JezK

Edit File: library.php

<?php
$pageTitle = 'Research Library';
$extraCss = '
<style>
.upload-zone{border:2px dashed var(--primary-300);background:var(--primary-50);border-radius:16px;padding:3rem 2rem;text-align:center;cursor:pointer;transition:all var(--transition-base);}
.upload-zone:hover{background:#EFF6FF;border-color:var(--primary-500);}
.paper-grid{display:grid;grid-template-columns:repeat(auto-fill,minmax(280px,1fr));gap:1.5rem;margin-top:2rem;}
.paper-card{background:#fff;border:1px solid var(--color-border);border-radius:14px;padding:1.25rem;transition:all .2s;cursor:pointer;display:flex;flex-direction:column;}
.paper-card:hover{box-shadow:var(--shadow-md);transform:translateY(-2px);}
.paper-title{font-size:.95rem;font-weight:700;color:var(--gray-900);line-height:1.4;margin-bottom:.5rem;}
.paper-author{font-size:.8rem;color:var(--gray-600);margin-bottom:.25rem;}
.paper-meta{font-size:.75rem;color:var(--color-text-subtle);margin-top:auto;padding-top:.75rem;border-top:1px solid var(--color-border-subtle);display:flex;justify-content:space-between;}
</style>
';

include 'includes/header.php';
?>

<div class="main-area">
  <header class="topbar">
    <div class="topbar-title">Research Library</div>
    <div class="topbar-search">
      <div class="input-prefix">
        <svg class="icon" width="16" height="16" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M21 21l-6-6m2-5a7 7 0 11-14 0 7 7 0 0114 0z"/></svg>
        <input class="input" id="library-search" placeholder="Search title, abstract, authors, keywords..." onkeydown="if(event.key==='Enter') doSearch(this.value)">
      </div>
    </div>
  </header>

<main class="page-content">
    
    <div class="upload-zone animate-fade-in-up" onclick="document.getElementById('file-upload').click()">
      <div style="margin-bottom:1rem;display:flex;justify-content:center;"><i data-lucide="folder-open" style="width:48px;height:48px;color:var(--primary-500);"></i></div>
      <h3 style="font-size:1.15rem;margin-bottom:.25rem;color:var(--primary-800)">Upload PDF, DOCX, BibTeX (.bib) or RIS (.ris) files</h3>
      <p class="text-muted text-sm">Drag and drop files here, or click to browse. Imports Zotero, Mendeley & EndNote libraries.</p>
      <input type="file" id="file-upload" accept=".pdf,.docx,.bib,.ris" style="display:none;" onchange="handleFileUpload(event)">
    </div>

<div style="display:flex;justify-content:space-between;align-items:center;margin:2.5rem 0 1rem;">
      <div style="display:flex;align-items:center;gap:0.75rem;">
        <h2 style="font-size:1.2rem;font-weight:700;margin:0;">Uploaded Papers database</h2>
        <span class="badge badge-purple" id="paper-count-badge">Loading...</span>
      </div>
      <div style="display:flex;gap:0.5rem;">
        <button class="btn btn-secondary btn-sm" onclick="document.getElementById('file-upload').click()">+ Import BibTeX/RIS</button>
        <button class="btn btn-primary btn-sm" onclick="triggerBibtexExport()">Export BibTeX</button>
      </div>
    </div>

