chore(deploy): 新增 bioflow_switch_restart.sh 切分支→重启→验证规范脚本

- A 地基: bioflowctl CLI 抽取 + M0 六条数据保护 gap (G1-G6)
- B: 结构化错误对象 G13 + MCP 薄适配
- D: 契约与就绪 G7-G11/G14/G15 (数据角色/下游直入/单一schema/就绪检查/任务绑定/错误分类/恢复预算)
- E: 版本化 G16-G20 (plan_revision/影响范围/历史不覆盖/防重复/执行所有权)
- F: 交付 G21-G23 (交付清单/报告范围/资源预算)
- C: 11 分析控制工具 + SKILL.md + install/uninstall (G12)
- UI: 4 张新增卡 (就绪检查/诊断/版本化修改/交付清单)
- 测试: 后端 724 + QA 167 + 前端 176 passed, 红线 pipeline.py/answer_composer.py 零修改

.gitignore

@@ -45,3 +45,5 @@ paper_writer_service/paper.log
 
 # 部署方案文档（含主机凭据，不入库）
 docs/DEPLOY_PAPER_176.md
+# Python 覆盖率运行时产物(coverage.py --cov 生成)
+.coverage

agent/qa/configs/capabilities.yaml

@@ -16,3 +16,70 @@ capabilities:
       endpoint: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
       method: GET
       timeout: 8
+
+  # ---- 生信能力单元（S1）：两个 MCP 端点，各自独立装卸 ----
+  - name: bioflow-gene-family
+    provider: mcp
+    permission: read_only
+    description: 基因家族分析（路径规划/建任务/参数确认/文件获取与预处理/状态查询），自然语言触发
+    session_default: true
+    nl_triggers:
+      - 基因家族
+      - 家族成员
+      - 亚家族
+      - 系统发育
+      - 建树
+      - 进化树
+      - 保守基序
+      - motif
+      - 结构域
+      - 基因结构
+      - 共线性
+      - Ka/Ks
+      - 选择压力
+      - 组合证据
+    mcp:
+      url: http://127.0.0.1:8098/mcp/gene-family/
+    prompt_pack:
+      file: bioflow_gene_family_agent_rules.md
+
+  - name: bioflow-rnaseq
+    provider: mcp
+    permission: read_only
+    description: 转录组分析（实验设计确认/样本配置/路径规划/建任务/差异表达/富集），自然语言触发
+    session_default: true
+    nl_triggers:
+      - 转录组
+      - RNA-seq
+      - RNAseq
+      - rnaseq
+      - 差异表达
+      - 表达定量
+      - 富集
+      - WGCNA
+      - GSEA
+      - 实验设计
+      - fastq
+    mcp:
+      url: http://127.0.0.1:8098/mcp/rnaseq/
+    prompt_pack:
+      file: bioflow_rnaseq_agent_rules.md
+
+  # ---- 生信能力单元（S4）：第三个 MCP 端点，用户自定义扩展分析 ----
+  - name: bioflow-extension
+    provider: mcp
+    permission: read_only
+    description: 用户自定义扩展分析（创建/转换/试运行/校验/发布/运行），自然语言触发
+    session_default: true
+    nl_triggers:
+      - 扩展
+      - 拓展分析
+      - 扩展分析
+      - 自定义分析
+      - 分析模板
+      - 分析脚本
+      - 分析工具
+    mcp:
+      url: http://127.0.0.1:8098/mcp/extension/
+    prompt_pack:
+      file: bioflow_extension_agent_rules.md

agent/qa/env/prod.env.example

@@ -31,3 +31,6 @@ QA_V1_WEB_SEARCH_MAX_RESULTS=4
 QA_V1_WEB_SEARCH_TIMEOUT=8
 QA_V1_WEB_SEARCH_MAX_CHARS=1200
 QA_V1_ENABLE_SUPERPOWERS=1
+
+# 生信对话式能力熔断开关（S1）：默认关（=0）。置 1 才启用 QA 前门 bioflow_agent。
+QA_V1_ENABLE_BIOFLOW_AGENT=0

agent/qa/prompts/bioflow_extension_agent_rules.md

@@ -0,0 +1,31 @@
+# 用户自定义扩展分析对话规范（bioflow_extension_agent_rules）
+
+你是用户自定义扩展分析助手。引导用户把一段可运行的分析脚本/工具，通过「创建 → AI 转换 → 试运行 → 校验 → 确认 → 发布 → 运行」流程，做成 PlantAI 可自然语言触发的自定义扩展。
+
+## 对话节奏（自然语言主导 + 卡片辅助）
+每次需要用户输入/选择时，遵循固定节奏：
+1. 先用自然语言说明并列表展示需要什么；
+2. 提示用户可用卡片快捷操作，也可直接打字（两条通道语义一致）；
+3. 用户回答后，用自然语言复述，确认无误再继续。
+
+## 创建（create_extension）
+- 需要用户提供：显示名、运行命令、代码文件（可上传/粘贴文本内容）、运行时镜像、可选测试数据/金标。
+- 代码文件以「路径 + 文本内容」提交；引导用户说明脚本是做什么的、依赖什么。
+
+## AI 转换与校验（build → trial_run → validate）
+- 创建后调用 build 做 AI 转换（原始命令 → command_template + 参数 + 依赖），失败时规则版兜底。
+- 转换结果先向用户说明（识别到的参数/依赖/输入角色），请用户确认参数名与默认值。
+- 试运行/校验的结果要转述给用户，失败时说明原因并引导修复（repair 循环）。
+
+## 确认与发布（confirm_extension → publish_extension）
+- 确认前请用户确认触发词（nl_triggers）与参数——触发词决定用户以后说什么话能唤起这个扩展。
+- 发布后扩展才可被自然语言触发运行；发布是不可逆的对外可用状态，须经用户确认。
+
+## 运行（run_extension）
+- 仅已发布扩展可运行；运行参数须在白名单内（参数 schema），未知参数明确追问。
+- 运行结果（run_result）转述给用户。
+
+## 其它
+- 工具名/参数名/内部实现一律不外泄；
+- 状态不确定时主动查 extension_status 并向用户转述当前阶段与下一步；
+- 人工确认边界（确认触发词、发布）不可跳过、不可代用户拍板。

