@neuralbridge/bio-pipelines-mcp 0.0.0-stage → 1.0.0

package/LICENSE

@@ -0,0 +1,202 @@
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package/NOTICE

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+NeuralBridge MCP servers
+Copyright 2026 NeuralBridge — https://neuralbridge.ru

package/README.md

@@ -1,3 +1,98 @@
-# Temporary Holding Version
+# @neuralbridge/bio-pipelines-mcp
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+MCP server for bioinformatics pipelines written for Nextflow, WDL (run with miniwdl) and Snakemake. It is the server
+behind the `nb-bio-pipelines` power of NeuralBridge IDE, and works with any MCP client over stdio.
+
+## Tools
+
+| Tool | What it does | Changes |
+|---|---|---|
+| `bio_detect` | Which of `nextflow`, `miniwdl`, `snakemake` are installed and their versions; with `dir`, lists `main.nf`, `nextflow.config`, `.wdl` files and Snakefiles | nothing |
+| `bio_lint` | `nextflow lint -o json`, `miniwdl check`, `snakemake --lint json`; findings as `file:line:column: message` | nothing (Snakemake evaluates the Snakefile) |
+| `bio_plan` | Dry run: Nextflow `run -preview -with-dag` (processes of the DAG), Snakemake `--dry-run` (jobs per rule), miniwdl `check` + required inputs + `run --json`; saves the exact command and file hashes as a plan | tool metadata (`.nextflow`, `.snakemake`) in the launch directory |
+| `bio_run` | Starts exactly the planned command in the background, once, and returns a run id | **runs the pipeline**: computes, writes results, may overwrite outputs |
+| `bio_run_status` | Running or finished, exit code, duration, progress, last 100 lines of the log | nothing |
+| `bio_run_stop_plan` | Shows what is running and for how long; saves a stop plan | a plan file in the data folder |
+| `bio_run_stop_apply` | Sends SIGTERM to the planned run, once | **stops the run** |
+| `bio_runs` | Runs started through this server, newest first | nothing |
+
+Read-only are only `bio_detect`, `bio_run_status` and `bio_runs`. `bio_lint` is not marked read-only because
+`snakemake --lint` executes the Snakefile, which is Python code; `bio_plan` evaluates the pipeline code of all three tools.
+`bio_run` and `bio_run_stop_apply` are marked destructive.
+
+### Plan, then run
+
+`bio_run` takes only a plan id. Before starting, it checks that the program still resolves to the same binary, that the
+launch directory exists and that the pipeline file, the `nextflow.config` files (pipeline and launch directory), the
+params file, the Snakemake config and profile files and the WDL inputs file have the same sha256 as at planning time.
+Then it runs exactly the saved arguments and removes the plan. Plans expire after 24 hours.
+
+The run is a detached process: its stdout and stderr go to `runs/<id>.log`, the PID and start time to `runs/<id>.json`.
+While the server is alive, it records the exit code when the process ends. If the server was restarted during a run,
+`bio_run_status` checks the PID (on Linux also its command line) and guesses the outcome from the end of the log. Records
+of finished runs, their logs and Nextflow reports are removed after 7 days.
+
+| Tool | Command started by `bio_run` |
+|---|---|
+| Nextflow | `nextflow run <main.nf> [-params-file F] [-profile P] [-work-dir D] [-resume] -with-report <data>/runs/<id>-report.html` |
+| Snakemake | `snakemake [targets] --snakefile S --directory D --nocolor --cores N [--configfile …] [--profile P] [--software-deployment-method …]` |
+| miniwdl | `miniwdl run <file.wdl> [-i inputs.json] [--task T] --dir <outputDir> --no-color` (a timestamp-named run directory is created under it) |
+
+Stopping sends SIGTERM to the program itself; Nextflow, Snakemake and miniwdl then cancel their running tasks and exit.
+
+## Local pipelines only, and what the tools download
+
+The server installs and downloads nothing. It starts only programs already installed, found on `PATH` or through
+`NB_BIO_NEXTFLOW`, `NB_BIO_MINIWDL`, `NB_BIO_SNAKEMAKE`.
+
+- **Pipelines must be local.** `pipeline` is an absolute path to `main.nf` (or the directory that contains it), a
+  Snakefile (or its project directory with `Snakefile` / `workflow/Snakefile`), or a `.wdl` file. Names like
+  `owner/repo`, which Nextflow would download from a git hosting service, and URLs are not accepted. Clone the pipeline
+  first and point to the local copy.
+- **Nextflow** downloads plugins and, on the very first start of its launcher, its own runtime into `~/.nextflow`. With
+  `offline: true` the server sets `NXF_OFFLINE=true`: Nextflow downloads no pipelines and no plugins (since 24.04), so the
+  plugins must already be installed. Tasks run with the executor configured in `nextflow.config`.
+- **Container images and Conda environments** used by the processes, rules or tasks are pulled or created by Nextflow,
+  Snakemake (only with `softwareDeployment`) and the container runtime of miniwdl when the run starts. miniwdl also
+  downloads input files given as URIs. The plan says so in its answer.
+- Snakemake software deployment (`--software-deployment-method conda|apptainer|env-modules`) is off unless requested.
+
+## Environment
+
+| Variable | Meaning |
+|---|---|
+| `NB_BIO_NEXTFLOW`, `NB_BIO_MINIWDL`, `NB_BIO_SNAKEMAKE` | Path of the program; default — the name on `PATH`. Each program is optional |
+| `PLUGIN_DATA` | Data folder for plans and runs; default — `nb-bio-pipelines` in the system temp folder. Mode 0700, files 0600 |
+
+Programs run without a shell, with closed stdin, `NO_COLOR=1` and a time limit (lint 5 minutes, plan 30 minutes, the
+run itself has none). Nextflow also gets `NXF_ANSI_LOG=false`, `NXF_DISABLE_CHECK_LATEST=true` (no check for a newer
+version) and `NXF_AGENT_MODE=false` (keeps the normal log format the progress parser reads). Credentials stay where the
+tools read them (their config files and the environment of the server). Answers mask passwords in URLs (`user:***@`),
+`password=` / `token:` pairs and bearer tokens; params files are shown by key names only. Logs of the server go to
+stderr.
+
+## Versions
+
+- `nextflow lint` needs Nextflow 25.04 or newer; with older versions `bio_lint` skips Nextflow files with a note.
+  `-preview` needs Nextflow 22.10 or newer.
+- `softwareDeployment` needs Snakemake 8 or newer. Dry-run job statistics are read from the `Job stats:` table.
+- miniwdl: `check`, `input-template` and `run --json` of current releases (1.x).
+
+## Run
+
+```bash
+npx -y @neuralbridge/bio-pipelines-mcp@1.0.0
+```
+
+Requires Node.js 20+.
+
+## Develop
+
+```bash
+npm install
+npm test   # build + unit and end-to-end tests with fake nextflow, miniwdl and snakemake programs
+```
+
+## License
+
+Apache-2.0. See `LICENSE` and `NOTICE`.

