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- 生信进度:后端新增 stage_progress 事件帧+进度解析白名单(rnaseq_qc/sample_qc), kernel 日志流式落盘(20行/1s flush+fsync),logs 分页端点(offset/limit/eof), 事件 seq 跨重启扫描续增(2026-09-17 断流修复);前端 FlowProgressCard 确定性/ 不确定两态进度条+点击定位到生信任务 TAB,BioJobsPane DAG 行展开滚动日志区 (3s 轮询),log_tail 4000 截断,重跑 stage_started 清零进度 - 图片注入:figures 三源重构(标准DOI图库主路径/遗留体系兜底/PMC兜底), [[FIG:]] 宽松归一化识别 PMC/PMID/DOI 三种形态,引文兜底扩展至 [PMCID:]/[DOI:] 且标记未满配额继续注入,注入预算 90s/10篇(175 实测校准), PMC graphic 无 content-type 宽松正则,空结果不缓存(176 冷连接三连败修复) - QA 启动自愈:start.sh 启动前等 Qdrant readyz(30min)+Neo4j TCP(10min); backend_guard 标签校验改子集判定 - 样本配对:同 inode 去重优先真实文件,R1/R2 归一配对一对一认领 - gitignore 新增 *.bak-*/*.before-*/bioflow_service/bioflow.db 测试:bioflow_service pytest 358/358,前端 bioflow vitest 205/205
262 lines
11 KiB
Python
262 lines
11 KiB
Python
"""app/services/bioflow/events.py —— 进程内事件总线（pub/sub 供 SSE）+ 持久事件日志。
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- 发布：runner/路由在任务状态变化时 publish(type, data)（事件类型清单 = 实施计划 §六
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12 类 + 内部 job_recovered）。
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- 订阅：async queue（供 SSE 端点）；内存环形缓冲（断线重连回放）。
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- 持久：events/{job_id}.jsonl 追加落盘（服务重启恢复回放；FR-BIO-031）。
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- 快照：snapshot(job_id) 构造断线重连首帧（TC-BIO-SSE-022/024）。
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服务层纪律：纯 dataclass/dict/stdlib，无 pydantic。
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"""
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from __future__ import annotations
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import asyncio
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import json
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import logging
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import os
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import threading
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from collections import deque
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from dataclasses import dataclass, field
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from pathlib import Path
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from typing import Any
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logger = logging.getLogger(__name__)
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EVENT_TYPES = (
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"job_created", "plan_ready", "stage_started", "stage_log", "stage_progress",
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"stage_done", "stage_failed", "stage_skipped", "stage_await_confirm",
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"stage_await_files",
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"job_done", "job_paused", "job_archived", "job_recovered",
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# 用户自定义扩展分析事件帧（契约 §4；并行链路，不触碰现有 job_* 语义）
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"extension_created", "extension_build", "extension_trial", "extension_repair",
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"extension_validate", "extension_published", "extension_candidates",
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"extension_confirm", "extension_run_started", "extension_run_log",
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"extension_run_done", "extension_run_failed",
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)
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# 断线重连时需要回放的关键状态事件（含历史事件全量）
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REPLAYABLE_TYPES = set(EVENT_TYPES)
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MEMORY_BUFFER_LIMIT = 500
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SNAPSHOT_TYPE = "snapshot"
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@dataclass(eq=False)
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class Subscriber:
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"""订阅者（eq=False：身份哈希，可入 set）。"""
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queue: asyncio.Queue = field(default_factory=asyncio.Queue)
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last_seq: int = -1
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job_filter: str | None = None
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def _stage_key(s: Any) -> str:
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"""job_created stages 元素 → 阶段名键（str 或 dict 统一；BUG-R1-04）。"""
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if isinstance(s, dict):
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return str(s.get("stage") or "")
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return str(s)
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def _stage_entry(s: Any) -> dict[str, Any]:
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"""job_created stages 元素 → 干净 {stage, status}（dict 保真透传）。
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runner 发布的 job_created.stages 元素为 {stage, status} dict；此前直接
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str(s) 会把 dict repr 串当阶段名（前端进度卡乱串，BUG-R1-04）。
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"""
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if isinstance(s, dict):
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return {"stage": str(s.get("stage") or ""), "status": str(s.get("status") or "waiting")}
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return {"stage": str(s), "status": "waiting"}
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class EventBus:
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"""进程内事件总线：publish → 订阅队列广播 + 内存环形缓冲 + jsonl 持久日志。"""
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def __init__(self, events_dir: str | Path) -> None:
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self.events_dir = Path(events_dir)
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self.events_dir.mkdir(parents=True, exist_ok=True)
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self._subscribers: set[Subscriber] = set()
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self._sub_lock = asyncio.Lock()
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self._buffer: deque[dict[str, Any]] = deque(maxlen=MEMORY_BUFFER_LIMIT)
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# 跨重启 seq 单调递增（BUG-FIX 2026-09-17）：旧进程事件已持久化在
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# events/*.jsonl，重启后 _seq 归零会让新事件 seq 小于浏览器 last_seq
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# 水位，前端回放被过滤、收不到 stage_await_files 等关键帧。
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# 启动时扫描历史日志取最大 seq 作为起始值。
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self._seq = self._scan_max_seq()
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self._file_lock = threading.Lock()
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def _scan_max_seq(self) -> int:
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"""扫描 events_dir 下全部 jsonl，取历史最大 seq（无文件/坏行 → 0）。"""
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max_seq = 0
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try:
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for path in self.events_dir.glob("*.jsonl"):
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try:
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for line in path.read_text(encoding="utf-8").splitlines():
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if not line.strip():
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continue
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try:
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seq = int(json.loads(line).get("seq") or 0)
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except (ValueError, TypeError):
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continue
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if seq > max_seq:
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max_seq = seq
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except OSError:
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continue
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except OSError: # pragma: no cover - 目录扫描失败(权限等)不影响启动
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return 0
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return max_seq
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# ---- 内部 ----
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def _events_file(self, job_id: str) -> Path:
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return self.events_dir / f"{job_id}.jsonl"
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def _append_file(self, event: dict[str, Any]) -> None:
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try:
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job_id = str((event.get("data") or {}).get("job_id") or "")
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with self._file_lock:
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with self._events_file(job_id).open("a", encoding="utf-8") as fh:
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fh.write(json.dumps(event, ensure_ascii=False) + "\n")
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except OSError:
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logger.warning("bioflow events: 持久化失败 %s", event.get("type"))
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# ---- 发布 ----
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def publish(self, event_type: str, data: dict[str, Any]) -> dict[str, Any]:
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"""发布事件（同步）：返回完整事件（含 seq），并唤醒所有订阅者。"""
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if event_type not in EVENT_TYPES:
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raise ValueError(f"未知事件类型: {event_type}")
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self._seq += 1
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event: dict[str, Any] = {
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"type": event_type,
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"seq": self._seq,