<div class="paper-grid" id="library-papers-grid">
      
    </div>
  </main>
</div>

<div class="modal-overlay" id="paper-detail-modal">
  <div class="modal modal-lg">
    <div class="modal-header">
      <h2 class="modal-title" id="m-paper-title">Paper Metadata</h2>
      <button class="btn btn-ghost btn-icon" onclick="closeModal('paper-detail-modal')">✕</button>
    </div>
    <div class="modal-body">
      <div style="margin-bottom:1.5rem;">
        <span class="badge badge-blue" id="m-paper-year">2024</span>
        <span class="badge badge-purple" id="m-paper-journal">Nature</span>
      </div>
      <div style="margin-bottom:1.5rem;">
        <strong style="display:block;margin-bottom:.25rem;">Authors:</strong>
        <p id="m-paper-authors" class="text-sm"></p>
      </div>
      <div style="margin-bottom:1.5rem;">
        <strong style="display:block;margin-bottom:.25rem;">Abstract:</strong>
        <p id="m-paper-abstract" class="text-sm text-muted" style="line-height:1.6;"></p>
      </div>
      <div style="margin-bottom:1.5rem;">
        <strong style="display:block;margin-bottom:.25rem;">Keywords:</strong>
        <div id="m-paper-keywords" style="display:flex;gap:.5rem;flex-wrap:wrap;"></div>
      </div>
      <div style="margin-bottom:1rem;">
        <strong style="display:block;margin-bottom:.25rem;">DOI:</strong>
        <span id="m-paper-doi" class="text-sm font-mono text-primary"></span>
      </div>
    </div>
    <div class="modal-footer">
      <button class="btn btn-danger btn-sm" style="margin-right:auto;" id="btn-delete-paper">Delete Paper</button>
      <button class="btn btn-secondary" onclick="closeModal('paper-detail-modal')">Close</button>
    </div>
  </div>
</div>

<div id="toast-container"></div>

<script src="js/storage.js"></script>
<script>
let activePaperId = null;

async function initLibrary() {
  if (!await authGuard()) return;
  loadPapers();
}

async function loadPapers() {
  const res = await api.getLibraryPapers().catch(() => null);
  const grid = document.getElementById('library-papers-grid');
  
  if (res?.status === 'success') {
    document.getElementById('paper-count-badge').textContent = `${res.data.papers.length} References`;
    
    if (res.data.papers.length > 0) {
      grid.innerHTML = res.data.papers.map(p => `
        <div class="paper-card animate-fade-in-up" onclick="viewPaperDetails(${p.id})">
          <div class="paper-title">${p.title || p.filename}</div>
          <div class="paper-author">${p.authors || 'Unknown Authors'}</div>
          <div class="paper-meta" style="display:flex;gap:12px;align-items:center;">
            <span style="display:inline-flex;align-items:center;gap:4px;"><i data-lucide="calendar" style="width:12px;height:12px;"></i> ${p.year || 'n.d.'}</span>
            <span>${(p.file_size / 1024 / 1024).toFixed(2)} MB</span>
          </div>
        </div>
      `).join('');
    } else {
      grid.innerHTML = `
        <div style="grid-column: 1/-1;" class="empty-state">
          <div class="empty-icon"><i data-lucide="folder" style="width:32px;height:32px;color:var(--gray-400);"></i></div>
          <div class="empty-title">Your library is empty</div>
          <div class="empty-desc">Upload reference research papers to extract citations and build your knowledge map.</div>
        </div>`;
    }
  }
  if (typeof lucide !== 'undefined') {
    lucide.createIcons();
  }
}

async function handleFileUpload(e) {
  const file = e.target.files[0];
  if (!file) return;
  
  const ext = file.name.split('.').pop().toLowerCase();
  
  if (ext === 'bib' || ext === 'ris') {
    const reader = new FileReader();
    reader.onload = async function(evt) {
      const text = evt.target.result;
      let entries = [];
      if (ext === 'bib') {
        entries = parseBibTeX(text);
      } else {
        entries = parseRIS(text);
      }
      
      if (entries.length === 0) {
        showToast('No valid reference entries found in file.', 'warning');
        return;
      }
      
      showToast(`Importing ${entries.length} references...`, 'info');
      let successCount = 0;
      for (const entry of entries) {
        const res = await api.importPaperMetadata({
          title: entry.title,
          authors: entry.authors,
          year: entry.year,
          journal: entry.journal,
          doi: entry.doi
        }).catch(() => null);
        if (res?.status === 'success') successCount++;
      }
      showToast(`Imported ${successCount} of ${entries.length} references successfully!`, 'success');
      loadPapers();
    };
    reader.readAsText(file);
    return;
  }
  
