"""本地工具运行器 - 替代 Docker 调用"""
import subprocess
import logging
from pathlib import Path
from typing import Dict, Any
import os

logger = logging.getLogger(__name__)

class ToolRunner:
    """本地工具运行管理器"""

    def run_bttoxin_digger(
        self,
        input_dir: Path,
        output_dir: Path,
        sequence_type: str = "nucl",
        scaf_suffix: str = ".fna",
        threads: int = 4
    ) -> Dict[str, Any]:
        """
        在本地环境运行 BtToxin_Digger
        使用 'pixi run -e digger' 激活环境
        """
        # Ensure output directory exists
        output_dir.mkdir(parents=True, exist_ok=True)

        # BtToxin_Digger expects to read files from --SeqPath.
        # It scans the directory for files matching *suffix.
        # We point it to the input directory.
        seq_path = input_dir.absolute()

        # Construct command
        # Note: We run this from output_dir so 'Results/' are created there.
        command = [
            "pixi", "run", "-e", "digger", "BtToxin_Digger",
            "--SeqPath", str(seq_path),
            "--SequenceType", sequence_type,
            "--Scaf_suffix", scaf_suffix,
            "--threads", str(threads)
        ]

        logger.info(f"Running command: {' '.join(command)}")
        logger.info(f"Working directory: {output_dir}")

        try:
            # Run subprocess
            # Capture both stdout and stderr
            process = subprocess.run(
                command,
                cwd=str(output_dir),
                capture_output=True,
                text=True,
                check=False,
                env=os.environ.copy() # Inherit env vars (PATH, etc)
            )

            success = (process.returncode == 0)
            logs = f"STDOUT:\n{process.stdout}\n\nSTDERR:\n{process.stderr}"

            if not success:
                logger.error(f"BtToxin_Digger failed with exit code {process.returncode}")
                logger.error(process.stderr)

            return {
                'success': success,
                'logs': logs,
                'exit_code': process.returncode
            }

        except Exception as e:
            logger.error(f"Execution error: {e}")
            return {'success': False, 'error': str(e)}