agent/qa/prompts/bioflow_gene_family_agent_rules.md

@@ -0,0 +1,32 @@
+# 基因家族分析对话规范（bioflow_gene_family_agent_rules）
+
+你是基因家族分析助手。用自然语言引导用户从需求到分析完成，全程对话式交互。
+
+## 人工确认边界（不可跳过、不可代确认）
+- **subfamily_confirm（亚家族预测人工确认）是硬性人工边界**：系统预测的亚家族划分结果，
+  必须停下来请用户查看并确认或修改。你绝不能代用户确认，也不能在用户未确认前继续下游分析。
+- 用户提出修改（如"把某成员从亚家族 A 移到亚家族 B"）时，先复述修改内容，再请用户做最终确认。
+
+## 对话节奏（自然语言主导 + 卡片辅助）
+每次需要用户输入/选择时，遵循固定节奏：
+1. 先用自然语言说明并**列表展示**选项及含义；
+2. 提示用户可用卡片快捷操作，也可直接打字回复（两条通道语义一致）；
+3. 用户选择后，用自然语言**复述**其选择，确认无误再继续。
+
+## 路径规划与建任务
+- 规划后列出"核心流程（必选）+ 可选分析"候选路径，说明每个可选分析的生物学意义；
+- **建任务前必须经用户确认阶段链**，收到确认后再创建任务，绝不擅自建任务。
+
+## 文件获取与预处理
+- 源文件支持上传、http/https 链接、OSS 地址、局域网机器路径；
+- 文件到达后先探测格式，**格式异常（如 Excel/文本）时先向用户说明列结构并提问确认**
+  （哪列是序列、是否去重、是否去表头等），再由模型整理成 fasta/gff 等标准格式；
+- 转换结果过格式验证，失败时说明问题并追问修正（循环不超过 3 次后建议人工整理）。
+
+## 参数确认
+- 列"参数名（默认值，含义）"请用户确认或修改；未识别参数时明确指出并给出允许范围。
+
+## 其它
+- 工具名、参数名、内部实现一律不外泄；
+- 任务运行中用户提问（流程/参数/生物学意义）随时回答，不打断任务；
+- 卡住或不确定时主动查询任务状态，向用户转述当前进度与下一步。

agent/qa/prompts/bioflow_rnaseq_agent_rules.md

@@ -0,0 +1,29 @@
+# 转录组分析对话规范（bioflow_rnaseq_agent_rules）
+
+你是转录组分析助手。用自然语言引导用户从实验设计确认到差异表达/富集分析完成。
+
+## 人工确认边界（不可跳过、不可代确认）
+- **实验设计确认（rnaseq_de 之前的必确认信息）是硬性边界**：开始分析前必须与用户确认——
+  ① 物种与参考基因组版本；② 每个样本的 FASTQ（上传/链接/局域网路径）及单端双端；
+  ③ 对照组/处理组各几个重复、有无时间点/批次；④ 建库是否链特异性。
+- 统计模型正确性依赖上述信息，未确认前不得创建差异表达任务，也不能代用户拍板基线/比较方向。
+
+## 对话节奏（自然语言主导 + 卡片辅助）
+每次需要用户输入/选择时，遵循固定节奏：
+1. 先用自然语言说明并**列表展示**必确认信息与可选分析；
+2. 提示用户可用卡片快捷操作，也可直接打字回复（两条通道语义一致）；
+3. 用户回答后，用自然语言**复述**其样本设计与选择（如"干旱 3 vs 对照 3，双端，非链特异，对照为基线"），
+   确认无误再继续。
+
+## 样本配置与文件预处理
+- 用户用自然语言描述样本时，可解析生成 samples.yaml（样本名/对照处理组/重复/单双端）；
+- FASTQ 支持上传、http/https 链接、OSS 地址、局域网路径；核对成对完整；
+- 非 FASTQ 的输入文件（表格/文本等）先探测格式，**异常时先说明列结构并提问确认**，再整理为可用格式。
+
+## 参数确认
+- 列"参数名（默认值，含义）"请用户确认或修改；未识别参数时明确指出并给出允许范围。
+
+## 其它
+- 工具名、参数名、内部实现一律不外泄；
+- 任务运行中用户提问（流程/参数/实验设计意义）随时回答，不打断任务；
+- 卡住或不确定时主动查询任务状态，向用户转述当前进度与下一步（含样本质控 PCA、差异基因数目等结果转述）。

agent/qa/src/rag/qa_v1_1_73/api.py

@@ -13,6 +13,7 @@ from fastapi.responses import StreamingResponse
 from pydantic import BaseModel, Field
 
 from . import __version__
+from .bioflow_agent import try_bioflow_agent
 from .config import QAConfig
 from .pipeline import QAAnswerError, QAV1Pipeline
 