package/dist/src/context.js

@@ -0,0 +1,23 @@
+// Copyright (c) NeuralBridge. Licensed under the Apache License, Version 2.0. See LICENSE.
+// Состояние сервера на время его жизни: окружение, кэш найденных программ и исход прогонов, запущенных этим
+// процессом сервера (код выхода известен сразу, до записи на диск). Используют все обработчики.
+import { PROGRAMS, resolveProgram } from './runner.js';
+export function createContext(env) {
+    return { env, programs: {}, exits: new Map(), children: new Map() };
+}
+/** Программа или `undefined`; неудачный поиск не кэшируется — пользователь может поставить программу без перезапуска. */
+export async function findProgram(ctx, kind) {
+    ctx.programs[kind] ??= resolveProgram(kind, ctx.env);
+    const program = await ctx.programs[kind];
+    if (!program) {
+        delete ctx.programs[kind];
+    }
+    return program;
+}
+export async function programOf(ctx, kind) {
+    const program = await findProgram(ctx, kind);
+    if (!program) {
+        throw new Error(PROGRAMS[kind].notFound);
+    }
+    return program;
+}

package/dist/src/index.js

@@ -0,0 +1,9 @@
+#!/usr/bin/env node
+// Copyright (c) NeuralBridge. Licensed under the Apache License, Version 2.0. See LICENSE.
+// Точка входа пакета `@neuralbridge/bio-pipelines-mcp`: сервер `server.ts` на транспорте stdio. Логи — только в
+// stderr: stdout занят протоколом.
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { createServer } from './server.js';
+const server = createServer();
+await server.connect(new StdioServerTransport());
+process.stderr.write('nb-bio-pipelines MCP server ready\n');

