backend/server.js

const express = require('express');
const multer  = require('multer');
const { spawn } = require('child_process');
const path    = require('path');
const fs      = require('fs');
const cors    = require('cors');
const archiver = require('archiver');
const https   = require('https');
const http    = require('http');

const app  = express();
const PORT = process.env.PORT || 3001;

// Store job metadata for downloading later
const jobStore = {};

// Google Drive API key — set as a Secret in HF Spaces Settings
// (Settings → Variables and Secrets → New Secret: GOOGLE_DRIVE_API_KEY)
const GDRIVE_API_KEY = process.env.GOOGLE_DRIVE_API_KEY || '';

app.use(cors());
app.use(express.json());
app.use(express.static(path.join(__dirname, '../frontend/dist')));

// ── Upload dir ────────────────────────────────────────────────────────────
const uploadDir = path.join(__dirname, 'uploads');
if (!fs.existsSync(uploadDir)) fs.mkdirSync(uploadDir, { recursive: true });

const storage = multer.diskStorage({
  destination: (req, file, cb) => cb(null, uploadDir),
  filename:    (req, file, cb) => {
    const u = Date.now() + '-' + Math.round(Math.random() * 1e9);
    cb(null, u + '-' + file.originalname);
  },
});
const upload = multer({ storage, limits: { fileSize: 500 * 1024 * 1024 } });

const R_SCRIPT_PATH = path.join(__dirname, '..', 'lc_ms_peak_picker.R');

// ── Helper: run R on one file ─────────────────────────────────────────────
function runRScript(inputFile, outputFile, params) {
  return new Promise((resolve, reject) => {
    const { ppm, sn, min_pw, max_pw, pref_k, pref_i, sample_name } = params;
    const args = [
      R_SCRIPT_PATH,
      '--input', inputFile, '--output', outputFile,
      '--ppm', ppm, '--sn', sn,
      '--min_pw', min_pw, '--max_pw', max_pw,
      '--pref_k', pref_k, '--pref_i', pref_i,
      '--sample_name', sample_name,
    ];
    const proc = spawn('Rscript', args);
    let errLog = '';
    proc.stdout.on('data', d => console.log(d.toString()));
    proc.stderr.on('data', d => { errLog += d; console.error(d.toString()); });
    proc.on('close', code => {
      if (code !== 0) return reject(new Error(`R failed for ${sample_name}: ${errLog}`));
      if (!fs.existsSync(outputFile)) return reject(new Error(`No output for ${sample_name}`));
      resolve(outputFile);
    });
  });
}

// ── Helper: process a list of jobs → { successOutputs, errors } ───────────
async function processJobs(jobs, params) {
  const results = await Promise.allSettled(
    jobs.map(j => runRScript(j.inputFile, j.outputFile, { ...params, sample_name: j.sample_name }))
  );
  const successOutputs = [], errors = [];
  jobs.forEach((j, i) => {
    if (results[i].status === 'fulfilled') {
      successOutputs.push({ path: j.outputFile, name: `${j.sample_name}.peaks` });
    } else {
      errors.push({ file: j.sample_name, reason: results[i].reason?.message });
    }
    if (fs.existsSync(j.inputFile)) fs.unlinkSync(j.inputFile);
  });
  return { successOutputs, errors };
}

// ── Helper: create ZIP on disk ──────────────────────────────────────────────
function createZipOnDisk(destPath, successOutputs, errors) {
  return new Promise((resolve, reject) => {
    const output = fs.createWriteStream(destPath);
    const archive = archiver('zip', { zlib: { level: 6 } });
    
    output.on('close', resolve);
    archive.on('error', reject);
    
    archive.pipe(output);
    successOutputs.forEach(({ path: p, name }) => archive.file(p, { name }));
    if (errors.length > 0) {
      archive.append(errors.map(e => `${e.file}: ${e.reason}`).join('\n'), { name: 'errors.txt' });
    }
    archive.finalize();
  }).then(() => {
    // Delete individual output files after zipping
    successOutputs.forEach(({ path: p }) => { if (fs.existsSync(p)) fs.unlinkSync(p); });
  });
}

// ── Helper: follow redirects and download a URL to disk ──────────────────
function downloadFile(url, destPath, redirectCount = 0) {
  return new Promise((resolve, reject) => {
    if (redirectCount > 10) return reject(new Error('Too many redirects'));
    const proto = url.startsWith('https') ? https : http;
    const req = proto.get(url, { headers: { 'User-Agent': 'Mozilla/5.0' } }, res => {
      if (res.statusCode === 301 || res.statusCode === 302 || res.statusCode === 307) {
        return downloadFile(res.headers.location, destPath, redirectCount + 1).then(resolve).catch(reject);
      }
      if (res.statusCode !== 200) {
        return reject(new Error(`HTTP ${res.statusCode} downloading file`));
      }
      const out = fs.createWriteStream(destPath);
      res.pipe(out);
      out.on('finish', () => out.close(resolve));
      out.on('error', reject);
    });
    req.on('error', reject);
  });
}

