Refactor: Unified pipeline execution, simplified UI, and fixed Docker config
- 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.
This commit is contained in:
zly
@@ -1,19 +1,4 @@
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from celery import Celery
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from .config import settings
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celery_app = Celery(
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"bttoxin",
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broker=settings.get_celery_broker_url(),
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backend=settings.get_celery_result_backend(),
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)
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celery_app.conf.update(
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task_track_started=True,
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worker_prefetch_multiplier=1,
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)
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"""Celery 配置"""
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"""Celery Configuration"""
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from celery import Celery
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from ..config import settings
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@@ -1,72 +0,0 @@
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"""Docker 客户端管理"""
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import docker
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from typing import Dict, Any
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from pathlib import Path
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import logging
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logger = logging.getLogger(__name__)
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class DockerManager:
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"""Docker 容器管理器"""
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def __init__(self, image: str = None):
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from ..config import settings
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self.client = docker.from_env()
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self.image = image or settings.DOCKER_IMAGE
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def ensure_image(self) -> bool:
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"""确保镜像存在"""
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try:
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self.client.images.get(self.image)
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return True
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except docker.errors.ImageNotFound:
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logger.info(f"Pulling image {self.image}...")
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self.client.images.pull(self.image)
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return True
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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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"""运行 BtToxin_Digger"""
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self.ensure_image()
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volumes = {
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str(input_dir.absolute()): {'bind': '/data', 'mode': 'ro'},
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str(output_dir.absolute()): {'bind': '/results', 'mode': 'rw'}
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}
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command = [
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"/usr/local/env-execute", "BtToxin_Digger",
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"--SeqPath", "/data",
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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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try:
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container = self.client.containers.run(
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self.image,
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command=command,
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volumes=volumes,
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platform="linux/amd64",
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detach=True,
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remove=False
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)
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result = container.wait()
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logs = container.logs().decode('utf-8')
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container.remove()
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return {
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'success': result['StatusCode'] == 0,
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'logs': logs,
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'exit_code': result['StatusCode']
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}
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except Exception as e:
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logger.error(f"Error: {e}")
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return {'success': False, 'error': str(e)}
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73
backend/app/core/tool_runner.py
Normal file
73
backend/app/core/tool_runner.py
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@@ -0,0 +1,73 @@
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"""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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