#!/usr/bin/env python3
"""Summary Skill - 综合报告生成技能"""

import argparse, hashlib, json, logging, os, sys
from datetime import datetime
from pathlib import Path
from typing import Dict, Optional
import yaml

logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
logger = logging.getLogger(__name__)

class SummarySkill:
    def __init__(self, config_path=None):
        self.config = self._load_config(config_path)
        self.commands, self.checksums = [], {}
        
    def _load_config(self, config_path):
        if config_path and os.path.exists(config_path):
            with open(config_path) as f: return yaml.safe_load(f)
        return {"skill": {"name": "summary", "version": "1.0.0"}, "parameters": {}, "dependencies": {"conda": {"channels": ["bioconda"], "packages": ["pandas"]}}}
    
    def _compute_checksum(self, filepath):
        sha256 = hashlib.sha256()
        with open(filepath, "rb") as f:
            for chunk in iter(lambda: f.read(8192), b""): sha256.update(chunk)
        return sha256.hexdigest()
    
    def _record_file(self, filepath, file_type="output"):
        if filepath.exists():
            self.checksums[str(filepath)] = {"sha256": self._compute_checksum(filepath), "size": filepath.stat().st_size, "type": file_type}
    
    def generate_report(self, output_dir):
        report_file = output_dir / "report.md"
        content = f"""# 基因家族分析综合报告

## 分析概要

本报告汇总了基因家族分析的完整结果，包括：
- 基因家族成员鉴定 (Identify)
- 系统发育分析 (Phylogeny)
- 保守基序分析 (Motif)
- 蛋白结构域分析 (Domain)
- 基因结构分析 (Structure)
- 启动子分析 (Promoter)
- 共线性分析 (Synteny)
- 核型分析 (Karyotype)
- 物种间比较 (Interspecies)
- 表达分析 (Expression)

## 基本信息
- **分析时间**: {datetime.now().strftime("%Y-%m-%d %H:%M:%S")}
- **技能版本**: {self.config["skill"]["version"]}

## 详细结果

请参考各分析阶段的独立报告。

## 可复现性

所有分析命令已记录在 `commands.sh` 中，环境配置见 `environment.yml`。
"""
        report_file.write_text(content)
        self._record_file(report_file)
        return report_file
    
    def write_reproducibility_bundle(self, output_dir):
        (output_dir / "commands.sh").write_text("#!/bin/bash\n# 综合报告\n")
        (output_dir / "environment.yml").write_text("name: summary\nchannels: [bioconda]\ndependencies: [pandas]")
        with open(output_dir / "checksums.sha256", "w") as f:
            for filepath, info in self.checksums.items(): f.write(f"{info['sha256']}  {filepath}\n")
    
    def run_demo(self, output_dir):
        output_dir.mkdir(parents=True, exist_ok=True)
        report = self.generate_report(output_dir)
        self.write_reproducibility_bundle(output_dir)
        return {"status": "success", "output_dir": str(output_dir), "report": str(report)}

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("--output", "-o", type=Path, required=True)
    parser.add_argument("--demo", action="store_true")
    args = parser.parse_args()
    skill = SummarySkill()
    result = skill.run_demo(args.output)
    print(json.dumps(result, indent=2))
    return 0

if __name__ == "__main__": sys.exit(main())