feat: migrate from Docker to pixi for BtToxin_Digger execution
- Add pixi.toml with digger and pipeline environments - Implement PixiRunner class replacing DockerContainerManager - Add run_digger_stage.py for standalone digger execution - Update run_single_fna_pipeline.py to use PixiRunner - Remove docker dependency from pyproject.toml - Delete docker_client.py (no longer needed) BREAKING CHANGE: Docker is no longer required. Use 'pixi install' instead.
This commit is contained in:
@@ -1,405 +0,0 @@
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"""Docker/Podman 容器管理（修正版，支持 arm64/macOS 与 linux/amd64）"""
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from __future__ import annotations
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import os
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import subprocess
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import logging
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import time
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from pathlib import Path
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from typing import Dict, Any, Optional, List
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import sys
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try:
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import docker # type: ignore
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except Exception: # 允许在无 docker SDK 环境下使用 podman fallback
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docker = None # type: ignore
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from ..core.config import settings
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logger = logging.getLogger(__name__)
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def _which(cmd: str) -> Optional[str]:
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from shutil import which
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return which(cmd)
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class DockerContainerManager:
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"""容器管理器 - 兼容 Docker 与 Podman。
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优先尝试 docker SDK；若不可用则回落到 podman CLI（或 docker CLI）。
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在 arm64 主机上默认以 --platform linux/amd64 运行镜像。
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"""
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def __init__(
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self,
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image: str = settings.DOCKER_IMAGE,
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platform: str = settings.DOCKER_PLATFORM,
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) -> None:
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self.image = image
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self.platform = platform
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self._engine: str = "docker"
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self._client = None
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# 首选 docker-py 客户端（若可用）
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if docker is not None:
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try:
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self._client = docker.from_env()
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# 探测 daemon
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self._client.ping()
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self._engine = "docker-sdk"
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except Exception as err:
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logger.info(f"docker SDK 不可用，将尝试 CLI 回落: {err}")
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self._client = None
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# CLI 回落：优先 podman，其次 docker
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if self._client is None:
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if _which("podman"):
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self._engine = "podman-cli"
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elif _which("docker"):
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self._engine = "docker-cli"
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else:
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raise RuntimeError("未找到可用的容器引擎（需要 podman 或 docker）")
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self._ensure_image()
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# ----------------------------- 公共方法 -----------------------------
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def run_command_in_container(
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self,
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command: List[str],
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volumes: Dict[str, Dict[str, str]],
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environment: Optional[Dict[str, str]] = None,
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working_dir: str = "/workspace",
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name: Optional[str] = None,
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detach: bool = False,
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remove: bool = True,
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) -> Dict[str, Any]:
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"""在容器中执行命令，返回执行结果。"""
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# 确保挂载目录存在且可写
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for host_path, spec in volumes.items():
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p = Path(host_path)
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p.mkdir(parents=True, exist_ok=True)
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try:
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p.chmod(0o777)
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except Exception:
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pass
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if self._engine == "docker-sdk" and self._client is not None:
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return self._run_with_docker_sdk(
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command, volumes, environment, working_dir, name, detach, remove
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)
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else:
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return self._run_with_cli(
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command, volumes, environment, working_dir, name, detach, remove
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)
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def update_database(self, log_dir: Path) -> Dict[str, Any]:
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"""在容器中更新 BtToxin_Digger 数据库。"""
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cmd = [
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"/usr/local/env-execute",
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"BtToxin_Digger",
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"--update-db",
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]
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vols = {str(log_dir): {"bind": "/logs", "mode": "rw"}}
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result = self.run_command_in_container(
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command=cmd, volumes=vols, working_dir="/tmp", name=f"bttoxin_update_db_{int(time.time())}"
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)
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if result.get("logs"):
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(log_dir / "update_db.log").write_text(result["logs"], encoding="utf-8")
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return result
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def validate_reads_filenames(
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self,
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input_dir: Path,
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platform: str,
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reads1_suffix: str,
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reads2_suffix: Optional[str] = None,
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suffix_len: int = 0,
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) -> Dict[str, Any]:
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files = list(input_dir.glob("*"))
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if platform == "illumina":
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r1 = [f for f in files if reads1_suffix and reads1_suffix in f.name]
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r2 = [f for f in files if reads2_suffix and reads2_suffix in f.name]
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if not r1 or not r2 or len(r1) != len(r2):
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return {"valid": False, "error": "Illumina R1/R2 配对数量不匹配或缺失"}
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for f1 in r1:
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strain = f1.name.replace(reads1_suffix, "")
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if not (input_dir / f"{strain}{reads2_suffix}").exists():
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return {"valid": False, "error": f"未找到配对文件: {strain}{reads2_suffix}"}
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return {
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"valid": True,
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"strain_count": len(r1),
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"suggested_suffix_len": suffix_len or len(reads1_suffix),
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}
