134 lines
5.1 KiB
Python
134 lines
5.1 KiB
Python
"""config.py —— 生信服务（bioflow-service 8098）环境变量驱动配置（pydantic-settings）。
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全部键可用环境变量覆盖（前缀 BIOFLOW_；LLM 沿用 docgen 的 DOCGEN_LLM_* 直连模式）。
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零硬编码纪律：不出现任何写死宿主路径；仓库内相对路径按 __file__ 推导 repo 根。
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"""
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from __future__ import annotations
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from functools import lru_cache
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from pathlib import Path
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from pydantic_settings import BaseSettings, SettingsConfigDict
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_REPO_ROOT = Path(__file__).resolve().parent.parent.parent # bioflow_service/.. = 仓库根
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def _resolve_root(v: str) -> str:
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"""仓库内相对路径按 __file__ 推导 repo 根解析为绝对路径。"""
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p = Path(v).expanduser()
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if not p.is_absolute():
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p = _REPO_ROOT / p
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return str(p)
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class Settings(BaseSettings):
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model_config = SettingsConfigDict(
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env_file=".env",
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env_file_encoding="utf-8",
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extra="ignore",
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env_prefix="BIOFLOW_",
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)
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# ---- 应用 ----
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app_name: str = "plantai-bioflow-service"
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version: str = "0.1.0"
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# ---- 阶段→镜像映射（A1 交付物，仓库内 bioflow_kernel/stage_image_map.json）----
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image_map_path: str = "bioflow_kernel/stage_image_map.json"
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# ---- 数据与任务目录 ----
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data_root: str = "bioflow_data" # 生信数据根（hmm/rag_db 等，只读挂载进容器）
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jobs_dir: str = "bioflow_data/jobs" # 任务目录根（input/workspace/events）
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db_path: str = "bioflow_data/bioflow.db" # 独立 SQLite（与 BFF 完全隔离，FR-BIO-028）
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archives_dir: str = "bioflow_data/archives"
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# ---- 执行 ----
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concurrency: int = 3 # 全局并发信号量上限（FR-BIO-031，可配）
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stage_timeout_sec: float = 36000.0 # 单阶段 docker 硬超时（秒，10h）
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docker_image_tag_suffix: str = "dev" # 镜像 tag 后缀（P0 交付物为 :dev）
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host_uid_env: str = "BIOFLOW_HOST_UID" # 宿主机 uid 环境变量名；未设置时回退服务进程 uid
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container_data_dir: str = "/bioflow-data"
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container_input_dir: str = "/job/input"
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container_workspace_dir: str = "/job/workspace"
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default_cpus: str = "4"
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default_memory: str = "32g"
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log_tail_lines: int = 80 # manifest 接口日志尾行数（≤80）
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max_upload_gb: float = 100.0 # 上传大小上限（GB；超限 413）
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upload_ext_allow: str = ".fasta,.fa,.faa,.fna,.pep,.cds,.gz,.gff,.gff3,.gtf,.txt,.tsv,.csv,.xlsx,.xls,.bed,.vcf,.vcf.gz,.bam,.cram,.sam,.hmm,.nwk,.newick,.treefile,.json,.yaml,.yml,.pdf"
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# ---- 规划（planner）----
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llm_plan_timeout: float = 60.0 # 规划 LLM 单次调用超时（秒）
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plan_candidates: int = 3 # 候选路径条数（2~3，FR-BIO-002）
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plan_max_rounds: int = 2 # LLM 输出硬校验失败的最多重试轮数
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# ---- 知识库（vstore/flow.py 本地实例；无 vstore 时自动降级 llm_only）----
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flow_docs_dir: str = "vstore/data/flow_docs"
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# ---- LLM（沿用 docgen deepseek 直连模式，DOCGEN_LLM_* 键）----
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docgen_llm_base_url: str = "https://api.deepseek.com/v1"
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docgen_llm_api_key: str = ""
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docgen_llm_model: str = "deepseek-chat"
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docgen_llm_timeout: float = 300.0
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# ---- 报告登记（BFF 反代端点；空=未配置，登记降级为仅落表）----
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service_url: str = "http://127.0.0.1:8098"
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# ---- 容器环境变量（BBA_*；零硬编码：路径全部从本配置推导）----
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@property
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def bba_env(self) -> dict[str, str]:
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"""docker run 注入的 BBA_* 环境（值全部来自配置推导，无写死宿主路径）。"""
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return {
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"BBA_PFAM_DIR": f"{self.container_data_dir}/hmm",
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"BBA_RAG_MAPPING_FILE": f"{self.container_data_dir}/rag_db/pfam_mapping.json",
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"BBA_DISABLE_RAG_PFAM_LOOKUP": "0",
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}
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@property
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def host_uid(self) -> int:
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"""--user 注入 uid：BIOFLOW_HOST_UID 环境变量优先，否则服务进程 uid。"""
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import os
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raw = os.environ.get(self.host_uid_env, "").strip()
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if raw:
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try:
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return int(raw)
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except ValueError:
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pass
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return os.getuid()
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@property
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def image_map_abs(self) -> str:
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return _resolve_root(self.image_map_path)
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@property
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def data_root_abs(self) -> str:
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return _resolve_root(self.data_root)
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@property
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def jobs_dir_abs(self) -> str:
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return _resolve_root(self.jobs_dir)
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@property
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def db_path_abs(self) -> str:
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return _resolve_root(self.db_path)
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@property
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def archives_dir_abs(self) -> str:
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return _resolve_root(self.archives_dir)
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@property
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def flow_docs_dir_abs(self) -> str:
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return _resolve_root(self.flow_docs_dir)
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@property
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def upload_ext_set(self) -> set[str]:
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return {ext.strip().lower() for ext in self.upload_ext_allow.split(",") if ext.strip()}
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@lru_cache(maxsize=1)
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def get_settings() -> Settings:
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return Settings()
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settings = get_settings()
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