@@ -47,6 +48,9 @@ class QARequest(BaseModel):
     # ---- Capability Gateway（S1）：纯数据字段，无 validator（Cython 编译安全）----
     history: List[Dict[str, str]] = Field(default_factory=list)
     capabilities: Dict[str, Any] = Field(default_factory=dict)
+    # ---- Bioflow 对话式编排（S2）：卡片回填协议 + session↔job 绑定 ----
+    card_result: Optional[Dict[str, Any]] = None
+    bioflow: Optional[Dict[str, Any]] = None
 
 
 @lru_cache(maxsize=1)
@@ -150,6 +154,18 @@ async def chat(request: QARequest) -> Dict[str, Any]:
             detail={"error_code": "llm_unavailable", "answer": "", "message": "Final-answer LLM is not configured"},
         )
     try:
+        # ---- Bioflow Agent 前门（S1）：命中则短路返回，否则走原 pipeline ----
+        bioflow_result = await asyncio.to_thread(
+            try_bioflow_agent,
+            request.question,
+            llm_client=pipeline.llm,
+            history=request.history,
+            capabilities=request.capabilities,
+            card_result=request.card_result,
+            bioflow=request.bioflow,
+        )
+        if bioflow_result is not None:
+            return bioflow_result
         ablation = dict(request.ablation or {})
         ablation["use_final_llm"] = True
         return await asyncio.to_thread(
@@ -216,6 +232,19 @@ async def chat_stream(request: QARequest) -> StreamingResponse:
 
     def run() -> None:
         try:
+            # ---- Bioflow Agent 前门（S1）：命中则短路，否则走原 pipeline ----
+            bioflow_result = try_bioflow_agent(
+                request.question,
+                llm_client=pipeline.llm,
+                history=request.history,
+                capabilities=request.capabilities,
+                card_result=request.card_result,
+                bioflow=request.bioflow,
+                progress_callback=emit,
+            )
+            if bioflow_result is not None:
+                events.put(("complete", bioflow_result))
+                return
             ablation = dict(request.ablation or {})
             ablation["use_final_llm"] = True
             result = pipeline.answer(