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if platform in ("pacbio", "oxford"):
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r = [f for f in files if reads1_suffix and reads1_suffix in f.name]
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if not r:
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return {"valid": False, "error": f"未找到匹配 {reads1_suffix} 的 reads 文件"}
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return {
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"valid": True,
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"strain_count": len(r),
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"suggested_suffix_len": suffix_len or len(reads1_suffix),
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}
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return {"valid": 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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log_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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bttoxin_db_dir: Optional[Path] = None,
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**kwargs: Any,
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) -> Dict[str, Any]:
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"""在容器中运行 BtToxin_Digger 主分析（单目录方案）。
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Args:
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bttoxin_db_dir: 外部 bt_toxin 数据库目录路径（可选）。
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若提供，将绑定到容器内 /usr/local/bin/BTTCMP_db/bt_toxin，
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覆盖容器内置的旧数据库。目录结构应为：
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bt_toxin/
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├── db/ (BLAST 索引文件)
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└── seq/ (序列源文件)
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"""
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# 1) 在宿主输出目录下准备 input_files，并复制输入文件
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work_input_dir = (output_dir / "input_files").resolve()
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work_input_dir.mkdir(parents=True, exist_ok=True)
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import shutil
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if sequence_type == "nucl":
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pattern = f"*{scaf_suffix}"
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elif sequence_type == "orfs":
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pattern = f"*{kwargs.get('orfs_suffix', '.ffn')}"
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elif sequence_type == "prot":
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pattern = f"*{kwargs.get('prot_suffix', '.faa')}"
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elif sequence_type == "reads":
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pattern = "*"
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else:
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pattern = "*"
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copied_files = 0
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for f in input_dir.glob(pattern):
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if f.is_file():
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shutil.copy2(f, work_input_dir / f.name)
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copied_files += 1
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logger.info(f"已复制 {copied_files} 个输入文件到 {work_input_dir}")
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base_cmd: List[str] = [
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"/usr/local/env-execute",
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"BtToxin_Digger",
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"--SeqPath",
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"/workspace/input_files",
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"--SequenceType",
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sequence_type,
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"--threads",
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str(threads),
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]
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if sequence_type == "nucl":
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base_cmd += ["--Scaf_suffix", scaf_suffix]
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elif sequence_type == "orfs":
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base_cmd += ["--orfs_suffix", kwargs.get("orfs_suffix", ".ffn")]
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elif sequence_type == "prot":
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base_cmd += ["--prot_suffix", kwargs.get("prot_suffix", ".faa")]
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elif sequence_type == "reads":
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platform = kwargs.get("platform", "illumina")
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base_cmd += ["--platform", platform]
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if platform == "illumina":
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r1 = kwargs.get("reads1_suffix", "_R1.fastq.gz")
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r2 = kwargs.get("reads2_suffix", "_R2.fastq.gz")
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sfx = kwargs.get("suffix_len") or len(r1)
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v = self.validate_reads_filenames(work_input_dir, platform, r1, r2, sfx)
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if not v.get("valid"):
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raise ValueError(f"Reads 文件验证失败: {v.get('error')}")
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sfx = v.get("suggested_suffix_len", sfx)
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base_cmd += ["--reads1", r1, "--reads2", r2, "--suffix_len", str(sfx)]
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elif platform in ("pacbio", "oxford"):
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r = kwargs.get("reads1_suffix", ".fastq.gz")
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gsize = kwargs.get("genome_size", "6.07m")
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sfx = kwargs.get("suffix_len") or len(r)
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v = self.validate_reads_filenames(work_input_dir, platform, r, None, sfx)
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if not v.get("valid"):
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raise ValueError(f"Reads 文件验证失败: {v.get('error')}")
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sfx = v.get("suggested_suffix_len", sfx)
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base_cmd += ["--reads1", r, "--genomeSize", gsize, "--suffix_len", str(sfx)]
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elif platform == "hybrid":
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short1 = kwargs.get("short1")
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short2 = kwargs.get("short2")
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long = kwargs.get("long")
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if not all([short1, short2, long]):
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raise ValueError("hybrid 需要 short1/short2/long 三个完整文件名")
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for fn in (short1, short2, long):
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if not (work_input_dir / fn).exists():
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raise ValueError(f"文件不存在: {fn}")
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base_cmd += [
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"--short1",
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short1,
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"--short2",
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short2,
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"--long",
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long,
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"--hout",
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"/workspace/Results/Assembles/Hybrid",
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]
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if kwargs.get("assemble_only"):
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base_cmd.append("--assemble_only")
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# 2) 挂载输出目录（含 input_files）、日志目录、以及可选的外部数据库
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volumes = {
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str(output_dir.resolve()): {"bind": "/workspace", "mode": "rw"},
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str(log_dir.resolve()): {"bind": "/data/logs", "mode": "rw"},
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}
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# 绑定外部 bt_toxin 数据库（覆盖容器内置旧库）
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if bttoxin_db_dir is not None:
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db_path = Path(bttoxin_db_dir).resolve()
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if db_path.exists() and (db_path / "db").exists():
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volumes[str(db_path)] = {
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"bind": "/usr/local/bin/BTTCMP_db/bt_toxin",
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"mode": "ro",
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}
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logger.info(f"绑定外部数据库: {db_path} -> /usr/local/bin/BTTCMP_db/bt_toxin")
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else:
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logger.warning(f"外部数据库目录不存在或结构不完整: {bttoxin_db_dir}")
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logger.info("开始 BtToxin_Digger 分析...")
