const area = document.getElementById('upload-area');
const inputFolder = document.getElementById('file-input');
const inputFiles = document.getElementById('file-input-files');
const overlay = document.getElementById('progress-overlay');
const uploadBar = document.getElementById('upload-bar');
const uploadText = document.getElementById('upload-text');
const uploadDetail = document.getElementById('upload-detail');
const processText = document.getElementById('process-text');
const processDetail = document.getElementById('process-detail');
const processLabel = document.getElementById('process-label');
const processBar = document.getElementById('process-bar');
const processTrack = document.getElementById('process-track');
const T = JSON.parse(document.getElementById('upload-i18n').textContent);
const dossierGUID = T.dossier;
let totalFileCount = 0;

area.onclick = e => {
  if (e.shiftKey) { inputFolder.click(); } else { inputFiles.click(); }
};
area.ondragover = e => { e.preventDefault(); area.classList.add('dragover'); };
area.ondragleave = () => area.classList.remove('dragover');
area.ondrop = async e => {
  e.preventDefault();
  area.classList.remove('dragover');
  const items = e.dataTransfer.items;
  if (items && items.length > 0) {
    overlay.style.display = 'flex';
    uploadBar.style.width = '0%';
    uploadText.textContent = T.reading_files;
    uploadDetail.textContent = '';
    processText.textContent = '';
    processDetail.textContent = '';
    processLabel.style.display = 'none';
    const files = await getAllFiles(items);
    if (files.length > 0) handleFiles(files);
    else overlay.style.display = 'none';
  }
};
inputFolder.onchange = e => handleFiles(Array.from(e.target.files));
inputFiles.onchange = e => handleFiles(Array.from(e.target.files));

async function getAllFiles(items) {
  const files = [];
  const entries = [];
  for (let i = 0; i < items.length; i++) {
    const entry = items[i].webkitGetAsEntry ? items[i].webkitGetAsEntry() : null;
    if (entry) entries.push(entry);
  }
  async function readEntry(entry, path) {
    if (entry.isFile) {
      return new Promise(resolve => {
        entry.file(f => {
          Object.defineProperty(f, 'relativePath', { value: path + f.name });
          files.push(f);
          resolve();
        });
      });
    } else if (entry.isDirectory) {
      const reader = entry.createReader();
      const readAll = () => new Promise(resolve => {
        reader.readEntries(async entries => {
          if (entries.length === 0) { resolve(); return; }
          for (const e of entries) await readEntry(e, path + entry.name + '/');
          await readAll();
          resolve();
        });
      });
      await readAll();
    }
  }
  for (const entry of entries) await readEntry(entry, '');
  return files;
}

function submitPaste() {
  const text = document.getElementById('paste-input').value.trim();
  if (!text) return;
  const blob = new Blob([text], { type: 'text/plain' });
  const ts = new Date().toISOString().replace(/[:.]/g, '-').slice(0, 19);
  const file = new File([blob], 'paste-' + ts + '.txt', { type: 'text/plain' });
  handleFiles([file]);
}

async function handleFiles(files) {
  if (!files.length) return;
  const category = '';
  overlay.style.display = 'flex';
  uploadBar.style.width = '0%';
  uploadText.textContent = '';
  processText.textContent = '';
  processDetail.textContent = '';
  processLabel.style.display = 'none';

  let geneticsFileId = null;
  let pdfFileIds = [];
  totalFileCount = files.length;
  let completed = 0;
  const concurrency = 10;

  async function uploadOne(file) {
    const name = file.relativePath || file.webkitRelativePath || file.name;
    const form = new FormData();
    form.append('file', file);
    form.append('path', name);
    form.append('category', category);
    try {
      const resp = await fetch('/dossier/' + dossierGUID + '/upload', { method: 'POST', body: form });
      const data = await resp.json();
      if (category === 'genetics' && data.id) geneticsFileId = data.id;
      if (category === 'pdf' && data.id) pdfFileIds.push(data.id);
    } catch (e) { console.error('Upload failed:', e); }
    completed++;
    uploadText.textContent = completed + ' / ' + files.length;
    uploadBar.style.width = (completed / files.length * 100) + '%';
  }

  const queue = [...files];
  const workers = [];
  for (let w = 0; w < Math.min(concurrency, queue.length); w++) {
    workers.push((async () => {
      while (queue.length > 0) {
        await uploadOne(queue.shift());
      }
    })());
  }
  await Promise.all(workers);

  if (geneticsFileId) {
    processText.textContent = T.processing_genetics;
    processDetail.textContent = T.analyzing_variants;
    await pollStatus(geneticsFileId);
    overlay.style.display = 'none';
    location.reload();
    return;
  }

