content.js

// content.js - Retraction Checker v2.0 (with citation scanning)

(function () {
  if (window.__retractionCheckerLoaded) return;
  window.__retractionCheckerLoaded = true;

  const CACHE_TTL = 86400000; // 24 hours

  // ─── DOI Utilities ────────────────────────────────────────────────────
  const DOI_PATTERNS = [
    /\b(10\.\d{4,9}\/[^\s"'<>]+)/gi,
    /doi\.org\/(10\.[^\s"'<>]+)/gi,
    /doi:\s*(10\.[^\s"'<>,;]+)/gi,
  ];

  const META_SELECTORS = [
    'meta[name="dc.identifier"]',
    'meta[name="DC.identifier"]',
    'meta[name="citation_doi"]',
    'meta[scheme="doi"]',
  ];

  function cleanDOI(doi) {
    return (doi || '').replace(/[.,;)\]>'"]+$/, '').toLowerCase().trim();
  }

  function extractPrimaryDOI() {
    for (const selector of META_SELECTORS) {
      const el = document.querySelector(selector);
      if (el) {
        const content = el.getAttribute('content') || el.getAttribute('href') || '';
        const match = content.match(/10\.\d{4,9}\/[^\s"'<>]+/);
        if (match) return cleanDOI(match[0]);
      }
    }
    const urlMatch = window.location.href.match(/10\.\d{4,9}\/[^\s"'<>?#&]+/);
    if (urlMatch) return cleanDOI(urlMatch[0]);
    const bodyText = document.body?.innerText?.substring(0, 3000) || '';
    for (const pattern of DOI_PATTERNS) {
      pattern.lastIndex = 0;
      const match = pattern.exec(bodyText);
      if (match) return cleanDOI(match[1] || match[0]);
    }
    return null;
  }

  // ─── CrossRef API ─────────────────────────────────────────────────────
  async function fetchCrossRef(doi) {
    const res = await fetch(
      `https://api.crossref.org/works/${encodeURIComponent(doi)}`,
      { headers: { 'User-Agent': 'RetractionChecker/2.0 (research-integrity-tool)' } }
    );
    if (!res.ok) return null;
    const data = await res.json();
    return data?.message || null;
  }

  function isRetractedWork(work) {
    if (!work) return { retracted: false };
    const type = (work.type || '').toLowerCase();
    const subtype = (work.subtype || '').toLowerCase();
    const title = (work.title?.[0] || '').toLowerCase();
    const updates = work.update || work.relation?.['is-retracted-by'];

    if (type === 'retraction' || subtype === 'retraction') {
      return { retracted: true, reason: 'Retraction notice type detected via CrossRef' };
    }
    if (updates && updates.length > 0) {
      const noticeUrl = updates[0]?.DOI ? `https://doi.org/${updates[0].DOI}` : work.URL;
      return { retracted: true, reason: 'Paper has a retraction update record', noticeUrl };
    }
    if (title.includes('retraction') || title.includes('retracted')) {
      return { retracted: true, reason: 'Title indicates retraction' };
    }
    return { retracted: false };
  }

  function extractPaperInfo(work) {
    if (!work) return null;
    return {
      title: work.title?.[0] || 'Unknown title',
      journal: work['container-title']?.[0] || '',
      year: work.issued?.['date-parts']?.[0]?.[0] || '',
      authors: (work.author || []).slice(0, 3)
        .map(a => `${a.given || ''} ${a.family || ''}`.trim()).join(', '),
    };
  }

