inject-headers.py

#!/usr/bin/env python3
"""
Inject navigation headers into HTML documentation pages.

Usage: python3 inject-headers.py <output_dir>

This script adds a consistent navigation header to all generated HTML pages,
with appropriate styling and links based on the page location (root, templates, guidelines).
"""

import sys
import re
import os
from pathlib import Path


# Version link placeholder — replaced at build time based on --dev flag
VERSION_LINK_PLACEHOLDER = '{{VERSION_LINK}}'

# Navigation header templates (use placeholder for version link)
HEADERS = {
    'root': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html" class="nav-current">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

    'tools': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools" class="nav-current">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

    'guidelines': f'''<header class="doc-header"><div class="doc-header-brand"><a href="../index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="../index.html">Home</a><a href="../specification.html">Specification</a><a href="../index.html#metadata-guidelines" class="nav-current">Metadata Guidelines</a><a href="../index.html#templates">Templates</a><a href="../sdrf-builder.html">Template Builder</a><a href="../index.html#tools">Tools</a><a href="../sdrf-explorer.html">Explorer</a><a href="../sdrf-editor.html">Editor</a><a href="../index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

    'templates': f'''<header class="doc-header"><div class="doc-header-brand"><a href="../index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="../index.html">Home</a><a href="../specification.html">Specification</a><a href="../index.html#metadata-guidelines">Metadata Guidelines</a><a href="../index.html#templates" class="nav-current">Templates</a><a href="../sdrf-builder.html">Template Builder</a><a href="../index.html#tools">Tools</a><a href="../sdrf-explorer.html">Explorer</a><a href="../sdrf-editor.html">Editor</a><a href="../index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

    'sample_guidelines': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines" class="nav-current">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

    'templates_guide': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates" class="nav-current">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>'''
}


def inject_header(filepath: str, header_html: str, is_dev: bool = False) -> None:
    """Inject navigation header into an HTML file."""
    with open(filepath, 'r', encoding='utf-8') as f:
        content = f.read()

    # Resolve version link: only show in dev builds (link back to stable)
    if is_dev:
        version_link = '<a href="/" class="version-link">Stable Version</a>'
    else:
        version_link = ''
    resolved_header = header_html.replace(VERSION_LINK_PLACEHOLDER, version_link)

    # Add has-doc-header class to body
    content = re.sub(r'<body class="([^"]*)"', r'<body class="has-doc-header \1"', content)
    content = re.sub(r'<body>', '<body class="has-doc-header">', content)

    # Insert header after opening body tag
    content = re.sub(r'(<body[^>]*>)', r'\1\n' + resolved_header, content)

    with open(filepath, 'w', encoding='utf-8') as f:
        f.write(content)


def inject_version_link_into_static(filepath: str, is_dev: bool) -> None:
    """Inject a 'Stable Version' link into static HTML pages for dev builds."""
    if not is_dev:
        return  # Stable builds don't show a version link

    with open(filepath, 'r', encoding='utf-8') as f:
        content = f.read()

    # Already has a version link — skip
    if 'class="version-link"' in content:
        return

    # Insert "Stable Version" link before the GitHub link
    stable_link = '<a href="/" class="version-link">Stable Version</a>'
    content = content.replace(
        '<a href="https://github.com/bigbio/proteomics-metadata-standard"',
        stable_link + '<a href="https://github.com/bigbio/proteomics-metadata-standard"'
    )

    with open(filepath, 'w', encoding='utf-8') as f:
        f.write(content)


def main():
    if len(sys.argv) < 2:
        print("Usage: python3 inject-headers.py <output_dir> [--dev]")
        sys.exit(1)

    is_dev = '--dev' in sys.argv
    output_dir = Path(sys.argv[1])

    print(f"Dev mode: {is_dev}")

    # Inject header into specification.html
    spec_file = output_dir / "specification.html"
    if spec_file.exists():
        print(f"Injecting header into: {spec_file}")
        inject_header(str(spec_file), HEADERS['root'], is_dev)

    # Inject header into tools.html
    tools_file = output_dir / "tools.html"
    if tools_file.exists():
        print(f"Injecting header into: {tools_file}")
        inject_header(str(tools_file), HEADERS['tools'], is_dev)

    # Inject header into sample-guidelines.html
    sg_file = output_dir / "sample-guidelines.html"
    if sg_file.exists():
        print(f"Injecting header into: {sg_file}")
        inject_header(str(sg_file), HEADERS['sample_guidelines'], is_dev)

    # Inject header into templates.html (templates guide)
    tpl_guide = output_dir / "templates.html"
    if tpl_guide.exists():
        print(f"Injecting header into: {tpl_guide}")
        inject_header(str(tpl_guide), HEADERS['templates_guide'], is_dev)

    # Inject headers into metadata-guidelines pages
    guidelines_dir = output_dir / "metadata-guidelines"
    if guidelines_dir.exists():
        for html_file in guidelines_dir.glob("*.html"):
            print(f"Injecting header into: {html_file}")
            inject_header(str(html_file), HEADERS['guidelines'], is_dev)

    # Inject headers into template pages
    templates_dir = output_dir / "templates"
    if templates_dir.exists():
        for html_file in templates_dir.glob("*.html"):
            print(f"Injecting header into: {html_file}")
            inject_header(str(html_file), HEADERS['templates'], is_dev)

    # Inject version link into static HTML pages for dev builds
    for static_page in ["index.html", "quickstart.html", "sdrf-terms.html",
                         "sdrf-explorer.html", "sdrf-editor.html", "sdrf-builder.html"]:
        static_file = output_dir / static_page
        if static_file.exists():
            print(f"Processing version link in: {static_file}")
            inject_version_link_into_static(str(static_file), is_dev)

    print("Header injection complete!")


if __name__ == "__main__":
    main()