  if (pdfFileIds.length > 0) {
    processText.textContent = T.processing_documents;
    processDetail.textContent = T.extracting_data;
    processLabel.style.display = '';
    await Promise.all(pdfFileIds.map(id => pollStatus(id)));
    overlay.style.display = 'none';
    location.reload();
    return;
  }

  if (category !== 'genetics') {
    fetch('/dossier/' + dossierGUID + '/process-imaging', { method: 'POST' });
    await pollProcessing();
  }
  overlay.style.display = 'none';
  location.reload();
}

async function pollStatus(fileId) {
  const maxAttempts = 60;
  for (let i = 0; i < maxAttempts; i++) {
    try {
      const resp = await fetch('/dossier/' + dossierGUID + '/files/' + fileId + '/status');
      const data = await resp.json();
      if (data.status === 'completed' || data.status === 'processed') { showToast(T.processing_complete, 'success'); return; }
      else if (data.status === 'failed') { showToast(T.processing_failed + ' ' + data.details, 'error'); return; }
    } catch (e) { console.error('Status check failed:', e); }
    await new Promise(r => setTimeout(r, 1000));
  }
  showToast(T.processing_timeout, 'error');
}

function showToast(message, type) {
  const toast = document.createElement('div');
  toast.textContent = message;
  toast.style.cssText = 'position:fixed;bottom:20px;right:20px;padding:16px 24px;border-radius:8px;color:white;font-weight:500;z-index:9999';
  toast.style.background = type === 'success' ? '#10b981' : '#ef4444';
  document.body.appendChild(toast);
  setTimeout(() => toast.remove(), 5000);
}

function deleteFile(fileId) {
  if (!confirm(T.confirm_delete)) return;
  fetch('/dossier/' + dossierGUID + '/files/' + fileId + '/delete', { method: 'POST' }).then(() => location.reload());
}

function undoImport(fileId) {
  if (!confirm(T.confirm_undo)) return;
  fetch('/dossier/' + dossierGUID + '/files/' + fileId + '/undo', { method: 'POST' })
    .then(resp => resp.json())
    .then(data => { showToast(data.status === 'ok' ? T.import_undone : T.undo_failed, data.status === 'ok' ? 'success' : 'error'); location.reload(); })
    .catch(() => { showToast(T.undo_failed, 'error'); });
}

function reprocessFile(fileId) {
  fetch('/dossier/' + dossierGUID + '/files/' + fileId + '/reprocess', { method: 'POST' })
    .then(resp => resp.json())
    .then(data => { if (data.status === 'ok') location.reload(); })
    .catch(() => { showToast(T.undo_failed, 'error'); });
}

async function pollProcessing() {
  while (true) {
    await new Promise(r => setTimeout(r, 300));
    let s;
    try { const resp = await fetch('/dossier/' + dossierGUID + '/process-status'); s = await resp.json(); } catch (e) { continue; }
    if (s.stage === 'idle' || s.stage === 'starting') continue;
    processLabel.style.display = '';
    processTrack.style.display = '';
    const total = totalFileCount || s.total || 1;
    if (s.stage === 'decrypting') {
      processText.textContent = T.preparing + ' ' + (s.processed || 0) + ' / ' + total;
      processDetail.textContent = '';
      processBar.style.width = ((s.processed || 0) / total * 100) + '%';
    } else if (s.stage === 'importing') {
      processText.textContent = T.importing + ' ' + (s.processed || 0) + ' / ' + total;
      const study = (s.study || '').replace(/&amp;/g, '&').replace(/&quot;/g, '"').trim();
      const series = (s.series || '').replace(/&amp;/g, '&').replace(/&quot;/g, '"').trim();
      processDetail.textContent = study + ' \u2014 ' + series;
      processBar.style.width = ((s.processed || 0) / total * 100) + '%';
    } else if (s.stage === 'importing_json') {
      processText.textContent = T.analyzing + ' ' + (s.processed || 0) + ' / ' + (s.total || total);
      processDetail.textContent = T.extracting_labs;
      processBar.style.width = ((s.processed || 0) / (s.total || total) * 100) + '%';
    } else if (s.stage === 'normalizing') {
      const nt = s.total || 1;
      processText.textContent = T.normalizing + ' ' + (s.processed || 0) + ' / ' + nt;
      processDetail.textContent = T.mapping_loinc;
      processBar.style.width = ((s.processed || 0) / nt * 100) + '%';
    } else if (s.stage === 'done') {
      if (s.error) showToast(T.import_error + ' ' + s.error, 'error');
      else if (s.slices > 0) showToast(T.imported + ' ' + s.studies + ' studies, ' + s.series_count + ' series, ' + s.slices + ' slices', 'success');
      else if (s.json_imported > 0) showToast(T.imported + ' ' + s.json_imported + ' files', 'success');
      return;
    }
  }
}