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Merge pull request #1 from pathoplexus/Create-GH-pages-for-PP-example-data
Create GH pages for PP example data
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‎.github/workflows/update-page.yml

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name: Generate Pathoplexus Example Data List
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on:
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push:
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branches:
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main
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install markdown
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- name: Create Python script
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run: |
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cat << EOF > generate_list.py
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import os
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import html
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from datetime import datetime
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import markdown
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def get_file_icon(file):
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ext = os.path.splitext(file)[1].lower()
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icon_map = {
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('.fasta', '.fa', '.fna'): '<i class="fas fa-dna" title="FASTA file"></i>',
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('.tsv', '.tab'): '<i class="fas fa-table" title="TSV file"></i>',
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('.py', '.js', '.css', '.html', '.json'): '<i class="fas fa-file-code" title="{} file"></i>',
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('.jpg', '.jpeg', '.png', '.gif', '.svg'): '<i class="fas fa-file-image" title="{} file"></i>',
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('.pdf', '.doc', '.docx', '.txt'): '<i class="fas fa-file-alt" title="{} file"></i>',
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}
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for extensions, icon in icon_map.items():
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if ext in extensions:
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return icon.format(ext[1:])
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return '<i class="fas fa-file"></i>'
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def get_readme_content():
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try:
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with open('README.md', 'r') as f:
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content = f.read()
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return markdown.markdown(content)
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except FileNotFoundError:
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return "<p>README.md not found.</p>"
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def generate_html():
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file_list = []
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for root, dirs, files in os.walk('example_files'):
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for file in files:
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if file != 'index.html' and not file.startswith('.'):
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path = os.path.join(root, file)
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size = os.path.getsize(path)
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mtime = os.path.getmtime(path)
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file_list.append((path, size, mtime))
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readme_content = get_readme_content()
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html_content = f'''
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<!DOCTYPE html>
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<html lang="en">
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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>Pathoplexus Example Files</title>
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<link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css" rel="stylesheet">
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<style>
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body {{ font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif; line-height: 1.6; padding: 20px; background-color: #f4f4f4; color: #333; }}
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.container {{ max-width: 800px; margin: 0 auto; background-color: #fff; padding: 20px; border-radius: 5px; box-shadow: 0 2px 5px rgba(0,0,0,0.1); }}
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table {{ width: 100%; border-collapse: collapse; margin-top: 20px; }}
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th, td {{ padding: 12px; text-align: left; border-bottom: 1px solid #e0e0e0; }}
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th {{ background-color: #f2f2f2; font-weight: bold; color: #2c3e50; }}
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tr:hover {{ background-color: #f5f5f5; }}
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a {{ color: #3498db; text-decoration: none; }}
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a:hover {{ color: #2980b9; }}
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.file-icon {{ margin-right: 10px; color: #7f8c8d; }}
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.file-size, .file-date {{ color: #7f8c8d; font-size: 0.9em; }}
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.readme-content {{ margin-bottom: 30px; padding: 20px; border-radius: 5px; }}
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.github-link {{ position: absolute; top: 10px; right: 10px; font-size: 24px; color: #333; }}
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</style>
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</head>
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<body>
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<div class="container">
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<a href="https://github.com/loculus-project/example_data" class="github-link" target="_blank" rel="noopener noreferrer">
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<i class="fab fa-github" title="View on GitHub"></i>
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</a>
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<div class="readme-content">
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{readme_content}
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</div>
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<table>
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<thead>
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<tr>
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<th>File Name</th>
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<th>Size</th>
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<th>Last Modified</th>
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</tr>
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</thead>
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<tbody>
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'''
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for file, size, mtime in sorted(file_list):
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file = file.replace("example_files/", "")
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icon = get_file_icon(file)
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size_str = f'{size/1024:.1f} KB' if size >= 1024 else f'{size} bytes'
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date_str = datetime.fromtimestamp(mtime).strftime('%Y-%m-%d %H:%M:%S')
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html_content += f'''
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<tr>
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<td><a href="example_files/{html.escape(file)}">{icon} {html.escape(file)}</a></td>
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<td class="file-size">{size_str}</td>
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<td class="file-date">{date_str}</td>
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</tr>
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'''
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html_content += '''
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</tbody>
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</table>
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</div>
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</body>
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</html>
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'''
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with open('index.html', 'w') as f:
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f.write(html_content)
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generate_html()
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EOF
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- name: Generate Pathoplexus example data list
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run: python generate_list.py
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- name: Commit and push to gh-pages
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run: |
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git config --global user.name 'GitHub Action'
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git config --global user.email '[email protected]'
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git checkout -b gh-pages
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git add index.html
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git commit -m "Update Pathoplexus example data list" || exit 0
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git push -f origin gh-pages

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