package/dist/src/inspect.js

@@ -0,0 +1,100 @@
+// Copyright (c) NeuralBridge. Licensed under the Apache License, Version 2.0. See LICENSE.
+// Обработчики `bio_detect` и `bio_lint`: какие программы установлены, какие пайплайны лежат в каталоге, и статическая
+// проверка `nextflow lint`, `miniwdl check`, `snakemake --lint`. Регистрация в MCP — `server.ts`.
+import { promises as fs } from 'node:fs';
+import { basename, dirname, join } from 'node:path';
+import { findProgram } from './context.js';
+import { parseMiniwdlCheck, parseNextflowLint, parseSnakemakeLint } from './parse.js';
+import { existingPath, findPipelineFiles, pipelineOf } from './paths.js';
+import { compareVersions, failure, MINUTE, PROGRAM_KINDS, PROGRAMS, programEnv, run } from './runner.js';
+/** `nextflow lint` появился в Nextflow 25.04. */
+export const NEXTFLOW_LINT_SINCE = '25.04.0';
+const LINT_TIMEOUT = 5 * MINUTE;
+const MAX_WDL = 20;
+const MAX_SNAKEFILES = 5;
+export async function detect(ctx, args) {
+    const lines = [];
+    for (const kind of PROGRAM_KINDS) {
+        const program = await findProgram(ctx, kind);
+        lines.push(program ? `${kind} ${program.version} (${program.path})` : `${kind}: not found. ${PROGRAMS[kind].notFound}`);
+    }
+    if (args.dir) {
+        const root = await existingPath(args.dir, '"dir"', 'dir');
+        const found = await findPipelineFiles(root);
+        const list = (title, files) => files.length ? [`${title}:`, ...files.map(f => `  ${f}`)] : [];
+        const files = [...list('Nextflow (main.nf, nextflow.config)', found.nextflow), ...list('WDL', found.wdl), ...list('Snakemake', found.snakemake)];
+        lines.push('', files.length ? `Pipelines under ${root}:\n${files.join('\n')}` : `No main.nf, nextflow.config, .wdl or Snakefile under ${root}.`);
+    }
+    return lines.join('\n');
+}
+/** Что проверять: файл — по имени; папка — все найденные пайплайны (Nextflow — папкой целиком). */
+async function lintTargets(path, only) {
+    const stat = await fs.stat(path);
+    const targets = [];
+    if (stat.isFile()) {
+        const name = basename(path);
+        const kind = /\.(nf|config)$/.test(name) ? 'nextflow' : name.endsWith('.wdl') ? 'miniwdl' : /^[Ss]nakefile$|\.smk$/.test(name) ? 'snakemake' : undefined;
+        if (!kind) {
+            throw new Error(`Cannot tell the pipeline language of ${path}: expected .nf, .config, .wdl, Snakefile or .smk.`);
+        }
+        targets.push({ kind, path, cwd: dirname(path) });
+    }
+    else {
+        const found = await findPipelineFiles(path);
+        if (found.nextflow.length) {
+            targets.push({ kind: 'nextflow', path, cwd: path });
+        }
+        for (const file of found.wdl.slice(0, MAX_WDL)) {
+            targets.push({ kind: 'miniwdl', path: join(path, file), cwd: dirname(join(path, file)) });
+        }
+        for (const file of found.snakemake.filter(f => !/(^|[\\/])rules[\\/]/.test(f)).slice(0, MAX_SNAKEFILES)) {
+            const pipeline = await pipelineOf('snakemake', join(path, file));
+            targets.push({ kind: 'snakemake', path: pipeline.file, cwd: pipeline.root });
+        }
+    }
+    return only ? targets.filter(t => t.kind === only) : targets;
+}
+async function lintOne(program, target, env) {
+    const options = { cwd: target.cwd, timeoutMs: LINT_TIMEOUT, env: programEnv(program.kind, env, { offline: true }) };
+    if (program.kind === 'nextflow') {
+        if (compareVersions(program.version, NEXTFLOW_LINT_SINCE) < 0) {
+            return `nextflow lint ${target.path}: skipped — "nextflow lint" needs Nextflow 25.04 or newer, found ${program.version}. Use bio_plan (nextflow -preview) to check that the script compiles.`;
+        }
+        const result = await run(program.path, ['lint', '-o', 'json', target.path], options);
+        const findings = parseNextflowLint(result.stdout);
+        if (!findings) {
+            throw failure('nextflow lint', result);
+        }
+        return `nextflow lint ${target.path}: ${findings.length ? `${findings.length} finding(s)\n${findings.join('\n')}` : 'no errors or warnings.'}`;
+    }
+    if (program.kind === 'miniwdl') {
+        const result = await run(program.path, ['check', target.path], options);
+        const { findings } = parseMiniwdlCheck(target.path, result.stdout, result.stderr);
+        const head = result.code === 0 ? 'parsed and type-checked' : 'FAILED to parse or type-check';
+        const extra = result.code !== 0 && !findings.some(f => f.startsWith('error:')) ? `\n${(result.stderr || result.stdout).trim()}` : '';
+        return `miniwdl check ${target.path}: ${head}${findings.length ? `, ${findings.length} finding(s)\n${findings.join('\n')}` : '.'}${extra}`;
+    }
+    const result = await run(program.path, ['--lint', 'json', '--snakefile', target.path, '--directory', target.cwd, '--nocolor'], options);
+    const findings = parseSnakemakeLint(result.stdout);
+    if (!findings) {
+        throw failure('snakemake --lint', result);
+    }
+    return `snakemake --lint ${target.path}: ${findings.length ? `${findings.length} finding(s)\n${findings.join('\n')}` : 'no lints.'}`;
+}
+export async function lint(ctx, args) {
+    const path = await existingPath(args.path, '"path"');
+    const targets = await lintTargets(path, args.program);
+    if (!targets.length) {
+        return `Nothing to lint under ${path}${args.program ? ` for ${args.program}` : ''}.`;
+    }
+    const sections = [];
+    for (const target of targets) {
+        const program = await findProgram(ctx, target.kind);
+        if (!program) {
+            sections.push(`${target.path}: skipped — ${PROGRAMS[target.kind].notFound}`);
+            continue;
+        }
+        sections.push(await lintOne(program, target, ctx.env).catch((error) => `${target.path}: ${error.message}`));
+    }
+    return sections.join('\n\n');
+}

