Initial commit
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Zhongwei Li
370
skills/biomni/scripts/generate_report.py
Executable file
370
skills/biomni/scripts/generate_report.py
Executable file
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#!/usr/bin/env python3
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"""
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Enhanced PDF report generation for biomni conversation histories.
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This script provides additional customization options for biomni reports:
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- Custom styling and branding
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- Formatted code blocks
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- Section organization
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- Metadata inclusion
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- Export format options (PDF, HTML, Markdown)
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Usage:
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python generate_report.py --input conversation.json --output report.pdf
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python generate_report.py --agent-object agent --output report.pdf --format html
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"""
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import argparse
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import json
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from pathlib import Path
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from typing import Dict, List, Optional, Any
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from datetime import datetime
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def format_conversation_history(
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messages: List[Dict[str, Any]],
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include_metadata: bool = True,
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include_code: bool = True,
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include_timestamps: bool = False
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) -> str:
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"""
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Format conversation history into structured markdown.
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Args:
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messages: List of conversation message dictionaries
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include_metadata: Include metadata section
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include_code: Include code blocks
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include_timestamps: Include message timestamps
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Returns:
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Formatted markdown string
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"""
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sections = []
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# Header
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sections.append("# Biomni Analysis Report\n")
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# Metadata
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if include_metadata:
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sections.append("## Metadata\n")
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sections.append(f"- **Generated**: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}")
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sections.append(f"- **Number of interactions**: {len(messages)}")
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sections.append("\n---\n")
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# Process messages
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sections.append("## Analysis\n")
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for i, msg in enumerate(messages, 1):
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role = msg.get('role', 'unknown')
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content = msg.get('content', '')
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if role == 'user':
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sections.append(f"### Task {i // 2 + 1}\n")
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sections.append(f"**Query:**\n```\n{content}\n```\n")
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elif role == 'assistant':
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sections.append(f"**Response:**\n")
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# Check if content contains code
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if include_code and ('```' in content or 'import ' in content):
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# Attempt to separate text and code
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parts = content.split('```')
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for j, part in enumerate(parts):
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if j % 2 == 0:
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# Text content
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if part.strip():
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sections.append(f"{part.strip()}\n")
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else:
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# Code content
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# Check if language is specified
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lines = part.split('\n', 1)
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if len(lines) > 1 and lines[0].strip() in ['python', 'r', 'bash', 'sql']:
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lang = lines[0].strip()
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code = lines[1]
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else:
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lang = 'python' # Default to python
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code = part
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sections.append(f"```{lang}\n{code}\n```\n")
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else:
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sections.append(f"{content}\n")
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sections.append("\n---\n")
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return '\n'.join(sections)
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def markdown_to_html(markdown_content: str, title: str = "Biomni Report") -> str:
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"""
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Convert markdown to styled HTML.
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Args:
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markdown_content: Markdown string
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title: HTML page title
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Returns:
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HTML string
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"""
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# Simple markdown to HTML conversion
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# For production use, consider using a library like markdown or mistune
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html_template = 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>{title}</title>
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<style>
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body {{
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font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, sans-serif;
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line-height: 1.6;
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max-width: 900px;
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margin: 0 auto;
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padding: 20px;
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color: #333;
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}}
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h1 {{
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color: #2c3e50;
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border-bottom: 3px solid #3498db;
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padding-bottom: 10px;
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}}
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h2 {{
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color: #34495e;
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margin-top: 30px;
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border-bottom: 2px solid #95a5a6;
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padding-bottom: 5px;
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}}
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h3 {{
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color: #555;
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}}
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code {{
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background-color: #f4f4f4;
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padding: 2px 6px;
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border-radius: 3px;
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font-family: 'Monaco', 'Menlo', 'Courier New', monospace;
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}}
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pre {{
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background-color: #f8f8f8;
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border: 1px solid #ddd;
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border-radius: 5px;
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padding: 15px;
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overflow-x: auto;
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}}
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pre code {{
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background-color: transparent;
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padding: 0;
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}}
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hr {{
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border: none;
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border-top: 1px solid #ddd;
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margin: 30px 0;
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}}
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.metadata {{
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background-color: #ecf0f1;
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padding: 15px;
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border-radius: 5px;
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margin-bottom: 20px;
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}}
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.task {{
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background-color: #e8f4f8;
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padding: 10px;
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border-left: 4px solid #3498db;
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margin: 20px 0;
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}}
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.footer {{
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margin-top: 50px;
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text-align: center;
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color: #7f8c8d;
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font-size: 0.9em;
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}}
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</style>
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</head>
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<body>
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<div class="content">
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{markdown_to_html_simple(markdown_content)}
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</div>
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<div class="footer">
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<p>Generated with Biomni | Stanford SNAP Lab</p>
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<p><a href="https://github.com/snap-stanford/biomni">github.com/snap-stanford/biomni</a></p>
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</div>
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</body>
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</html>
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"""
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return html_template
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def markdown_to_html_simple(md: str) -> str:
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"""Simple markdown to HTML converter (basic implementation)."""