  // ─── Retraction Check (single DOI, cached) ────────────────────────────
  async function checkRetraction(doi) {
    const cacheKey = `rc2_${doi}`;
    try {
      const cached = await chrome.storage.local.get(cacheKey);
      if (cached[cacheKey] && Date.now() - cached[cacheKey].timestamp < CACHE_TTL) {
        return cached[cacheKey].result;
      }
    } catch (_) {}

    let result = { retracted: false, doi };
    try {
      const work = await fetchCrossRef(doi);
      if (work) {
        const { retracted, reason, noticeUrl } = isRetractedWork(work);
        const info = extractPaperInfo(work);
        result = {
          retracted,
          doi,
          source: 'CrossRef',
          paperInfo: info,
          details: retracted ? {
            ...info,
            reason,
            notice_url: noticeUrl || work.URL || `https://doi.org/${doi}`,
          } : null,
          _references: (work.reference || [])
            .map(r => r.DOI ? cleanDOI(r.DOI) : null)
            .filter(Boolean),
          _refCount: (work.reference || []).length,
        };
      }
    } catch (e) {
      console.warn('[RetractionChecker] CrossRef error:', e.message);
    }

    try {
      await chrome.storage.local.set({ [cacheKey]: { result, timestamp: Date.now() } });
    } catch (_) {}
    return result;
  }

  // ─── Citation Scan ────────────────────────────────────────────────────
  async function checkCitations(referenceDOIs, onProgress) {
    const results = [];
    const BATCH = 5;
    const DELAY = 300;

    for (let i = 0; i < referenceDOIs.length; i += BATCH) {
      const batch = referenceDOIs.slice(i, i + BATCH);
      const batchResults = await Promise.all(batch.map(doi => checkRetraction(doi)));
      results.push(...batchResults);
      onProgress(Math.min(results.length, referenceDOIs.length), referenceDOIs.length);
      if (i + BATCH < referenceDOIs.length) {
        await new Promise(r => setTimeout(r, DELAY));
      }
    }
    return results;
  }

  // ─── Banner UI ────────────────────────────────────────────────────────
  function injectStyles() {
    if (document.getElementById('rc-styles')) return;
    const style = document.createElement('style');
    style.id = 'rc-styles';
    style.textContent = `
      @keyframes rcSlideIn {
        from { transform:translateY(-100%); opacity:0; }
        to   { transform:translateY(0);     opacity:1; }
      }
      @keyframes rcPulse { 0%,100%{opacity:1} 50%{opacity:0.5} }
      #rc-banner * { box-sizing:border-box; }
      #rc-banner a { color:#fde68a; text-decoration:underline; }
      #rc-banner button:hover { opacity:0.8; }
      .rc-cite-item {
        background:rgba(0,0,0,0.25); border-radius:6px;
        padding:8px 10px; margin-top:6px; font-size:11px; line-height:1.5;
      }
      .rc-progress-bar {
        height:3px; background:rgba(255,255,255,0.15);
        border-radius:2px; margin-top:8px; overflow:hidden;
      }
      .rc-progress-fill {
        height:100%; background:rgba(255,255,255,0.5);
        border-radius:2px; transition:width 0.3s ease;
      }
    `;
    document.head.appendChild(style);
  }

  function removeBanners() {
    document.getElementById('rc-banner')?.remove();
    document.getElementById('rc-loading')?.remove();
  }

  function showLoadingBanner() {
    removeBanners();
    injectStyles();
    const el = document.createElement('div');
    el.id = 'rc-loading';
    el.style.cssText = `
      position:fixed;top:0;left:0;right:0;z-index:2147483647;
      background:#1e3a5f;color:white;
      font-family:-apple-system,BlinkMacSystemFont,'Segoe UI',sans-serif;
      font-size:13px;padding:10px 20px;text-align:center;
      animation:rcPulse 1.5s ease-in-out infinite;
    `;
    el.textContent = '🔍 Checking retraction status…';
    document.body.prepend(el);
  }

  function showMainBanner(result, citationSummary) {
    removeBanners();
    injectStyles();

    const isRetracted = result.retracted;
    const hasBadCitations = citationSummary?.retractedCount > 0;
    const isScanning = citationSummary?.scanning;