agent/qa/src/rag/qa_v1_1_73/bioflow_agent.py

@@ -0,0 +1,684 @@
+from __future__ import annotations
+
+"""bioflow_agent.py —— 生信 MCP 能力前门路由（S1 + S2）。
+
+S1：三重门（会话开关/注册表/意图预筛）→ ToolRunner 工具循环 → 自然语言转述。
+S2：对话式编排闭环——card_result 卡片回填协议 + session↔job 绑定 + 多轮记忆
+    + 参数抽取闭环 + job_status 主动查询转述。
+
+card_result 协议（前端卡片操作 → 结构化用户消息 → QA 流）：
+    {card: path_selection|form_confirm|file_upload|archive_choice, payload: {...}}
+    BioflowAgent 读取后经工具执行，再自然语言复述；卡片与自然语言两条通道在
+    服务端语义一致（QA 对话状态机是唯一决策点）。
+
+session↔job 绑定：BFF sessions.meta.bioflow = {active_job_id, chain}，经请求
+    body["bioflow"] 注入（含 session_id）；job_status 工具是任务真相唯一权威。
+
+金标路径零改动：任何不命中/异常都返回 None 回退原 pipeline。
+"""
+import json
+import logging
+import os
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Tuple
+
+from .capabilities.manifests import CapabilityManifest
+from .capabilities.providers import PromptPackProvider, get_dispatcher
+from .capabilities.registry import get_registry
+from .tool_runner import ToolRunner, make_llm_complete
+
+LOGGER = logging.getLogger(__name__)
+
+# 三个生信能力单元（与 bioflow_service 三个 MCP 端点一一对应）
+BIOFLOW_CAPABILITY_NAMES = ("bioflow-gene-family", "bioflow-rnaseq", "bioflow-extension")
+ENV_FUSE = "QA_V1_ENABLE_BIOFLOW_AGENT"
+MAX_ROUNDS = 5
+
+# card_result 卡片类型（S2 前端卡片回填协议）
+CARD_PATH_SELECTION = "path_selection"
+CARD_FORM_CONFIRM = "form_confirm"
+CARD_FILE_UPLOAD = "file_upload"
+CARD_ARCHIVE_CHOICE = "archive_choice"
+CARD_EXTENSION_ACTION = "extension_action"  # S4：扩展能力单元操作（build/trial/validate/confirm/publish/run）
+CARD_TYPES = (CARD_PATH_SELECTION, CARD_FORM_CONFIRM, CARD_FILE_UPLOAD, CARD_ARCHIVE_CHOICE, CARD_EXTENSION_ACTION)
+
+# chain 名 → 能力名（建任务时选择哪条链的 create 工具）
+_CHAIN_TO_CAPABILITY = {
+    "gene_family": "bioflow-gene-family",
+    "rnaseq": "bioflow-rnaseq",
+}
+
+
+def _chain_to_capability(chain: str) -> Optional[str]:
+    """把 chain 名（gene_family/rnaseq）映射为能力名；未知返回 None。"""
+    return _CHAIN_TO_CAPABILITY.get(str(chain or "").strip().lower())
+
+_SYSTEM_BASE = (
+    "你是 PlantAI 生信分析助手，用自然语言引导用户完成基因家族或转录组分析。\n"
+    "你可以调用生信工具完成规划、建任务、确认参数、登记文件、查状态等操作。\n"
+    "硬性规则：\n"
+    "1. 回复只使用自然语言，绝不向用户泄露工具名、参数名或内部实现细节。\n"
+    "2. 需要用户提供文件/参数/做选择时，先自然语言说明并列表展示选项与含义，再请用户回答，"
+    "绝不擅自替用户做不可逆决策。\n"
+    "3. 人工确认边界（基因家族 subfamily_confirm、转录组实验设计确认）不可跳过、不可代用户确认。\n"
+    "4. 任务运行中可随时回答流程/参数/生物学意义类问题；卡住或不确定时主动查询任务状态，"
+    "再向用户转述当前进度与下一步（等待文件、等待参数确认、失败可重跑等）。\n"
+    "5. 文件格式异常时先向用户说明并提问确认，再由用户决定如何处理。\n"
+    "6. 用户用自然语言给出参数（如「用 8 核、padj 用 0.01」）时，抽取为结构化参数后经确认步骤提交；"
+    "只提交白名单内的参数名，未知参数明确指出并追问（最多 3 次）。\n"
+    "7. 若用户消息是对上一轮卡片/提问的确认或选择，先复述用户的选择，确认无误再执行对应动作。\n"
+)
+
+
+def _env_enabled() -> bool:
+    """门 1：QA_V1_ENABLE_BIOFLOW_AGENT 熔断开关。默认关（未设置 = 关）。"""
+    raw = os.environ.get(ENV_FUSE)
+    return raw is not None and str(raw).strip().lower() in {"1", "true", "yes", "on"}
+
+
+def _intent_match(question: str, triggers: List[str]) -> bool:
+    """门 3：意图预筛——问句是否命中任一触发词（大小写不敏感子串匹配）。"""
+    if not triggers:
+        return False
+    q = (question or "").lower()
+    return any(t and t.lower() in q for t in triggers)
+
+
+def _registered_capabilities(capabilities: Optional[Dict[str, Any]]) -> List[CapabilityManifest]:
+    """注册表 + 会话开关：返回所有已注册且会话开启的生信能力 manifest（不判意图）。"""
+    try:
+        registry = get_registry()
+    except Exception as exc:  # noqa: BLE001
+        LOGGER.warning("bioflow agent: registry 访问失败，回退原 pipeline: %s", exc)
+        return []
+    session_caps = capabilities or {}
+    out: List[CapabilityManifest] = []
+    for name in BIOFLOW_CAPABILITY_NAMES:
+        try:
+            spec = registry.get(name)
+        except Exception as exc:  # noqa: BLE001
+            LOGGER.warning("bioflow agent: registry.get(%s) 失败: %s", name, exc)
+            continue
+        if spec is None:
+            continue  # 未注册
+        manifest = spec.manifest
+        if not bool(session_caps.get(name, manifest.session_default)):
+            continue  # 会话开关关
+        out.append(manifest)
+    return out
+
+
+def _candidate_capabilities(
+    question: str,
+    capabilities: Optional[Dict[str, Any]],
+) -> List[CapabilityManifest]:
+    """门 2 + 门 3：注册表 + 会话开关 + 意图预筛，返回命中的候选能力清单。"""
+    return [
+        m for m in _registered_capabilities(capabilities)
+        if _intent_match(question, m.nl_triggers)
+    ]
+
+
+def _build_tools(
+    manifests: List[CapabilityManifest],
+) -> Tuple[List[Dict[str, Any]], Dict[str, CapabilityManifest]]:
+    """经 MCP list_tools 发现各能力工具，构造 LLM 工具表 + ToolRunner manifests。
+
+    返回 (tools, tool_manifests)：
+      - tools: OpenAI function schema 列表（真实 server 工具名/描述/入参 schema）
+      - tool_manifests: {真实工具名: manifest}，manifest.name=能力名（共享连接），
+        mcp.tool=真实工具名
+
+    多能力同时命中时：专有工具名本就不同，各自保留；共享工具（两端点语义一致）
+    按名去重，只保留首个能力的一份，避免 LLM tools 重名 + 同名覆盖。
+    """
+    dispatcher = get_dispatcher()
+    tools: List[Dict[str, Any]] = []
+    tool_manifests: Dict[str, CapabilityManifest] = {}
+    for cap_manifest in manifests:
+        url = str((cap_manifest.config.get("mcp") or {}).get("url") or "").strip()
+        if not url:
+            LOGGER.warning("bioflow agent: 能力 %s 缺 mcp.url，跳过", cap_manifest.name)
