np_app/README.md

NP Replica

This project provides a local Chinese web replica of the core NUPACK analysis/input workflow.

Run

docker compose up --build -d

Open http://127.0.0.1:18765.

Reverse Proxy

The service listens on port 18765. You can later reverse proxy np.lihato.icu to this port from your public server.

Endpoints

• GET /
• GET /health
• GET /api/example
• POST /api/analyze
• POST /api/jobs
• GET /api/jobs/<job_id>

Persistent Shares

Shared result links are stored in Redis when NP_REDIS_URL is enabled. The compose file maps Redis data to ./runtime/redis and enables AOF/RDB persistence, so shares survive container recreation and service restarts. Back up or migrate ./runtime/redis if you move the deployment.

Notes

• tube mode supports strand concentrations and SetSpec(max_size=...).

• complex mode supports explicit complex definitions such as A+B.

• Pair matrices are returned as a preview block to keep responses manageable.

• The Docker image compiles ViennaRNA RNAplot from rna/ViennaRNA-2.7.2.tar.gz and embeds SVG structure plots into MFE results.

• Multistrand MFE plots now use a split-strand layout by default when a structure contains +, with RNAplot retained as the fallback path.

• The web UI now supports Chinese and English switching, browser-side history, result export, and async polling for submitted jobs.

• Docker now starts three services: np-replica, np-worker, and redis.

• Async jobs use Redis-backed storage and queueing when NP_REDIS_URL is configured; otherwise the app falls back to the older in-memory mode.

• The browser-facing API and page behavior stay the same after enabling Redis-backed jobs.

• Worker concurrency is controlled by NP_WORKER_CONCURRENCY and defaults to 2.

• Per-job native thread usage is capped by NP_PER_JOB_THREAD_LIMIT and defaults to 1 to prevent a single analysis from monopolizing the machine.

• NP_STRUCTURE_PLOT_MODE supports auto (default), split, and rnaplot.

• Static pages are served with ETag-based browser caching; JSON API responses remain uncached.

• The force-directed structure viewer lazy-loads D3 only when that view is opened, so the initial page load is not blocked by the external CDN.

• /health uses Redis queue length plus a running-job set instead of scanning every historical job on each poll.

  现在 docker-compose.yml 面向 64 核 / 64G WSL 服务器的并发策略是：

  • 最多同时跑 16 个任务
  • 每个任务最多用 4 个计算线程
  • 后续任务进入队列等待
  • 理论上最多占用约 64 个 native 计算线程，避免 16 × 8 这类过度超卖

  如果后面你发现机器还会被压满，最直接的调法就是在 docker-compose.yml 里继续压：

  • 把 NP_WORKER_CONCURRENCY 改小
  • 或保持并发不变，把 NP_PER_JOB_THREAD_LIMIT 改成 2 或 1