    const bg = isRetracted
      ? 'linear-gradient(135deg,#7f1d1d,#991b1b)'
      : hasBadCitations
        ? 'linear-gradient(135deg,#78350f,#92400e)'
        : 'linear-gradient(135deg,#14532d,#166534)';

    const icon = isRetracted ? '⚠️' : hasBadCitations ? '🔶' : '✅';
    const mainTitle = isRetracted
      ? 'RETRACTED PAPER'
      : hasBadCitations
        ? `CITES ${citationSummary.retractedCount} RETRACTED PAPER${citationSummary.retractedCount > 1 ? 'S' : ''}`
        : 'Paper Verified';
    const mainSub = isRetracted
      ? (result.details?.reason || 'This paper has been retracted.')
      : isScanning
        ? `Scanning ${citationSummary.total} citations for retractions…`
        : citationSummary
          ? (hasBadCitations
            ? `Found in ${citationSummary.retractedCount} of ${citationSummary.checked} citations checked.`
            : `No retractions found · ${citationSummary.checked} of ${citationSummary.total} citations checked`)
          : 'No retraction notice found in CrossRef.';

    // Retracted citations expandable list
    let citesHTML = '';
    if (hasBadCitations && citationSummary.retractedItems.length > 0) {
      const items = citationSummary.retractedItems.map(r => `
        <div class="rc-cite-item">
          <strong>${r.paperInfo?.title || r.doi}</strong><br>
          ${r.paperInfo?.journal ? `📰 ${r.paperInfo.journal}` : ''}
          ${r.paperInfo?.year ? ` · ${r.paperInfo.year}` : ''}
          ${r.details?.notice_url
            ? ` · <a href="${r.details.notice_url}" target="_blank">View notice →</a>`
            : ` · <a href="https://doi.org/${r.doi}" target="_blank">doi.org →</a>`}
          <br><span style="opacity:0.6;font-size:10px;">${r.details?.reason || 'Retracted'}</span>
        </div>`).join('');

      citesHTML = `
        <div id="rc-cites-panel" style="display:none;margin-top:8px;max-height:200px;overflow-y:auto;">${items}</div>
        <button id="rc-toggle-btn" onclick="
          var p=document.getElementById('rc-cites-panel');
          var b=document.getElementById('rc-toggle-btn');
          if(p.style.display==='none'){p.style.display='block';b.textContent='▲ Hide retracted citations';}
          else{p.style.display='none';b.textContent='▼ Show '+${citationSummary.retractedCount}+' retracted citations';}
        " style="margin-top:6px;background:rgba(255,255,255,0.15);border:1px solid rgba(255,255,255,0.3);
                 color:white;padding:4px 12px;border-radius:4px;cursor:pointer;font-size:11px;">
          ▼ Show ${citationSummary.retractedCount} retracted citation${citationSummary.retractedCount > 1 ? 's' : ''}
        </button>`;
    }

    // Scanning progress bar
    let progressHTML = '';
    if (isScanning) {
      const pct = citationSummary.total ? Math.round((citationSummary.checked / citationSummary.total) * 100) : 0;
      progressHTML = `
        <div class="rc-progress-bar"><div class="rc-progress-fill" id="rc-progress" style="width:${pct}%"></div></div>
        <div style="font-size:10px;opacity:0.55;margin-top:3px;" id="rc-progress-label">
          ${citationSummary.checked} / ${citationSummary.total} citations checked
        </div>`;
    }