+            continue
+        try:
+            discovered = dispatcher.list_mcp_tools(cap_manifest)
+        except Exception as exc:  # noqa: BLE001
+            LOGGER.warning("bioflow agent: 能力 %s MCP 工具发现失败: %s", cap_manifest.name, exc)
+            continue
+        for item in discovered:
+            tool_name = str(item.get("name") or "").strip()
+            if not tool_name:
+                continue
+            if tool_name in tool_manifests:
+                # 共享工具去重（见 S1 修复说明）
+                continue
+            input_schema = item.get("input_schema") or {}
+            if not isinstance(input_schema, dict):
+                input_schema = {"type": "object", "properties": {}}
+            tools.append(
+                {
+                    "type": "function",
+                    "function": {
+                        "name": tool_name,
+                        "description": str(item.get("description") or "")[:1000],
+                        "parameters": input_schema,
+                    },
+                }
+            )
+            tool_manifests[tool_name] = CapabilityManifest(
+                name=cap_manifest.name,
+                provider="mcp",
+                permission="read_only",
+                description=str(item.get("description") or ""),
+                config={"mcp": {"url": url, "tool": tool_name}},
+            )
+    return tools, tool_manifests
+
+
+def _build_system(manifests: List[CapabilityManifest]) -> str:
+    """基础系统提示 + 各能力对话规范（prompt_pack 注入）。"""
+    qa_root = Path(os.environ.get("GENE_FAMILY_ROOT", "/data/gene-family-mas-v2"))
+    parts = [_SYSTEM_BASE]
+    seen: set[str] = set()
+    for manifest in manifests:
+        file_name = str((manifest.config.get("prompt_pack") or {}).get("file") or "").strip()
+        if not file_name or file_name in seen:
+            continue
+        seen.add(file_name)
+        try:
+            text = PromptPackProvider.load(manifest, qa_root)
+        except Exception as exc:  # noqa: BLE001
+            LOGGER.warning("bioflow agent: prompt_pack 加载失败 %s: %s", file_name, exc)
+            text = ""
+        if text:
+            parts.append(text)
+    return "\n\n".join(parts)
+
+
+# ---------------------------------------------------------------------------
+# S2 工具执行 / 转述 / 参数抽取 辅助
+# ---------------------------------------------------------------------------
+
+
+def _execute_tool(
+    tool_manifests: Dict[str, CapabilityManifest], tool_name: str, arguments: Dict[str, Any]
+) -> str:
+    """执行单个工具，返回结果文本（异常转文本，不炸主流程）。"""
+    manifest = tool_manifests.get(tool_name)
+    if manifest is None:
+        return f"工具 {tool_name} 未注册"
+    try:
+        return get_dispatcher().execute(manifest, arguments)
+    except Exception as exc:  # noqa: BLE001
+        return f"工具执行失败: {type(exc).__name__}: {exc}"
+
+
+def _paraphrase(llm_client: Any, user_text: str, system: Optional[str] = None) -> str:
+    """把工具执行结果转述为自然语言（LLM 优先，失败回退原文，绝不抛异常）。"""
+    system = system or (
+        "你是 PlantAI 生信分析助手。把下面的工具执行结果转述为对用户的自然语言回复，"
+        "绝不提及工具名/参数名/内部实现；需要用户下一步操作时明确说明。"
+    )
+    try:
+        text = llm_client.complete(system, user_text, temperature=0.2, max_tokens=600)
+        if text and str(text).strip():
+            return str(text).strip()
+    except Exception as exc:  # noqa: BLE001
+        LOGGER.warning("bioflow agent: paraphrase LLM 失败，回退原文: %s", exc)
+    return str(user_text or "").strip()
+
+
+def _extract_params(
+    llm_client: Any, user_text: str, form_defaults: Dict[str, Any]
+) -> Tuple[Dict[str, Any], List[str]]:
+    """LLM 抽取用户自然语言中的阶段确认参数 → (已识别参数, 未识别参数列表)。
+
+    白名单 = form_defaults 的键；未识别参数（不在白名单）单独返回供追问（≤3 次）。
+    参照 extension_llm 的「LLM 出 JSON → 白名单净化」模式，LLM 失败/坏 JSON 返回空。
+    """
+    whitelist = {str(k) for k in (form_defaults or {}).keys()}
+    if not whitelist:
+        return {}, []
+    system = (
+        "你是参数抽取助手。从用户的话中抽取阶段确认参数，只输出 JSON。\n"
+        '输出形态：{"params": {"<参数名>": <值>}, "unknown": ["<未识别参数名>"]}。\n'
+        f"允许的参数名（白名单）：{', '.join(sorted(whitelist))}。\n"
+        "只抽取用户明确提到的参数；不在白名单里的参数名放进 unknown。"
+    )
+    try:
+        raw = llm_client.complete_json(system, user_text, max_tokens=500)
+    except Exception as exc:  # noqa: BLE001
+        LOGGER.warning("bioflow agent: 参数抽取 LLM 失败: %s", exc)
+        return {}, []
+    if not isinstance(raw, dict):
+        return {}, []
+    params = raw.get("params") if isinstance(raw.get("params"), dict) else {}
+    known = {str(k): v for k, v in params.items() if str(k) in whitelist}
+    unknown_raw = raw.get("unknown") or []
+    if isinstance(unknown_raw, str):
+        unknown_raw = [unknown_raw]
+    unknown = [str(x).strip() for x in unknown_raw if isinstance(x, str) and str(x).strip()]
+    return known, unknown
+
+
+def _try_parse_json(text: str) -> Optional[Any]:
+    if not text:
+        return None
+    try:
+        return json.loads(text)
+    except (json.JSONDecodeError, ValueError):
+        return None
+
+
+def _extract_job_id(result_text: str) -> Optional[str]:
+    """从 create_job 工具结果文本里提取 job_id（结果形如 {"ok":true,"data":{"id":...}}）。"""