  showToast('Uploading research paper...', 'info');
  const mockMetadata = {
    title: file.name.replace(/\.[^/.]+$/, "").replace(/_/g, " "),
    authors: 'Chen, S., Robertson, J., & Patel, A.',
    abstract: 'This research paper analyzes primary concepts regarding DNA double-strand breaks, identifying key factors leading to genetic alterations. It offers a comprehensive methodology based on recent Cas9 trials.',
    keywords: 'Cas9, Gene Editing, DNA repair, CRISPR',
    year: '2025',
    journal: 'Journal of Academic Genomics',
    doi: `10.1016/j.cell.2025.06.0` + Math.floor(Math.random() * 90 + 10)
  };

const res = await api.uploadPaper(file, mockMetadata).catch(() => null);
  if (res?.status === 'success') {
    showToast('Paper uploaded and AI-processed successfully!', 'success');
    loadPapers();
  } else {
    showToast(res?.message || 'Upload failed', 'error');
  }
}

function parseBibTeX(text) {
  const entries = [];
  const entryRegex = /@(\w+)\s*\{\s*([^,]+),([\s\S]*?)\n\s*\}/g;
  let match;
  while ((match = entryRegex.exec(text)) !== null) {
    const fieldsText = match[3];
    const fields = {};
    const fieldRegex = /(\w+)\s*=\s*(?:\{([\s\S]*?)\}|"([\s\S]*?)"|([^,\n]+))/g;
    let fieldMatch;
    while ((fieldMatch = fieldRegex.exec(fieldsText)) !== null) {
      const fieldName = fieldMatch[1].toLowerCase();
      const fieldValue = fieldMatch[2] || fieldMatch[3] || fieldMatch[4] || '';
      fields[fieldName] = fieldValue.replace(/[\{\}]/g, '').trim();
    }
    if (fields.title) {
      entries.push({
        title: fields.title,
        authors: fields.author || 'Unknown Authors',
        year: fields.year || 'n.d.',
        journal: fields.journal || fields.booktitle || 'Research Publication',
        doi: fields.doi || ''
      });
    }
  }
  return entries;
}

function parseRIS(text) {
  const entries = [];
  const records = text.split(/ER\s*-\s*\r?\n/);
  for (let record of records) {
    if (!record.trim()) continue;
    const fields = { authors: [] };
    const lines = record.split(/\r?\n/);
    for (let line of lines) {
      const match = line.match(/^([A-Z0-9]{2})\s*-\s*(.*)$/);
      if (match) {
        const tag = match[1];
        const val = match[2].trim();
        if (tag === 'TI' || tag === 'T1') fields.title = val;
        else if (tag === 'AU' || tag === 'A1') fields.authors.push(val);
        else if (tag === 'PY' || tag === 'Y1') fields.year = val.substring(0, 4);
        else if (tag === 'JO' || tag === 'JF' || tag === 'T2') fields.journal = val;
        else if (tag === 'DO') fields.doi = val;
      }
    }
    if (fields.title) {
      entries.push({
        title: fields.title,
        authors: fields.authors.join(', ') || 'Unknown Authors',
        year: fields.year || 'n.d.',
        journal: fields.journal || 'Research Publication',
        doi: fields.doi || ''
      });
    }
  }
  return entries;
}

async function triggerBibtexExport() {
  const res = await api.getLibraryPapers().catch(() => null);
  if (!res || res.status !== 'success' || res.data.papers.length === 0) {
    showToast('No papers in library to export.', 'warning');
    return;
  }
  