    const info = result.details || result.paperInfo;
    const banner = document.createElement('div');
    banner.id = 'rc-banner';
    banner.style.cssText = `
      position:fixed;top:0;left:0;right:0;z-index:2147483647;
      background:${bg};color:white;
      font-family:-apple-system,BlinkMacSystemFont,'Segoe UI',sans-serif;
      box-shadow:0 4px 24px rgba(0,0,0,0.4);
      animation:rcSlideIn 0.4s cubic-bezier(0.16,1,0.3,1);
    `;
    banner.innerHTML = `
      <div style="max-width:960px;margin:0 auto;padding:12px 18px;display:flex;align-items:flex-start;gap:12px;">
        <span style="font-size:22px;line-height:1;flex-shrink:0;margin-top:2px;">${icon}</span>
        <div style="flex:1;min-width:0;">
          <div style="font-weight:700;font-size:13px;letter-spacing:0.06em;text-transform:uppercase;">${mainTitle}</div>
          <div style="font-size:12px;margin-top:2px;opacity:0.9;">${mainSub}</div>
          ${info?.title ? `<div style="font-size:11px;margin-top:5px;opacity:0.75;">
            <strong>${info.title}</strong>
            ${info.journal ? ` · ${info.journal}` : ''}
            ${info.year ? ` · ${info.year}` : ''}
            ${result.details?.notice_url ? ` · <a href="${result.details.notice_url}" target="_blank">View retraction notice →</a>` : ''}
          </div>` : ''}
          ${citesHTML}
          ${progressHTML}
          <div style="font-size:10px;margin-top:6px;opacity:0.45;">DOI: ${result.doi} · Powered by CrossRef</div>
        </div>
        <button onclick="document.getElementById('rc-banner').remove()"
          style="background:rgba(255,255,255,0.2);border:none;color:white;
                 width:26px;height:26px;border-radius:50%;cursor:pointer;font-size:14px;flex-shrink:0;">✕</button>
      </div>`;
    document.body.prepend(banner);

    // Auto-dismiss clean banners
    if (!isRetracted && !hasBadCitations && !isScanning) {
      setTimeout(() => banner?.remove(), 7000);
    }
  }

  function updateProgress(checked, total) {
    const pct = Math.round((checked / total) * 100);
    const fill = document.getElementById('rc-progress');
    const label = document.getElementById('rc-progress-label');
    if (fill) fill.style.width = `${pct}%`;
    if (label) label.textContent = `${checked} / ${total} citations checked`;
  }

  // ─── Main ──────────────────────────────────────────────────────────────
  async function run() {
    const primaryDOI = extractPrimaryDOI();
    if (!primaryDOI) return;

    chrome.runtime.sendMessage({ type: 'DOI_FOUND', doi: primaryDOI });
    showLoadingBanner();

    // Step 1: Check the current paper
    const result = await checkRetraction(primaryDOI);
    const { alwaysShow } = await chrome.storage.local.get('alwaysShow');
    const referenceDOIs = result._references || [];
    const totalRefs = result._refCount || 0;

    // Show banner after main check, before citation scan
    const shouldShow = result.retracted || alwaysShow || referenceDOIs.length > 0;
    if (shouldShow) {
      showMainBanner(result, referenceDOIs.length > 0
        ? { scanning: true, checked: 0, total: referenceDOIs.length, retractedCount: 0, retractedItems: [] }
        : null);
    } else {
      removeBanners();
    }

    chrome.runtime.sendMessage({ type: 'CHECK_RESULT', result, citationTotal: totalRefs });

    // Step 2: Scan citations
    if (referenceDOIs.length === 0) return;

    const citationResults = await checkCitations(referenceDOIs, (checked, total) => {
      updateProgress(checked, total);
    });

    const retractedCitations = citationResults.filter(r => r.retracted);
    const citationSummary = {
      scanning: false,
      checked: citationResults.length,
      total: totalRefs,
      retractedCount: retractedCitations.length,
      retractedItems: retractedCitations,
    };

    if (result.retracted || retractedCitations.length > 0 || alwaysShow) {
      showMainBanner(result, citationSummary);
    } else {
      removeBanners();
    }

    chrome.runtime.sendMessage({ type: 'CITATION_RESULT', result, citationSummary });
  }

  if (document.readyState === 'loading') {
    document.addEventListener('DOMContentLoaded', () => setTimeout(run, 900));
  } else {
    setTimeout(run, 900);
  }
})();