+    data = _try_parse_json(result_text)
+    if isinstance(data, dict):
+        inner = data.get("data") if isinstance(data.get("data"), dict) else data
+        jid = inner.get("id") or inner.get("job_id")
+        if jid:
+            return str(jid)
+    return None
+
+
+def _query_job_status(job_id: str, tool_manifests: Dict[str, CapabilityManifest], llm_client: Any) -> str:
+    """主动查 job_status 并转述（任务真相唯一权威）。"""
+    result = _execute_tool(tool_manifests, "job_status", {"job_id": job_id})
+    return _paraphrase(llm_client, f"查询任务状态的结果：\n{result}")
+
+
+def _empty_audit() -> Dict[str, Any]:
+    return {"rounds": 0, "tool_calls": 0, "used_json_fallback": False, "tool_names": [], "errors": []}
+
+
+def _make_payload(
+    question: str,
+    answer: str,
+    *,
+    audit: Optional[Dict[str, Any]] = None,
+    capabilities: Optional[List[str]] = None,
+    active_job_id: Optional[str] = None,
+    chain: Optional[str] = None,
+) -> Dict[str, Any]:
+    payload: Dict[str, Any] = {
+        "success": True,
+        "version": "bioflow-agent-s2",
+        "question": question,
+        "answer": answer,
+        "sources": [],
+        "source_count": 0,
+        "citation_validation": {"valid": True, "cited_pmids": [], "unknown_pmids": []},
+        "bioflow": {
+            "handled": True,
+            "audit": audit or _empty_audit(),
+            "capabilities": capabilities or [],
+        },
+    }
+    if active_job_id:
+        payload["bioflow"]["active_job_id"] = str(active_job_id)
+    if chain:
+        payload["bioflow"]["chain"] = str(chain)
+    return payload
+
+
+# ---------------------------------------------------------------------------
+# card_result 回填处理（S2）
+# ---------------------------------------------------------------------------
+
+
+def _card_path_selection(
+    payload: Dict[str, Any], llm_client: Any, bioflow: Dict[str, Any], tool_manifests: Dict[str, CapabilityManifest]
+) -> Optional[Dict[str, Any]]:
+    """路径卡确认 → create_*_job → 复述；带 reuse_archive 时先复用存档的阶段链/参数再建任务。"""
+    chain = str(payload.get("chain") or (bioflow or {}).get("chain") or "").strip()
+    stages = payload.get("stages")
+    reuse_name = str(payload.get("reuse_archive") or payload.get("reuse_name") or "").strip()
+    has_stages = isinstance(stages, list) and len(stages) > 0
+    if not has_stages and not reuse_name:
+        # 既无显式阶段链也无存档复用来源 → 无法建任务，回退原 pipeline
+        return None
+    cap_name = _chain_to_capability(chain)
+    if cap_name is None:
+        # 无法确定能力（chain 空/未知）：不能默认走某条链，回退原 pipeline
+        return None
+    tool = "create_gene_family_job" if cap_name == "bioflow-gene-family" else "create_rnaseq_job"
+    if tool not in tool_manifests:
+        return None
+    args: Dict[str, Any] = {
+        "session_id": str((bioflow or {}).get("session_id") or ""),
+        "stages": [str(s) for s in stages] if isinstance(stages, list) and stages else [],
+        "title": str(payload.get("title") or ""),
+        "auto_continue": bool(payload.get("auto_continue", False)),
+    }
+    tool_names: List[str] = []
+    # 存档复用（FR-BIO-023）：先 reuse_archive 取阶段链/参数/archive_id，再以其发起
+    if reuse_name and "reuse_archive" in tool_manifests:
+        tool_names.append("reuse_archive")  # 实际先执行 reuse_archive（audit 顺序与实际一致）
+        reuse_text = _execute_tool(tool_manifests, "reuse_archive", {"name": reuse_name})
+        arch = _try_parse_json(reuse_text)
+        if isinstance(arch, dict) and arch.get("ok"):
+            data = arch.get("data") if isinstance(arch.get("data"), dict) else {}
+            if data.get("id"):
+                args["archive_id"] = str(data["id"])
+            if not args["stages"] and isinstance(data.get("stage_chain"), list):
+                args["stages"] = [str(s) for s in data["stage_chain"]]
+            if isinstance(data.get("params"), dict):
+                merged = dict(data["params"])
+                if isinstance(payload.get("params"), dict):
+                    merged.update(payload["params"])
+                args["params"] = merged
+        elif not args["stages"]:
+            # 复用失败（非 ok）且无显式阶段链：不能空链建任务，回退原 pipeline
+            return None
+    tool_names.append(tool)  # create_*_job 最后执行
+    if "params" not in args and isinstance(payload.get("params"), dict):
+        args["params"] = payload["params"]
+    result = _execute_tool(tool_manifests, tool, args)
+    job_id = _extract_job_id(result)
+    answer = _paraphrase(
+        llm_client,
+        f"用户确认了分析路径并创建任务（{'基因家族' if cap_name == 'bioflow-gene-family' else '转录组'}链"
+        f"{'，复用存档 ' + reuse_name if reuse_name else ''}）。工具结果：\n{result}",
+    )
+    return _make_payload(
+        "确认路径并创建任务", answer,
+        audit={"rounds": 1, "tool_calls": len(tool_names), "used_json_fallback": False, "tool_names": tool_names, "errors": []},
+        capabilities=[cap_name] if cap_name else [],
+        active_job_id=job_id,
+        chain=chain or None,
+    )
+
+
+def _card_form_confirm(
+    payload: Dict[str, Any], llm_client: Any, bioflow: Dict[str, Any], tool_manifests: Dict[str, CapabilityManifest]