// ── Helper: fetch JSON from HTTPS ─────────────────────────────────────────
function fetchJSON(url) {
  return new Promise((resolve, reject) => {
    https.get(url, { headers: { 'User-Agent': 'Mozilla/5.0' } }, res => {
      let data = '';
      res.on('data', c => data += c);
      res.on('end', () => {
        try { resolve(JSON.parse(data)); }
        catch (e) { reject(new Error('Invalid JSON from Drive API: ' + data.slice(0, 200))); }
      });
    }).on('error', reject);
  });
}

// ── Helper: extract Drive folder ID from URL ──────────────────────────────
function extractFolderId(url) {
  const patterns = [/\/folders\/([a-zA-Z0-9_-]{10,})/, /[?&]id=([a-zA-Z0-9_-]{10,})/];
  for (const p of patterns) { const m = url.match(p); if (m) return m[1]; }
  return null;
}

// ── Helper: list mzML/mzXML files in a public Drive folder via API ────────
async function listDriveFiles(folderId, pageToken = '', allFiles = []) {
  const q = encodeURIComponent(`'${folderId}' in parents and trashed = false`);
  const fields = encodeURIComponent('nextPageToken,files(id,name,mimeType,size)');
  let url = `https://www.googleapis.com/drive/v3/files?q=${q}&fields=${fields}&pageSize=100&key=${GDRIVE_API_KEY}`;
  if (pageToken) url += `&pageToken=${encodeURIComponent(pageToken)}`;

  const data = await fetchJSON(url);

  if (data.error) {
    const msg = data.error.message || JSON.stringify(data.error);
    throw new Error(`Drive API error: ${msg}`);
  }

  const supported = (data.files || []).filter(f => {
    const n = f.name.toLowerCase();
    return n.endsWith('.mzml') || n.endsWith('.mzxml');
  });
  allFiles.push(...supported);

  if (data.nextPageToken) {
    return listDriveFiles(folderId, data.nextPageToken, allFiles);
  }
  return allFiles;
}

// ── Helper: download a file from Drive API (handles large file confirmations)
async function downloadDriveFile(fileId, destPath) {
  // Using Drive API v3 alt=media — works for public files with API key
  const url = `https://www.googleapis.com/drive/v3/files/${fileId}?alt=media&key=${GDRIVE_API_KEY}`;
  await downloadFile(url, destPath);
}

// ═══════════════════════════════════════════════════════════════════════════
// ROUTES
// ═══════════════════════════════════════════════════════════════════════════

// ── Batch upload endpoint ─────────────────────────────────────────────────
app.post('/api/peak-picker/batch', upload.array('files', 100), async (req, res) => {
  if (!req.files?.length) return res.status(400).json({ error: 'No files uploaded.' });

  const params = {
    ppm: req.body.ppm || '15', sn: req.body.sn || '1.5',
    min_pw: req.body.min_pw || '5', max_pw: req.body.max_pw || '20',
    pref_k: req.body.pref_k || '0', pref_i: req.body.pref_i || '0',
  };
  const jobs = req.files.map(f => ({
    inputFile:  f.path,
    outputFile: path.join(uploadDir, `${f.filename}.peaks`),
    sample_name: path.parse(f.originalname).name,
  }));

  const { successOutputs, errors } = await processJobs(jobs, params);
  if (!successOutputs.length) return res.status(500).json({ error: 'All files failed.', details: errors });

  const jobId = Date.now().toString(36) + '-' + Math.random().toString(36).substr(2, 5);
  let finalPath = '';
  let finalName = '';

  if (successOutputs.length === 1 && !errors.length) {
    finalPath = successOutputs[0].path;
    finalName = successOutputs[0].name;
  } else {
    finalPath = path.join(uploadDir, `${jobId}.zip`);
    finalName = 'peak_picker_results.zip';
    await createZipOnDisk(finalPath, successOutputs, errors);
  }

  jobStore[jobId] = { path: finalPath, name: finalName, count: successOutputs.length, timestamp: Date.now() };
  
  // Cleanup old jobs (older than 2 hours) to prevent disk filling up
  if (Math.random() < 0.1) {
    const TWO_HOURS = 2 * 60 * 60 * 1000;
    const now = Date.now();
    Object.keys(jobStore).forEach(k => {
      const job = jobStore[k];
      if (job.timestamp && (now - job.timestamp > TWO_HOURS)) {
        try {
          if (fs.existsSync(job.path)) {
            fs.unlinkSync(job.path);
          }
          delete jobStore[k];
          console.log(`Cleaned up expired job: ${k}`);
        } catch (e) {
          console.error(`Failed to clean up job ${k}:`, e.message);
        }
      }
    });
  }

  res.json({ success: true, jobId, count: successOutputs.length, total: jobs.length, errors });
});