package/dist/src/parse.js

@@ -0,0 +1,144 @@
+/** JSON из вывода, перед которым программа могла напечатать что-то ещё. */
+function jsonOf(text) {
+    const start = text.indexOf('{');
+    if (start < 0) {
+        return undefined;
+    }
+    try {
+        return JSON.parse(text.slice(start));
+    }
+    catch {
+        return undefined;
+    }
+}
+/** `nextflow lint -o json`: `{ errors: [...], warnings: [...] }` с полями filename, startLine, startColumn, message. */
+export function parseNextflowLint(stdout) {
+    const parsed = jsonOf(stdout);
+    if (!parsed || typeof parsed !== 'object') {
+        return undefined;
+    }
+    const line = (severity, item) => `${severity}: ${String(item.filename ?? '?')}:${Number(item.startLine ?? 0)}:${Number(item.startColumn ?? 0)}: ${String(item.message ?? '').replace(/\s+/g, ' ').trim()}`;
+    const list = (value) => Array.isArray(value) ? value : [];
+    return [...list(parsed.errors).map(e => line('error', e)), ...list(parsed.warnings).map(w => line('warning', w))];
+}
+/**
+ * `miniwdl check`: в stdout — схема документа с замечаниями «(Ln 2, Col 7) UnusedDeclaration, …» и строками `call`;
+ * ошибки разбора и типов — в stderr «(file.wdl Ln 3 Col 5) …».
+ */
+export function parseMiniwdlCheck(file, stdout, stderr) {
+    const findings = [];
+    let calls = 0;
+    for (const line of stdout.split('\n')) {
+        const warning = /^\s*\(Ln (\d+), Col (\d+)\)\s*(.*)$/.exec(line);
+        if (warning) {
+            findings.push(`warning: ${file}:${warning[1]}:${warning[2]}: ${warning[3].trim()}`);
+        }
+        else if (/^\s+call\s+\S/.test(line)) {
+            calls++;
+        }
+    }
+    for (const line of stderr.split('\n')) {
+        const error = /^\((.+?) Ln (\d+) Col (\d+)\)\s*(.*)$/.exec(line.trim());
+        if (error) {
+            findings.push(`error: ${error[1]}:${error[2]}:${error[3]}: ${error[4].trim()}`);
+        }
+    }
+    return { calls, findings };
+}
+/** `snakemake --lint json`: `{ snakefiles: [{ for: { snakefile }, lints }], rules: [{ for: { rule, line, snakefile }, lints }] }`. */
+export function parseSnakemakeLint(stdout) {
+    const parsed = jsonOf(stdout);
+    if (!parsed || typeof parsed !== 'object' || (!('snakefiles' in parsed) && !('rules' in parsed))) {
+        return undefined;
+    }
+    const out = [];
+    const groups = (value) => Array.isArray(value) ? value : [];
+    for (const group of [...groups(parsed.snakefiles), ...groups(parsed.rules)]) {
+        const where = `${String(group.for?.snakefile ?? '?')}${group.for?.line !== undefined && group.for.line !== null ? `:${Number(group.for.line)}` : ''}`;
+        const rule = group.for?.rule ? ` rule ${String(group.for.rule)}:` : '';
+        for (const lint of Array.isArray(group.lints) ? group.lints : []) {
+            out.push(`lint: ${where}:${rule} ${String(lint.title ?? '')} — ${String(lint.body ?? '').replace(/\s+/g, ' ').trim()}`);
+        }
+    }
+    return out;
+}
+/** Таблица «Job stats» сухого прогона Snakemake: число заданий по правилам и итог. */
+export function parseSnakemakeJobStats(text) {
+    const lines = text.split('\n');
+    const start = lines.findIndex(line => line.trim() === 'Job stats:');
+    if (start < 0) {
+        return undefined;
+    }
+    const rules = [];
