c75c85c53b
- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency. - Backend: Changed output format to ZIP and added auto-cleanup of intermediate files. - Backend: Fixed language parameter passing in API and tasks. - Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views. - Frontend: Implemented simulated progress bar for better UX. - Frontend: Restored One-click load button and added result file structure documentation. - Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml. - Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.
74 lines
2.3 KiB
Python
74 lines
2.3 KiB
Python
"""本地工具运行器 - 替代 Docker 调用"""
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import subprocess
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import logging
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from pathlib import Path
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from typing import Dict, Any
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import os
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logger = logging.getLogger(__name__)
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class ToolRunner:
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"""本地工具运行管理器"""
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def run_bttoxin_digger(
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self,
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input_dir: Path,
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output_dir: Path,
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sequence_type: str = "nucl",
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scaf_suffix: str = ".fna",
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threads: int = 4
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) -> Dict[str, Any]:
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"""
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在本地环境运行 BtToxin_Digger
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使用 'pixi run -e digger' 激活环境
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"""
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# Ensure output directory exists
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output_dir.mkdir(parents=True, exist_ok=True)
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# BtToxin_Digger expects to read files from --SeqPath.
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# It scans the directory for files matching *suffix.
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# We point it to the input directory.
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seq_path = input_dir.absolute()
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# Construct command
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# Note: We run this from output_dir so 'Results/' are created there.
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command = [
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"pixi", "run", "-e", "digger", "BtToxin_Digger",
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"--SeqPath", str(seq_path),
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"--SequenceType", sequence_type,
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"--Scaf_suffix", scaf_suffix,
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"--threads", str(threads)
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]
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logger.info(f"Running command: {' '.join(command)}")
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logger.info(f"Working directory: {output_dir}")
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try:
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# Run subprocess
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# Capture both stdout and stderr
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process = subprocess.run(
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command,
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cwd=str(output_dir),
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capture_output=True,
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text=True,
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check=False,
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env=os.environ.copy() # Inherit env vars (PATH, etc)
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)
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success = (process.returncode == 0)
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logs = f"STDOUT:\n{process.stdout}\n\nSTDERR:\n{process.stderr}"
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if not success:
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logger.error(f"BtToxin_Digger failed with exit code {process.returncode}")
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logger.error(process.stderr)
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return {
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'success': success,
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'logs': logs,
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'exit_code': process.returncode
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}
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except Exception as e:
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logger.error(f"Execution error: {e}")
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return {'success': False, 'error': str(e)}
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