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final_cmd = base_cmd
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working_dir = "/workspace"
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result = self.run_command_in_container(
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command=final_cmd,
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volumes=volumes,
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working_dir=working_dir,
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name=f"bttoxin_digger_{int(time.time())}",
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)
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# 保存容器日志
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logs_path = log_dir / "digger_execution.log"
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if result.get("logs"):
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logs_path.write_text(result["logs"], encoding="utf-8")
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logger.info(f"容器日志已保存: {logs_path}")
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# 验证输出
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results_dir = output_dir / "Results"
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if result.get("success") and results_dir.exists():
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files = [f for f in results_dir.rglob("*") if f.is_file()]
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result["output_files"] = len(files)
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else:
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result["output_files"] = 0
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return result
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# ----------------------------- 内部实现 -----------------------------
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def _ensure_image(self) -> None:
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if self._engine == "docker-sdk" and self._client is not None:
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try:
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self._client.images.get(self.image)
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return
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except Exception:
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logger.info(f"拉取镜像 {self.image} (platform={self.platform}) ...")
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self._client.images.pull(self.image, platform=self.platform)
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else:
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# CLI 模式：先尝试拉取
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cli = "podman" if self._engine == "podman-cli" else "docker"
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try:
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subprocess.run(
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[cli, "pull", "--platform", self.platform, self.image],
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check=True,
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stdout=subprocess.PIPE,
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stderr=subprocess.STDOUT,
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text=True,
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)
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except Exception as err:
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logger.warning(f"{cli} pull 失败: {err}")
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def _run_with_docker_sdk(
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self,
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command: List[str],
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volumes: Dict[str, Dict[str, str]],
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environment: Optional[Dict[str, str]],
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working_dir: str,
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name: Optional[str],
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detach: bool,
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remove: bool,
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) -> Dict[str, Any]:
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assert self._client is not None
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try:
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# 注意：docker SDK 在 detach=False 时返回的是日志字节串，而非容器对象。
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# 这里统一以 detach=True 运行，然后等待并抓取日志，最后按需删除容器。
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container = self._client.containers.run(
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image=self.image,
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command=command,
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volumes=volumes,
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environment=environment or {},
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working_dir=working_dir,
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platform=self.platform,
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name=name,
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user="0:0", # 以 root 运行，避免挂载目录权限问题
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detach=True,
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remove=False, # 获取日志后再删
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stdout=True,
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stderr=True,
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)
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exit_info = container.wait()
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code = exit_info.get("StatusCode", 1)
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logs = container.logs().decode("utf-8", errors="ignore")
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if remove:
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try:
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container.remove()
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except Exception:
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pass
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return {"success": code == 0, "exit_code": code, "logs": logs, "status": "completed" if code == 0 else "failed"}
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except Exception as e:
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logger.error(f"docker SDK 运行失败: {e}", exc_info=True)
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return {"success": False, "error": str(e), "exit_code": -1, "status": "error"}
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def _run_with_cli(
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self,
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command: List[str],
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volumes: Dict[str, Dict[str, str]],
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environment: Optional[Dict[str, str]],
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working_dir: str,
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name: Optional[str],
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detach: bool,
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remove: bool,
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) -> Dict[str, Any]:
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cli = "podman" if self._engine == "podman-cli" else "docker"
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cmd: List[str] = [cli, "run", "--rm" if remove and not detach else ""]
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cmd = [c for c in cmd if c]
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cmd += ["--platform", self.platform]
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# 以 root 运行，避免权限问题
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cmd += ["--user", "0:0"]
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if name:
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cmd += ["--name", name]
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for host, spec in volumes.items():
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bind = spec.get("bind")
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mode = spec.get("mode", "rw")
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# Podman(Linux) 下附加 :Z 处理 SELinux 标注；其他平台保持不变
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mount_mode = mode
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if self._engine == "podman-cli" and os.name == "posix" and sys.platform.startswith("linux"):
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mount_mode = f"{mode},Z"
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cmd += ["-v", f"{host}:{bind}:{mount_mode}"]
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for k, v in (environment or {}).items():
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cmd += ["-e", f"{k}={v}"]
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cmd += ["-w", working_dir, self.image]
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cmd += command
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try:
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if detach:
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# 后台运行：CLI 简化返回
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p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)
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return {"success": True, "status": "running", "pid": p.pid}
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else:
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proc = subprocess.run(cmd, capture_output=True, text=True)
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out = (proc.stdout or "") + (proc.stderr or "")
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return {"success": proc.returncode == 0, "exit_code": proc.returncode, "logs": out, "status": "completed" if proc.returncode == 0 else "failed"}
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except Exception as e:
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logger.error(f"{cli} 运行失败: {e}", exc_info=True)
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return {"success": False, "error": str(e), "exit_code": -1, "status": "error"}
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Block a user