+    for (const line of lines.slice(start + 1)) {
+        const row = /^\s*(\S+)\s+(\d+)\s*$/.exec(line);
+        if (row) {
+            if (row[1] === 'total') {
+                return { total: Number(row[2]), rules };
+            }
+            rules.push({ name: row[1], count: Number(row[2]) });
+        }
+        else if (line.trim() && !/^[-\s]+$/.test(line) && !/^\s*job\s+count\s*$/.test(line)) {
+            break;
+        }
+    }
+    return rules.length ? { total: rules.reduce((sum, r) => sum + r.count, 0), rules } : undefined;
+}
+/** Процессы в DAG Nextflow в формате Mermaid: узлы процессов — `v3(["NAME"])`; операторы без `-verbose` — `(( ))`. */
+export function parseNextflowDag(mermaid) {
+    const names = new Set();
+    for (const match of mermaid.matchAll(/\b[a-z]?\d+\(\["?([^"\]]+)"?\]\)/g)) {
+        names.add(match[1].trim());
+    }
+    return [...names];
+}
+/**
+ * Прогресс Nextflow по логу без ANSI: строки «[ab/123456] Submitted process > NAME (1)», «Cached process >», а в
+ * ANSI-сводке «[ab/123456] process > NAME (3) [100%] 3 of 3 ✔» — берётся последняя строка каждого процесса.
+ */
+export function nextflowProgress(log) {
+    const ansi = new Map();
+    const counts = new Map();
+    let executor = '';
+    for (const line of log.split('\n')) {
+        const exec = /^executor\s*>\s*(.+)$/.exec(line.trim());
+        if (exec) {
+            executor = `executor > ${exec[1].trim()}`;
+        }
+        const bar = /\[[0-9a-f-]{2}\/[0-9a-f-]{6}\]\s+process\s*>\s*(\S+)(.*\[\s*\d+%\].*)$/.exec(line);
+        if (bar) {
+            ansi.set(bar[1], `${bar[1]}${bar[2]}`.replace(/\s+/g, ' ').trim());
+            continue;
+        }
+        const plain = /\[[0-9a-f]{2}\/[0-9a-f]{6}\]\s+(Submitted|Re-submitted|Cached) process\s*>\s*(\S+)/.exec(line);
+        if (plain) {
+            const entry = counts.get(plain[2]) ?? { submitted: 0, cached: 0 };
+            if (plain[1] === 'Cached') {
+                entry.cached++;
+            }
+            else {
+                entry.submitted++;
+            }
+            counts.set(plain[2], entry);
+        }
+    }
+    const rows = ansi.size
+        ? [...ansi.values()]
+        : [...counts.entries()].map(([name, c]) => `${name}: ${c.submitted} submitted${c.cached ? `, ${c.cached} cached` : ''}`);
+    return executor && rows.length ? [executor, ...rows] : rows;
+}
+/** Прогресс Snakemake: последняя строка «3 of 5 steps (60%) done». */
+export function snakemakeProgress(log) {
+    const matches = [...log.matchAll(/^\s*(\d+ of \d+ steps \(\d+%\) done)/gm)];
+    return matches.length ? [matches[matches.length - 1][1]] : [];
+}
+/** Исход по хвосту лога, когда код выхода неизвестен (сервер перезапускался во время прогона). */
+export function inferOutcome(program, log) {
+    const patterns = {
+        nextflow: { ok: /^Succeeded\s*:|Workflow completed successfully|^Completed at:/m, fail: /^ERROR ~|Execution aborted|Workflow failed/m },
+        snakemake: { ok: /\(100%\) done|Nothing to be done/, fail: /Exiting because a job execution failed|^Error in rule|WorkflowError/m },
+        miniwdl: { ok: /"outputs"\s*:/, fail: /\bfailed\b.*\btask\b|"error"\s*:|Traceback/i },
+    };
+    const { ok, fail } = patterns[program];
+    return fail.test(log) ? 'failed' : ok.test(log) ? 'succeeded' : undefined;
+}