// ── Google Drive endpoint ─────────────────────────────────────────────────
app.post('/api/peak-picker/gdrive', async (req, res) => {
  const { folderUrl, ppm, sn, min_pw, max_pw, pref_k, pref_i } = req.body;

  if (!folderUrl) return res.status(400).json({ error: 'No Google Drive folder URL provided.' });

  // Check API key is configured
  if (!GDRIVE_API_KEY) {
    return res.status(500).json({
      error: 'Google Drive API key is not configured on the server. Please add GOOGLE_DRIVE_API_KEY as a Secret in HF Spaces Settings.',
    });
  }

  const folderId = extractFolderId(folderUrl);
  if (!folderId) return res.status(400).json({ error: 'Could not parse folder ID from URL.' });

  // 1. List files
  let fileList;
  try {
    fileList = await listDriveFiles(folderId);
  } catch (err) {
    return res.status(500).json({ error: `Failed to list Drive folder: ${err.message}` });
  }

  if (!fileList.length) {
    return res.status(404).json({
      error: 'No .mzML or .mzXML files found in this folder. Make sure the folder is shared as "Anyone with the link can view" and contains supported files.',
    });
  }

  // 2. Download all files
  const params = { ppm: ppm||'15', sn: sn||'1.5', min_pw: min_pw||'5', max_pw: max_pw||'20', pref_k: pref_k||'0', pref_i: pref_i||'0' };
  const jobs = [];
  const downloadErrors = [];

  await Promise.allSettled(fileList.map(async ({ id, name }) => {
    const u = Date.now() + '-' + Math.round(Math.random() * 1e9);
    const localPath = path.join(uploadDir, `${u}-${name}`);
    try {
      await downloadDriveFile(id, localPath);
      jobs.push({
        inputFile:  localPath,
        outputFile: path.join(uploadDir, `${u}-${path.parse(name).name}.peaks`),
        sample_name: path.parse(name).name,
      });
    } catch (err) {
      downloadErrors.push({ file: name, reason: err.message });
    }
  }));

  if (!jobs.length) return res.status(500).json({ error: 'Failed to download any files.', details: downloadErrors });

  // 3. Process all
  const { successOutputs, errors } = await processJobs(jobs, params);
  const allErrors = [...downloadErrors, ...errors];

  if (!successOutputs.length) return res.status(500).json({ error: 'All files failed to process.', details: allErrors });

  const jobId = Date.now().toString(36) + '-' + Math.random().toString(36).substr(2, 5);
  let finalPath = '';
  let finalName = '';

  if (successOutputs.length === 1 && !allErrors.length) {
    finalPath = successOutputs[0].path;
    finalName = successOutputs[0].name;
  } else {
    finalPath = path.join(uploadDir, `${jobId}.zip`);
    finalName = 'peak_picker_results.zip';
    await createZipOnDisk(finalPath, successOutputs, allErrors);
  }

  jobStore[jobId] = { path: finalPath, name: finalName, count: successOutputs.length, timestamp: Date.now() };

  res.json({ success: true, jobId, count: successOutputs.length, total: jobs.length, errors: allErrors });
});

// ── Download endpoint ─────────────────────────────────────────────────────
app.get('/api/peak-picker/download/:jobId', (req, res) => {
  const job = jobStore[req.params.jobId];
  if (!job || !fs.existsSync(job.path)) {
    return res.status(404).send('Download link expired or invalid.');
  }
  res.download(job.path, job.name);
});

// ── Check if API key is configured (called by frontend on tab switch) ─────
app.get('/api/gdrive-status', (req, res) => {
  res.json({ configured: Boolean(GDRIVE_API_KEY) });
});

// Error handling middleware (catches Multer and other unhandled errors)
app.use((err, req, res, next) => {
  if (err instanceof multer.MulterError) {
    if (err.code === 'LIMIT_UNEXPECTED_FILE') {
      return res.status(400).json({ error: 'Too many files uploaded. Maximum is 100 files.' });
    }
    return res.status(400).json({ error: `Upload error: ${err.message}` });
  }
  console.error('Unhandled error:', err);
  res.status(500).json({ error: err.message || 'Internal server error.' });
});

// Catch-all → React
app.get('*', (req, res) => {
  res.sendFile(path.join(__dirname, '../frontend/dist/index.html'));
});

app.listen(PORT, () => console.log(`Server running on http://localhost:${PORT}`));