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"data": dict(data),
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}
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self._buffer.append(event)
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self._append_file(event)
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# 广播给订阅者（跨线程安全：queue.put_nowait 本身线程安全）
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for sub in list(self._subscribers):
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if sub.job_filter is not None and sub.job_filter != str(data.get("job_id") or ""):
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continue
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try:
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sub.queue.put_nowait(event)
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except asyncio.QueueFull: # pragma: no cover - 防御
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logger.warning("bioflow events: 订阅队列满，丢弃事件 %s", event_type)
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return event
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def publish_async(self, event_type: str, data: dict[str, Any]) -> None:
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"""异步发布（供路由协程调用，publish 本身为同步安全实现）。"""
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self.publish(event_type, data)
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# ---- 订阅（SSE 端点）----
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async def subscribe(self, job_filter: str | None = None, last_seq: int = -1) -> Subscriber:
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sub = Subscriber(last_seq=last_seq, job_filter=job_filter)
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async with self._sub_lock:
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self._subscribers.add(sub)
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return sub
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async def unsubscribe(self, sub: Subscriber) -> None:
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async with self._sub_lock:
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self._subscribers.discard(sub)
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# ---- 断线重连回放 ----
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def snapshot(self, job_id: str) -> dict[str, Any] | None:
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"""构造任务快照（首帧 data.type=snapshot；TC-BIO-SSE-022）。
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从持久日志读该任务全部事件，拼出 job + stages 当前状态。
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事件不存在（未知任务）返回 None。
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"""
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path = self._events_file(job_id)
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if not path.exists():
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return None
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events: list[dict[str, Any]] = []
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try:
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for line in path.read_text(encoding="utf-8").splitlines():
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if not line.strip():
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continue
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try:
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ev = json.loads(line)
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if ev.get("type") in REPLAYABLE_TYPES:
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events.append(ev)
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except ValueError:
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continue
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except OSError:
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return None
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if not events:
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return None
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# 由事件序列推导 job/stages 状态
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job_status = "created"
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stage_states: dict[str, dict[str, Any]] = {}
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for ev in events:
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t, d = ev["type"], ev.get("data") or {}
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if t == "job_created":
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job_status = "created"
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for s in d.get("stages") or []:
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key = _stage_key(s)
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if key:
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stage_states.setdefault(key, _stage_entry(s))
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elif t == "stage_started":
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st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
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st["status"] = "running"
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elif t == "stage_done":
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st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
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st["status"] = "done"
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elif t == "stage_failed":
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st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
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st["status"] = "failed"
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elif t == "stage_skipped":
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st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
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st["status"] = "skipped"
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elif t == "stage_progress":
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st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
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pct = d.get("percent")
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if isinstance(pct, (int, float)):
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st["progress"] = max(float(st.get("progress") or 0.0), float(pct))
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msg = d.get("message")
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if msg:
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st["progressMessage"] = str(msg)
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elif t == "stage_await_confirm":
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st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
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st["status"] = "waiting_confirm"
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elif t == "stage_await_files":
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st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
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st["status"] = "await_files"
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elif t == "job_done":
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job_status = "done"
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elif t == "job_paused":
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job_status = "paused"
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elif t == "job_archived":
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job_status = "archived"
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return {
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"type": SNAPSHOT_TYPE,
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"job_id": job_id,
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"job": {"status": job_status},
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"stages": [stage_states[k] for k in stage_states],
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"last_seq": events[-1]["seq"] if events else 0,
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}
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def replay(self, job_id: str, after_seq: int = -1) -> list[dict[str, Any]]:
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"""回放任务历史事件（seq > after_seq；断线重连补齐；TC-BIO-SSE-023/024）。"""
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path = self._events_file(job_id)
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if not path.exists():
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return []
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out: list[dict[str, Any]] = []
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try:
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for line in path.read_text(encoding="utf-8").splitlines():
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if not line.strip():
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continue
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try:
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ev = json.loads(line)
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if ev.get("type") in REPLAYABLE_TYPES and int(ev.get("seq") or 0) > after_seq:
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out.append(ev)
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except (ValueError, TypeError):
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continue
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except OSError:
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return []
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return out
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def memory_replay(self, after_seq: int = -1) -> list[dict[str, Any]]:
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"""内存环形缓冲回放（进程重启后内存为空，此时走持久回放）。"""
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return [ev for ev in self._buffer if int(ev.get("seq") or 0) > after_seq]
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