout_path', 'stderr_path', 'stdout_size', 'stderr_size',
+                'command', 'script_path', 'session_id', 'workdir', 'exit_code',
+                'account', 'qos', 'time_limit', 'notes',
+            ];
+            for (const field of fields) {
+                if (job[field] !== undefined) {
+                    updates.push(`${field} = ?`);
+                    values.push(job[field]);
+                }
+            }
+            updates.push('updated_at = ?');
+            values.push(now);
+            values.push(job.job_id);
+            this.db.prepare(`UPDATE slurm_jobs SET ${updates.join(', ')} WHERE job_id = ?`).run(...values);
+        }
+        else {
+            this.db
+                .prepare(`INSERT INTO slurm_jobs (
+            job_id, name, state, submit_time, start_time, end_time,
+            partition, nodes, num_nodes, num_tasks, cpus_per_task, mem,
+            stdout_path, stderr_path, stdout_size, stderr_size,
+            command, script_path, session_id, workdir, exit_code,
+            account, qos, time_limit, notes, discovered_at, updated_at
+          ) VALUES (
+            ?, ?, ?, ?, ?, ?,
+            ?, ?, ?, ?, ?, ?,
+            ?, ?, ?, ?,
+            ?, ?, ?, ?, ?,
+            ?, ?, ?, ?, ?, ?
+          )`)
+                .run(job.job_id, job.name ?? null, job.state ?? 'UNKNOWN', job.submit_time ?? now, job.start_time ?? null, job.end_time ?? null, job.partition ?? null, job.nodes ?? null, job.num_nodes ?? null, job.num_tasks ?? null, job.cpus_per_task ?? null, job.mem ?? null, job.stdout_path ?? null, job.stderr_path ?? null, job.stdout_size ?? null, job.stderr_size ?? null, job.command ?? null, job.script_path ?? null, job.session_id ?? null, job.workdir ?? null, job.exit_code ?? null, job.account ?? null, job.qos ?? null, job.time_limit ?? null, job.notes ?? null, now, now);
+        }
+    }
+    updateJobNotes(jobId, notes) {
+        const now = new Date().toISOString();
+        const result = this.db
+            .prepare('UPDATE slurm_jobs SET notes = ?, updated_at = ? WHERE job_id = ?')
+            .run(notes, now, jobId);
+        return result.changes > 0;
+    }
+    getJob(jobId) {
+        return this.db.prepare('SELECT * FROM slurm_jobs WHERE job_id = ?').get(jobId) ?? null;
+    }
+    listJobs(opts) {
+        const conditions = [];
+        const values = [];
+        if (opts?.state) {
+            conditions.push('state = ?');
+            values.push(opts.state);
+        }
+        if (opts?.session_id) {
+            conditions.push('session_id = ?');
+            values.push(opts.session_id);
+        }
+        if (opts?.search) {
+            conditions.push('(job_id LIKE ? OR name LIKE ? OR command LIKE ? OR notes LIKE ?)');
+            const pattern = `%${opts.search}%`;
+            values.push(pattern, pattern, pattern, pattern);
+        }
+        const where = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';
+        const limitRaw = opts?.limit ?? 100;
+        const offsetRaw = opts?.offset ?? 0;
+        const limit = Number.isFinite(limitRaw) ? Math.min(1000, Math.max(1, Math.floor(limitRaw))) : 100;
+        const offset = Number.isFinite(offsetRaw) ? Math.max(0, Math.floor(offsetRaw)) : 0;
+        return this.db
+            .prepare(`SELECT * FROM slurm_jobs ${where} ORDER BY submit_time DESC LIMIT ? OFFSET ?`)
+            .all(...values, limit, offset);
+    }
+    getActiveJobIds() {
+        const rows = this.db
+            .prepare("SELECT job_id FROM slurm_jobs WHERE state IN ('PENDING', 'RUNNING', 'COMPLETING', 'SUSPENDED')")
+            .all();
+        return rows.map((r) => r.job_id);
+    }
+    getJobCount(state) {
+        if (state) {
+            return this.db.prepare('SELECT COUNT(*) as count FROM slurm_jobs WHERE state = ?').get(state).count;
+        }
+        return this.db.prepare('SELECT COUNT(*) as count FROM slurm_jobs').get().count;
+    }
+    close() {
+        this.db.close();
+    }
+}
+exports.SlurmJobDB = SlurmJobDB;
+//# sourceMappingURL=slurm-db.js.map

package/dist/lib/slurm-db.js.map

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package/dist/lib/slurm-mcp.d.ts