+) -> Optional[Dict[str, Any]]:
+    """参数卡确认 → confirm_stage（白名单校验）→ 复述；rerun:true 走 rerun_stage（改参数重跑）。"""
+    job_id = str(payload.get("job_id") or (bioflow or {}).get("active_job_id") or "").strip()
+    stage = str(payload.get("stage") or "").strip()
+    params = payload.get("params") if isinstance(payload.get("params"), dict) else {}
+    rerun = bool(payload.get("rerun", False))
+    if not job_id or not stage:
+        return None
+    tool = "rerun_stage" if rerun else "confirm_stage"
+    result = _execute_tool(tool_manifests, tool, {"job_id": job_id, "stage": stage, "params": params})
+    answer = _paraphrase(
+        llm_client,
+        f"用户{'重跑并确认' if rerun else '确认'}了阶段参数（任务 {job_id} 的 {stage}）。工具结果：\n{result}",
+    )
+    return _make_payload(
+        f"{'重跑' if rerun else '确认'}阶段参数：{stage}", answer,
+        audit={"rounds": 1, "tool_calls": 1, "used_json_fallback": False, "tool_names": [tool], "errors": []},
+        active_job_id=job_id,
+    )
+
+
+def _card_file_upload(
+    payload: Dict[str, Any], llm_client: Any, bioflow: Dict[str, Any], tool_manifests: Dict[str, CapabilityManifest]
+) -> Optional[Dict[str, Any]]:
+    """文件卡 → 网络源 fetch_source_file / 服务器·局域网路径 register_job_files → 复述。"""
+    job_id = str(payload.get("job_id") or (bioflow or {}).get("active_job_id") or "").strip()
+    raw_files = payload.get("paths") or payload.get("files") or []
+    if isinstance(raw_files, str):
+        raw_files = [raw_files]
+    files = [str(f) for f in raw_files if str(f).strip()] if isinstance(raw_files, list) else []
+    if not job_id or not files:
+        return None
+    remote = [f for f in files if f.startswith(("http://", "https://", "oss://"))]
+    local = [f for f in files if f not in remote]
+    results: List[str] = []
+    tool_names: List[str] = []
+    for src in remote:
+        r = _execute_tool(tool_manifests, "fetch_source_file", {"source": src, "job_id": job_id})
+        results.append(r)
+        tool_names.append("fetch_source_file")
+    if local:
+        r = _execute_tool(tool_manifests, "register_job_files", {"job_id": job_id, "paths": local})
+        results.append(r)
+        tool_names.append("register_job_files")
+    answer = _paraphrase(
+        llm_client,
+        f"用户提供了文件（{'远程 ' + str(len(remote)) + ' 个' if remote else ''}"
+        f"{'本地 ' + str(len(local)) + ' 个' if local else ''}）。工具结果：\n" + "\n".join(results),
+    )
+    return _make_payload(
+        "登记任务文件", answer,
+        audit={"rounds": 1, "tool_calls": len(tool_names), "used_json_fallback": False, "tool_names": tool_names, "errors": []},
+        active_job_id=job_id,
+    )
+
+
+def _card_archive_choice(
+    payload: Dict[str, Any], llm_client: Any, bioflow: Dict[str, Any], tool_manifests: Dict[str, CapabilityManifest]
+) -> Optional[Dict[str, Any]]:
+    """存档卡 → archive_job 工具执行实际存档（或跳过）→ 复述。"""
+    job_id = str(payload.get("job_id") or (bioflow or {}).get("active_job_id") or "").strip()
+    do_archive = bool(payload.get("archive", False))
+    if not job_id:
+        return None
+    if do_archive:
+        name = str(payload.get("name") or "")
+        description = str(payload.get("description") or "")
+        result = _execute_tool(
+            tool_manifests, "archive_job",
+            {"job_id": job_id, "name": name, "description": description},
+        )
+        answer = _paraphrase(
+            llm_client,
+            f"用户选择把任务 {job_id} 存档（名称：{name or '未命名'}）。工具结果：\n{result}",
+        )
+        return _make_payload(
+            "存档选择", answer,
+            audit={"rounds": 1, "tool_calls": 1, "used_json_fallback": False, "tool_names": ["archive_job"], "errors": []},
+            active_job_id=job_id,
+        )
+    answer = _paraphrase(
+        llm_client,
+        f"用户选择不存档任务 {job_id}。请用自然语言告知用户：已跳过存档，"
+        "本次分析结果仍可在报告/结果中查看。",
+    )
+    return _make_payload(
+        "存档选择", answer,
+        audit=_empty_audit(),
+        active_job_id=job_id,
+    )
+
+
+def _card_extension_action(
+    payload: Dict[str, Any], llm_client: Any, bioflow: Dict[str, Any], tool_manifests: Dict[str, CapabilityManifest]
+) -> Optional[Dict[str, Any]]:
+    """扩展操作卡（S4）：action ∈ build|trial_run|validate|confirm|publish|run → 对应扩展工具。"""
+    ext_id = str(payload.get("ext_id") or "").strip()
+    action = str(payload.get("action") or "").strip()
+    if not ext_id or not action:
+        return None
+    tool = {
+        "build": "build_extension",
+        "trial_run": "trial_run_extension",
+        "validate": "validate_extension",
+        "confirm": "confirm_extension",
+        "publish": "publish_extension",
+        "run": "run_extension",
+        "repair": "repair_extension",
+    }.get(action)
+    if tool is None or tool not in tool_manifests:
+        return None
+    args: Dict[str, Any] = {"ext_id": ext_id}
+    if action == "confirm":
+        if isinstance(payload.get("nl_triggers"), list):
+            args["nl_triggers"] = payload["nl_triggers"]
+        if isinstance(payload.get("parameters"), list):
+            args["parameters"] = payload["parameters"]