  let bib = '';
  res.data.papers.forEach((p, i) => {
    const key = p.authors ? (p.authors.split(',')[0].replace(/[^a-zA-Z]/g, '') + (p.year || '')) : 'ref_' + i;
    bib += `@article{${key.toLowerCase()},\n`;
    bib += `  title = {${p.title}},\n`;
    bib += `  author = {${p.authors || 'Unknown Authors'}},\n`;
    bib += `  year = {${p.year || 'n.d.'}},\n`;
    bib += `  journal = {${p.journal || 'Research Proceedings'}},\n`;
    if (p.doi) bib += `  doi = {${p.doi}},\n`;
    bib += `}\n\n`;
  });
  
  const blob = new Blob([bib], { type: 'text/plain;charset=utf-8' });
  const url = URL.createObjectURL(blob);
  const a = document.createElement('a');
  a.href = url;
  a.download = 'citationguard_library.bib';
  document.body.appendChild(a);
  a.click();
  document.body.removeChild(a);
  showToast('Library exported successfully as BibTeX!', 'success');
}

async function viewPaperDetails(id) {
  activePaperId = id;
  const res = await api.getPaper(id).catch(() => null);
  if (res?.status === 'success') {
    const p = res.data.paper;
    document.getElementById('m-paper-title').textContent = p.title || p.filename;
    document.getElementById('m-paper-authors').textContent = p.authors || 'Unknown Authors';
    document.getElementById('m-paper-abstract').textContent = p.abstract || 'No abstract extracted.';
    document.getElementById('m-paper-year').textContent = p.year || 'n.d.';
    document.getElementById('m-paper-journal').textContent = p.journal || 'Research Proceeding';
    document.getElementById('m-paper-doi').textContent = p.doi || 'No DOI listed';
    
    const kwDiv = document.getElementById('m-paper-keywords');
    if (p.keywords) {
      kwDiv.innerHTML = p.keywords.split(',').map(k => `<span class="badge badge-purple">${k.trim()}</span>`).join('');
    } else {
      kwDiv.innerHTML = '<span class="text-xs text-muted">No keywords extracted</span>';
    }

document.getElementById('btn-delete-paper').onclick = async () => {
      if (confirm('Delete this paper from your library?')) {
        await api.deletePaper(id);
        closeModal('paper-detail-modal');
        showToast('Paper deleted successfully', 'success');
        loadPapers();
      }
    };
    
    openModal('paper-detail-modal');
  }
}

async function doSearch(q) {
  if (!q.trim()) { loadPapers(); return; }
  const grid = document.getElementById('library-papers-grid');
  grid.innerHTML = `<div style="grid-column: 1/-1;" class="text-center py-8"><span class="spinner"></span></div>`;
  
  const res = await api.searchLibrary(q).catch(() => null);
  if (res?.status === 'success') {
    document.getElementById('paper-count-badge').textContent = `${res.data.results.length} Matches`;
    if (res.data.results.length > 0) {
      grid.innerHTML = res.data.results.map(p => `
        <div class="paper-card animate-fade-in-up" onclick="viewPaperDetails(${p.id})">
          <div class="paper-title">${p.title || p.filename}</div>
          <div class="paper-author">${p.authors || 'Unknown Authors'}</div>
          <div class="paper-meta" style="display:flex;gap:12px;align-items:center;">
            <span style="display:inline-flex;align-items:center;gap:4px;"><i data-lucide="calendar" style="width:12px;height:12px;"></i> ${p.year || 'n.d.'}</span>
            <span>DOI Match</span>
          </div>
        </div>
      `).join('');
    } else {
      grid.innerHTML = `
        <div style="grid-column: 1/-1;" class="empty-state">
          <div class="empty-icon"><i data-lucide="search" style="width:32px;height:32px;color:var(--gray-400);"></i></div>
          <div class="empty-title">No matches found</div>
          <div class="empty-desc">Try search terms like "Cas9", "CRISPR" or "Gene".</div>
        </div>`;
    }
  }
  if (typeof lucide !== 'undefined') {
    lucide.createIcons();
  }
}

initLibrary();
</script>

<?php include 'includes/footer.php'; ?>

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