@@ -0,0 +1,12 @@
+/**
+ * LabGate SLURM MCP Server
+ *
+ * A Model Context Protocol server that exposes SLURM job tracking tools
+ * to Claude Code. Runs as a standalone process using stdio transport.
+ *
+ * Usage: node dist/lib/slurm-mcp.js [--db <path>]
+ *
+ * Environment variables:
+ *   LABGATE_SLURM_DB  – Path to the SLURM SQLite database (default: ~/.labgate/slurm.db)
+ */
+export declare function main(): Promise<void>;

package/dist/lib/slurm-mcp.js

@@ -0,0 +1,347 @@
+"use strict";
+/**
+ * LabGate SLURM MCP Server
+ *
+ * A Model Context Protocol server that exposes SLURM job tracking tools
+ * to Claude Code. Runs as a standalone process using stdio transport.
+ *
+ * Usage: node dist/lib/slurm-mcp.js [--db <path>]
+ *
+ * Environment variables:
+ *   LABGATE_SLURM_DB  – Path to the SLURM SQLite database (default: ~/.labgate/slurm.db)
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.main = main;
+const mcp_js_1 = require("@modelcontextprotocol/sdk/server/mcp.js");
+const stdio_js_1 = require("@modelcontextprotocol/sdk/server/stdio.js");
+const slurm_db_js_1 = require("./slurm-db.js");
+const config_js_1 = require("./config.js");
+const fs_1 = require("fs");
+const zod_1 = require("zod");
+// ── Resolve DB path ──────────────────────────────────────
+function resolveDbPath() {
+    // CLI arg
+    const dbArgIdx = process.argv.indexOf('--db');
+    if (dbArgIdx >= 0 && process.argv[dbArgIdx + 1]) {
+        return process.argv[dbArgIdx + 1];
+    }
+    // Environment variable
+    if (process.env.LABGATE_SLURM_DB) {
+        return process.env.LABGATE_SLURM_DB;
+    }
+    // Default
+    return (0, config_js_1.getSlurmDbPath)();
+}
+// ── Helpers ──────────────────────────────────────────────
+function tailReadFile(filePath, maxLines) {
+    if (!(0, fs_1.existsSync)(filePath))
+        return '';
+    const st = (0, fs_1.statSync)(filePath);
+    const maxBytes = 1_048_576; // 1MB
+    const readSize = Math.min(st.size, maxBytes);
+    if (readSize === 0)
+        return '';
+    const buf = Buffer.alloc(readSize);
+    let fd = null;
+    try {
+        fd = (0, fs_1.openSync)(filePath, 'r');
+        (0, fs_1.readSync)(fd, buf, 0, readSize, Math.max(0, st.size - readSize));
+    }
+    finally {
+        if (fd !== null) {
+            try {
+                (0, fs_1.closeSync)(fd);
+            }
+            catch { /* best effort */ }
+        }
+    }
+    let text = buf.toString('utf-8');
+    if (st.size > readSize) {
+        const firstNewline = text.indexOf('\n');
+        if (firstNewline >= 0)
+            text = text.slice(firstNewline + 1);
+    }
+    const lines = text.split('\n');
+    return lines.slice(-maxLines).join('\n');
+}
+function clampInt(value, fallback, min, max) {
+    if (!Number.isFinite(value))
+        return fallback;
+    return Math.min(max, Math.max(min, Math.floor(value)));
+}
+function normalizeJobId(value) {
+    return String(value || '').trim();
+}
+// ── MCP Server ───────────────────────────────────────────
+async function main() {
+    const dbPath = resolveDbPath();
+    let db;
+    try {
+        db = new slurm_db_js_1.SlurmJobDB(dbPath);
+    }
+    catch (err) {
+        console.error(`Failed to open SLURM database at ${dbPath}: ${err.message}`);
+        process.exit(1);
+    }
+    const server = new mcp_js_1.McpServer({
+        name: 'labgate-slurm',
+        version: '1.0.0',
+    }, {
+        capabilities: {
+            tools: {},
+        },
+        instructions: 'LabGate SLURM job tracker. Use these tools to check the status of SLURM jobs, ' +
+            'read their output files, and cancel jobs. Jobs are automatically discovered by ' +
+            'polling squeue/sacct.',
+    });
+    // ── Tool: list_slurm_jobs ──────────────────────────────
+    server.registerTool('list_slurm_jobs', {
+        title: 'List SLURM Jobs',
+        description: 'List SLURM jobs tracked by LabGate. Returns job ID, name, state, runtime, ' +
+            'partition, nodes, and output file paths. Filter by state or search by name/ID.',
+        inputSchema: {
+            state: zod_1.z.string().optional().describe('Filter by state: PENDING, RUNNING, COMPLETED, FAILED, CANCELLED, TIMEOUT'),
+            search: zod_1.z.string().optional().describe('Search by job ID, name, or command'),
+            limit: zod_1.z.number().int().min(1).max(500).optional().default(20).describe('Max number of jobs to return'),
+        },
+    }, async ({ state, search, limit }) => {
+        const safeLimit = clampInt(limit, 20, 1, 500);
+        const jobs = db.listJobs({
+            state: state || undefined,
+            search: search || undefined,
+            limit: safeLimit,
+        });
+        const summary = jobs.map((j) => ({
+            job_id: j.job_id,
+            name: j.name,
+            state: j.state,
+            partition: j.partition,
+            nodes: j.nodes,
+            submit_time: j.submit_time,
+            start_time: j.start_time,
+            end_time: j.end_time,
+            exit_code: j.exit_code,
+            stdout_path: j.stdout_path,
+            stderr_path: j.stderr_path,
+            stdout_size: j.stdout_size,
+            stderr_size: j.stderr_size,
+            command: j.command,
+            notes: j.notes,
+        }));
+        return {
+            content: [
+                {
+                    type: 'text',
+                    text: jobs.length === 0
+                        ? 'No SLURM jobs found.'
+                        : JSON.stringify(summary, null, 2),
+                },
+            ],
+        };
+    });
+    // ── Tool: get_slurm_job ────────────────────────────────
+    server.registerTool('get_slurm_job', {
+        title: 'Get SLURM Job Details',
+        description: 'Get detailed information about a specific SLURM job by its ID.',
+        inputSchema: {
+            job_id: zod_1.z.string().describe('The SLURM job ID'),
+        },
+    }, async ({ job_id }) => {
+        const normalizedJobId = normalizeJobId(job_id);
+        if (!normalizedJobId) {
+            return {
+                content: [{ type: 'text', text: 'job_id must be a non-empty string.' }],
+                isError: true,
+            };
+        }
+        const job = db.getJob(normalizedJobId);
+        if (!job) {
+            return {
+                content: [{ type: 'text', text: `Job ${normalizedJobId} not found.` }],
