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LukasWallrichclaude
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claude
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Update all components with latest changes
Includes updates to annotator, explorer, preprocessing, and shared components. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
1 parent 0db3d89 commit 0849f95

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‎annotator/css/annotator.css‎

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‎annotator/index.html‎

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<head>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>FReD Annotator - Annotate Reading Lists</title>
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<title>FLoRA Annotator - Annotate Reading Lists</title>
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<!-- Stylesheets -->
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<link rel="stylesheet" href="../shared/css/theme.css">
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<div style="display: flex; align-items: center; gap: 1rem;">
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<img src="https://forrt.org/author/forrt/avatar_hu8bc9dda6369ea35e3d2850cf7115c3e5_11296_270x270_fill_q100_h2_lanczos_center_2.webp" alt="FORRT Logo" style="height: 50px; border-radius: 8px;">
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<div>
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<h1 style="margin: 0;">FReD Annotator</h1>
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<h1 style="margin: 0;">FLoRA Annotator</h1>
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<p style="margin: 0; opacity: 0.9; font-size: 0.9rem;">Annotate Reading Lists with Replication Information</p>
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</div>
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</div>
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Smith, J. (2020). Study title. Journal Name. https://doi.org/10.1234/example
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10.5678/another-doi"
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></textarea>
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<!-- DOI Lookup Section -->
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<div class="doi-lookup-section" style="margin-top: 0.75rem; padding: 0.75rem; background: var(--fred-bg-alt); border-radius: 6px;">
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<div style="display: flex; align-items: center; gap: 0.5rem; flex-wrap: wrap;">
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<span style="font-size: 0.875rem; color: var(--fred-text-muted);">Don't have DOIs?</span>
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<button class="btn btn-sm btn-secondary" id="btn-lookup-dois" title="Look up DOIs for references without them">
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Look up DOIs via CrossRef
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</button>
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<input type="email"
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id="crossref-email"
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class="form-control"
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placeholder="your@email.com (required by CrossRef)"
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style="flex: 1; min-width: 200px; max-width: 300px; font-size: 0.875rem; padding: 0.35rem 0.5rem;">
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</div>
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<small class="text-muted" style="display: block; margin-top: 0.5rem;">
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This will query CrossRef to find DOIs for references that don't already contain them.
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</small>
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</div>
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<!-- Retraction Check Option -->
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<div class="retraction-check-section" style="margin-top: 0.75rem; padding: 0.75rem; background: var(--fred-bg-alt); border-radius: 6px; border: 1px solid var(--fred-border);">
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<label style="display: flex; align-items: flex-start; gap: 0.5rem; cursor: pointer;">
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<input type="checkbox" id="check-retractions" style="margin-top: 0.2rem;">
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<div>
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<span style="font-size: 0.875rem; font-weight: 500; color: var(--fred-text);">Check for retracted articles</span>
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<small class="text-muted" style="display: block; margin-top: 0.25rem;">
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Query the Retraction Watch database to identify retracted papers. This will slow down processing as it requires downloading the database (~15MB).
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</small>
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</div>
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</label>
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</div>
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</div>
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<!-- File Upload -->
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<div class="form-group">
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<label class="form-label" for="file-upload">Or upload a file</label>
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<input type="file" id="file-upload" class="form-control" accept=".pdf,.bib,.ris,.txt">
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<small class="text-muted">Supported formats: PDF, BibTeX (.bib), RIS (.ris), plain text (.txt)</small>
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<div class="file-upload-wrapper">
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<label for="file-upload" class="custom-file-upload">
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Choose File
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</label>
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<input type="file" id="file-upload" accept=".pdf,.bib,.ris,.txt">
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<span class="file-chosen" id="file-chosen">No file chosen</span>
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</div>
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<small class="text-muted" style="display: block; margin-top: 0.5rem;">Supported formats: PDF, BibTeX (.bib), RIS (.ris), plain text (.txt)</small>
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</div>
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<!-- Action Buttons -->
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<div class="btn-group mt-2">
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<div class="btn-group mt-2" id="process-buttons">
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<!-- Initial state: single Process button -->
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<button class="btn btn-primary" id="btn-process">Process References</button>
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<!-- After DOIs added: Add/Replace buttons (hidden initially) -->
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<button class="btn btn-primary" id="btn-add-refs" style="display: none;">Add to Selection</button>
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<button class="btn btn-secondary" id="btn-replace-refs" style="display: none;">Replace Selection</button>
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<button class="btn btn-secondary" id="btn-clear">Clear</button>
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</div>
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</div>
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<!-- Tab: Study Selection -->
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<div class="tab-content" id="tab-selection">
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<div class="card">
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<div class="card-header">Studies Found in FReD</div>
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<div class="card-header">Studies Found in FLoRA</div>