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lines = md.split('\n')
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html_lines = []
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in_code_block = False
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in_list = False
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for line in lines:
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# Code blocks
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if line.startswith('```'):
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if in_code_block:
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html_lines.append('</code></pre>')
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in_code_block = False
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else:
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lang = line[3:].strip()
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html_lines.append(f'<pre><code class="language-{lang}">')
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in_code_block = True
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continue
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if in_code_block:
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html_lines.append(line)
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continue
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# Headers
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if line.startswith('# '):
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html_lines.append(f'<h1>{line[2:]}</h1>')
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elif line.startswith('## '):
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html_lines.append(f'<h2>{line[3:]}</h2>')
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elif line.startswith('### '):
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html_lines.append(f'<h3>{line[4:]}</h3>')
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# Lists
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elif line.startswith('- '):
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if not in_list:
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html_lines.append('<ul>')
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in_list = True
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html_lines.append(f'<li>{line[2:]}</li>')
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else:
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if in_list:
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html_lines.append('</ul>')
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in_list = False
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# Horizontal rule
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if line.strip() == '---':
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html_lines.append('<hr>')
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# Bold
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elif '**' in line:
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line = line.replace('**', '<strong>', 1).replace('**', '</strong>', 1)
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html_lines.append(f'<p>{line}</p>')
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# Regular paragraph
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elif line.strip():
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html_lines.append(f'<p>{line}</p>')
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else:
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html_lines.append('<br>')
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if in_list:
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html_lines.append('</ul>')
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return '\n'.join(html_lines)
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def generate_report(
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conversation_data: Dict[str, Any],
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output_path: Path,
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format: str = 'markdown',
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title: Optional[str] = None
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):
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"""
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Generate formatted report from conversation data.
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Args:
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conversation_data: Conversation history dictionary
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output_path: Output file path
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format: Output format ('markdown', 'html', or 'pdf')
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title: Report title
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"""
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messages = conversation_data.get('messages', [])
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if not title:
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title = f"Biomni Analysis - {datetime.now().strftime('%Y-%m-%d')}"
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# Generate markdown
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markdown_content = format_conversation_history(messages)
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if format == 'markdown':
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output_path.write_text(markdown_content)
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print(f"✓ Markdown report saved to {output_path}")
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elif format == 'html':
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html_content = markdown_to_html(markdown_content, title)
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output_path.write_text(html_content)
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print(f"✓ HTML report saved to {output_path}")
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elif format == 'pdf':
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# For PDF generation, we'd typically use a library like weasyprint or reportlab
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# This is a placeholder implementation
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print("PDF generation requires additional dependencies (weasyprint or reportlab)")
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print("Falling back to HTML format...")
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html_path = output_path.with_suffix('.html')
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html_content = markdown_to_html(markdown_content, title)
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html_path.write_text(html_content)
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print(f"✓ HTML report saved to {html_path}")
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print(" To convert to PDF:")
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print(f" 1. Install weasyprint: pip install weasyprint")
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print(f" 2. Run: weasyprint {html_path} {output_path}")
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else:
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raise ValueError(f"Unsupported format: {format}")
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def main():
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"""Main entry point for CLI usage."""
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parser = argparse.ArgumentParser(
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description="Generate enhanced reports from biomni conversation histories"
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)
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parser.add_argument(
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'--input',
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type=Path,
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required=True,
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help='Input conversation history JSON file'
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)
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parser.add_argument(
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'--output',
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type=Path,
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required=True,
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help='Output report file path'
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)
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parser.add_argument(
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'--format',
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choices=['markdown', 'html', 'pdf'],
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default='markdown',
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help='Output format (default: markdown)'
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)
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parser.add_argument(
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'--title',
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type=str,
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help='Report title (optional)'
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)
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args = parser.parse_args()
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# Load conversation data
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try:
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with open(args.input, 'r') as f:
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conversation_data = json.load(f)
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except FileNotFoundError:
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print(f"❌ Input file not found: {args.input}")
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return 1
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except json.JSONDecodeError:
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print(f"❌ Invalid JSON in input file: {args.input}")
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return 1
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# Generate report
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try:
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generate_report(
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conversation_data,
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args.output,
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format=args.format,
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title=args.title
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)
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return 0
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except Exception as e:
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print(f"❌ Error generating report: {e}")
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return 1
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if __name__ == '__main__':
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import sys
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sys.exit(main())
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