+                isError: true,
+            };
+        }
+        return {
+            content: [{ type: 'text', text: JSON.stringify(job, null, 2) }],
+        };
+    });
+    // ── Tool: get_slurm_output ─────────────────────────────
+    server.registerTool('get_slurm_output', {
+        title: 'Read SLURM Job Output',
+        description: 'Read the stdout or stderr output file of a SLURM job. Returns the last N lines.',
+        inputSchema: {
+            job_id: zod_1.z.string().describe('The SLURM job ID'),
+            stream: zod_1.z.enum(['stdout', 'stderr']).optional().default('stdout').describe('Which output stream to read'),
+            tail_lines: zod_1.z.number().optional().default(100).describe('Number of lines to read from the end'),
+        },
+    }, async ({ job_id, stream, tail_lines }) => {
+        const normalizedJobId = normalizeJobId(job_id);
+        if (!normalizedJobId) {
+            return {
+                content: [{ type: 'text', text: 'job_id must be a non-empty string.' }],
+                isError: true,
+            };
+        }
+        const safeTailLines = clampInt(tail_lines, 100, 1, 5000);
+        const job = db.getJob(normalizedJobId);
+        if (!job) {
+            return {
+                content: [{ type: 'text', text: `Job ${normalizedJobId} not found.` }],
+                isError: true,
+            };
+        }
+        const filePath = stream === 'stderr' ? job.stderr_path : job.stdout_path;
+        if (!filePath) {
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: `No ${stream} path recorded for job ${normalizedJobId}.`,
+                    },
+                ],
+            };
+        }
+        if (!(0, fs_1.existsSync)(filePath)) {
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: `Output file ${filePath} does not exist (yet).`,
+                    },
+                ],
+            };
+        }
+        const st = (0, fs_1.statSync)(filePath);
+        if (st.size === 0) {
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: `Output file ${filePath} exists but is empty (0 bytes).`,
+                    },
+                ],
+            };
+        }
+        const content = tailReadFile(filePath, safeTailLines);
+        return {
+            content: [
+                {
+                    type: 'text',
+                    text: `=== ${stream} for job ${normalizedJobId} (last ${safeTailLines} lines, file size: ${st.size} bytes) ===\n${content}`,
+                },
+            ],
+        };
+    });
+    // ── Tool: cancel_slurm_job ─────────────────────────────
+    server.registerTool('cancel_slurm_job', {
+        title: 'Cancel SLURM Job',
+        description: 'Cancel a pending or running SLURM job using scancel.',
+        inputSchema: {
+            job_id: zod_1.z.string().describe('The SLURM job ID to cancel'),
+        },
+    }, async ({ job_id }) => {
+        const normalizedJobId = normalizeJobId(job_id);
+        if (!normalizedJobId) {
+            return {
+                content: [{ type: 'text', text: 'job_id must be a non-empty string.' }],
+                isError: true,
+            };
+        }
+        const job = db.getJob(normalizedJobId);
+        if (!job) {
+            return {
+                content: [{ type: 'text', text: `Job ${normalizedJobId} not found.` }],
+                isError: true,
+            };
+        }
+        if (slurm_db_js_1.TERMINAL_STATES.has(job.state)) {
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: `Job ${normalizedJobId} is already in terminal state: ${job.state}`,
+                    },
+                ],
+            };
+        }
+        const { execFile } = await import('child_process');
+        const { promisify } = await import('util');
+        const execFileAsync = promisify(execFile);
+        try {
+            await execFileAsync('scancel', [normalizedJobId], { timeout: 10_000 });
+            db.upsertJob({ job_id: normalizedJobId, state: 'CANCELLED' });
+            return {
+                content: [
+                    { type: 'text', text: `Job ${normalizedJobId} has been cancelled.` },
+                ],
+            };
+        }
+        catch (err) {
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: `Failed to cancel job ${normalizedJobId}: ${err.message}`,
+                    },
+                ],
+                isError: true,
+            };
+        }
+    });
+    // ── Tool: set_slurm_job_notes ─────────────────────────
+    server.registerTool('set_slurm_job_notes', {
+        title: 'Set SLURM Job Notes',
+        description: 'Add or update a text note on a SLURM job. Use this to annotate jobs with context or observations.',
+        inputSchema: {
+            job_id: zod_1.z.string().describe('The SLURM job ID'),
+            notes: zod_1.z.string().nullable().describe('Note text, or null to clear'),
+        },
+    }, async ({ job_id, notes }) => {
+        const id = normalizeJobId(job_id);
+        if (!id) {
+            return {
+                content: [{ type: 'text', text: 'job_id must be a non-empty string.' }],
+                isError: true,
+            };
+        }
+        const job = db.getJob(id);
+        if (!job) {
+            return {
+                content: [{ type: 'text', text: `Job ${id} not found.` }],
+                isError: true,
+            };
+        }
+        db.updateJobNotes(id, notes);
+        return {
+            content: [
+                {
+                    type: 'text',
+                    text: notes ? `Notes set for job ${id}.` : `Notes cleared for job ${id}.`,
+                },
+            ],
+        };
+    });
+    // ── Connect and start ──────────────────────────────────
+    const transport = new stdio_js_1.StdioServerTransport();
+    await server.connect(transport);
+    // Clean up on exit
+    process.on('SIGINT', () => {
+        db.close();
+        process.exit(0);
+    });
+    process.on('SIGTERM', () => {
+        db.close();
+        process.exit(0);
+    });
+}
+function isDirectRun() {
+    const argv1 = process.argv[1] || '';
+    return /(?:^|\/|\\)slurm-mcp(?:\.js)?$/.test(argv1);
+}
+if (isDirectRun()) {
+    main().catch((err) => {
+        console.error('MCP server error:', err);
+        process.exit(1);
+    });
+}
+//# sourceMappingURL=slurm-mcp.js.map