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<div class="card-body">
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<!-- Coverage Summary -->
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<div id="coverage-chart" style="margin-bottom: 1rem;"></div>
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<!-- Database Browser -->
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<div class="card">
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<div class="card-header">Browse FReD Database</div>
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<div class="card-header">Browse FLoRA Database</div>
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<div class="card-body">
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<p class="text-muted">Select additional studies to include in your report.</p>
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<table id="database-table" class="display" style="width:100%">
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<thead>
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<tr>
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<th>DOI</th>
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<th></th>
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<th>Reference</th>
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<th>Title</th>
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</tr>
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</thead>
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<tbody></tbody>
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Replication Report
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<div class="btn-group">
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<button class="btn btn-sm btn-secondary" id="btn-copy-report">Copy HTML</button>
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<button class="btn btn-sm btn-secondary" id="btn-toggle-markdown">Show Markdown</button>
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<button class="btn btn-sm btn-secondary" id="btn-copy-markdown">Copy Markdown</button>
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<button class="btn btn-sm btn-primary" id="btn-print">Print / Save PDF</button>
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</div>
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</div>
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</div>
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</div>
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<!-- Replicability Plot -->
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<div class="card">
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<div class="card-header">Effect Size Comparison</div>
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<div class="card-body">
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<div class="plot-container" id="replicability-plot"></div>
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</div>
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</div>
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</div>
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</main>
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<!-- Footer -->
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<footer style="background: var(--fred-bg-alt); padding: 1rem 0; margin-top: 2rem; text-align: center; color: var(--fred-text-muted);">
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<div class="container">
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<p>FReD Annotator | <a href="https://forrt.org" target="_blank">FORRT</a> | Data last updated: <span id="data-updated">Loading...</span></p>
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<p>FLoRA Annotator | <a href="https://forrt.org" target="_blank">FORRT</a> | Data last updated: <span id="data-updated">Loading...</span></p>
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</div>
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</footer>
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<!-- Welcome Modal -->
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<div class="modal-overlay" id="welcome-modal">
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<div class="modal">
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<div class="modal-header">
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<h3>Welcome to FReD Annotator</h3>
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<h3>Welcome to FLoRA Annotator</h3>
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<button class="modal-close" onclick="document.getElementById('welcome-modal').classList.remove('active')">&times;</button>
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</div>
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<div class="modal-body">
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<p>
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The <strong>FReD Annotator</strong> helps you identify which studies in your reading list
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The <strong>FLoRA Annotator</strong> helps you identify which studies in a reference list, journal article or reading list
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have been replicated and what the outcomes were.
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</p>
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<h4>How to use:</h4>
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<li><strong>Study Selection:</strong> Review matched studies and select additional ones</li>
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<li><strong>Report:</strong> Generate an annotated report to share or save</li>
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</ol>
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<h4>Legend</h4>
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<ul style="list-style: none; padding-left: 0;">
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<li><span style="color: darkgreen;">&#x2714;</span> <strong>Success:</strong> All replications succeeded</li>
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<li><span style="color: darkred;">&#x2716;</span> <strong>Failure:</strong> All replications failed</li>
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<li>&#x2753; <strong>Mixed:</strong> Mixed results across replications</li>
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<li>&#x2754; <strong>N/A:</strong> Original study not significant</li>
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<li>&#x270F; <strong>Not Coded:</strong> Outcome not yet coded</li>
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</ul>
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</div>
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<div class="modal-footer">
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<button class="btn btn-primary" onclick="document.getElementById('welcome-modal').classList.remove('active')">Get Started</button>
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<label style="display: flex; align-items: center; gap: 0.5rem; font-size: 0.875rem; cursor: pointer;">
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<input type="checkbox" id="welcome-dont-show">
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Don't show this again
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</label>
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<button class="btn btn-primary" id="welcome-close-btn">Get Started</button>
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</div>
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</div>
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</div>
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<script src="../shared/js/success-criteria.js"></script>
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<script src="../shared/js/data-loader.js"></script>
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<script src="js/doi-parser.js"></script>
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<script src="js/retraction-checker.js"></script>
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<script src="js/report-generator.js"></script>
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<script src="js/app.js"></script>
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</body>

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