package/dist/lib/slurm-mcp.js.map

@@ -0,0 +1 @@
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package/dist/lib/slurm-poller.d.ts

@@ -0,0 +1,36 @@
+import { SlurmJobDB, SlurmJob } from './slurm-db.js';
+export interface PollResult {
+    squeueJobs: number;
+    sacctJobs: number;
+    errors: string[];
+}
+export interface SlurmPollerOptions {
+    db: SlurmJobDB;
+    pollIntervalMs?: number;
+    sacctLookbackHours?: number;
+    username?: string;
+}
+export declare class SlurmPoller {
+    private db;
+    private pollIntervalMs;
+    private sacctLookbackHours;
+    private username;
+    private timer;
+    private sacctTimer;
+    private backoffMs;
+    private squeueSupportsJson;
+    private readonly localHost;
+    constructor(opts: SlurmPollerOptions);
+    start(): void;
+    stop(): void;
+    pollOnce(): Promise<PollResult>;
+    private pollSqueue;
+    parseSqueueJson(output: string): Partial<SlurmJob>[];
+    parseSqueueDelimited(output: string, delimiter?: string): Partial<SlurmJob>[];
+    private pollSacct;
+    parseSacctOutput(output: string): Partial<SlurmJob>[];
+    private upsertWithSessionCorrelation;
+    private findMatchingSession;
+    private updateOutputFileStats;
+    private exec;
+}