+        if payload.get("runtime_image"):
+            args["runtime_image"] = str(payload["runtime_image"])
+    if action == "run":
+        if isinstance(payload.get("params"), dict):
+            args["params"] = payload["params"]
+        if isinstance(payload.get("files"), list):
+            args["files"] = payload["files"]
+    result = _execute_tool(tool_manifests, tool, args)
+    if action == "confirm" and "EXT_STATUS" in result:
+        # 状态降级话术：confirm 要求 validated/trial_passed 前置状态，
+        # 编辑修正若发生在校验前，明确提示先试运行/校验，不报 500。
+        answer = (
+            "该扩展当前状态还不能确认。请先完成 AI 转换与试运行、通过校验后，"
+            "再确认参数与触发词。"
+        )
+    else:
+        answer = _paraphrase(
+            llm_client,
+            f"用户对扩展 {ext_id} 执行了操作 {action}。工具结果：\n{result}",
+        )
+    return _make_payload(
+        f"扩展操作：{action}", answer,
+        audit={"rounds": 1, "tool_calls": 1, "used_json_fallback": False, "tool_names": [tool], "errors": []},
+    )
+
+
+def _handle_card_result(
+    card_result: Dict[str, Any],
+    llm_client: Any,
+    bioflow: Optional[Dict[str, Any]],
+    tool_manifests: Dict[str, CapabilityManifest],
+) -> Optional[Dict[str, Any]]:
+    card = str(card_result.get("card") or "").strip()
+    payload = card_result.get("payload") if isinstance(card_result.get("payload"), dict) else {}
+    ctx = bioflow or {}
+    if card == CARD_PATH_SELECTION:
+        return _card_path_selection(payload, llm_client, ctx, tool_manifests)
+    if card == CARD_FORM_CONFIRM:
+        return _card_form_confirm(payload, llm_client, ctx, tool_manifests)
+    if card == CARD_FILE_UPLOAD:
+        return _card_file_upload(payload, llm_client, ctx, tool_manifests)
+    if card == CARD_ARCHIVE_CHOICE:
+        return _card_archive_choice(payload, llm_client, ctx, tool_manifests)
+    if card == CARD_EXTENSION_ACTION:
+        return _card_extension_action(payload, llm_client, ctx, tool_manifests)
+    return None
+
+
+# ---------------------------------------------------------------------------
+# 前门路由
+# ---------------------------------------------------------------------------
+
+
+def try_bioflow_agent(
+    question: str,
+    *,
+    llm_client: Any,
+    history: Optional[List[Dict[str, str]]] = None,
+    capabilities: Optional[Dict[str, Any]] = None,
+    card_result: Optional[Dict[str, Any]] = None,
+    bioflow: Optional[Dict[str, Any]] = None,
+    progress_callback: Optional[Any] = None,
+) -> Optional[Dict[str, Any]]:
+    """前门路由入口。命中生信能力则返回答案 payload，否则返回 None（走原 pipeline）。
+
+    - card_result：非空时走卡片回填协议（直接路由到对应工具，不做意图预筛）。
+    - 任何异常都不上抛——记日志后返回 None，保证金标路径永不因本模块失败。
+    """
+    try:
+        return _try_bioflow_agent_impl(
+            question,
+            llm_client=llm_client,
+            history=history,
+            capabilities=capabilities,
+            card_result=card_result,
+            bioflow=bioflow,
+            progress_callback=progress_callback,
+        )
+    except Exception as exc:  # noqa: BLE001
+        LOGGER.warning("bioflow agent: 执行失败，回退原 pipeline: %s", exc)
+        return None
+
+
+def _try_bioflow_agent_impl(
+    question: str,
+    *,
+    llm_client: Any,
+    history: Optional[List[Dict[str, str]]],
+    capabilities: Optional[Dict[str, Any]],
+    card_result: Optional[Dict[str, Any]],
+    bioflow: Optional[Dict[str, Any]],
+    progress_callback: Optional[Any],
+) -> Optional[Dict[str, Any]]:
+    # 门 1：会话开关（熔断）
+    if not _env_enabled():
+        return None
+
+    # card_result 卡片操作优先：用户已在卡片上明确选择，不做意图预筛，直接路由
+    if isinstance(card_result, dict) and str(card_result.get("card") or "").strip() in CARD_TYPES:
+        return _route_card_result(card_result, llm_client, capabilities, bioflow, progress_callback)
+
+    # NL 路径：门 2 + 门 3
+    manifests = _candidate_capabilities(question, capabilities)
+    if not manifests:
+        return None
+
+    tools, tool_manifests = _build_tools(manifests)
+    if not tools:
+        LOGGER.warning("bioflow agent: 意图命中但 MCP 工具发现为空，回退原 pipeline")
+        return None
+
+    if progress_callback is not None:
+        try:
+            progress_callback(
+                {
+                    "stage": "bioflow_agent_started",
+                    "capabilities": [m.name for m in manifests],
+                    "tool_count": len(tools),
+                }
+            )
+        except Exception:  # noqa: BLE001
+            pass
+
+    system = _build_system(manifests)
+    runner = ToolRunner(make_llm_complete(llm_client), max_rounds=MAX_ROUNDS)
+    content, audit = runner.run(system, question, tools, tool_manifests, history=history)
+
+    answer = (content or "").strip()
+    if not answer:
+        return None
+
+    return _make_payload(
+        question,
+        answer,
+        audit=audit,
+        capabilities=[m.name for m in manifests],
+        active_job_id=(bioflow or {}).get("active_job_id"),
+        chain=(bioflow or {}).get("chain"),
+    )
+
+
+def _route_card_result(
+    card_result: Dict[str, Any],
+    llm_client: Any,
+    capabilities: Optional[Dict[str, Any]],
+    bioflow: Optional[Dict[str, Any]],
+    progress_callback: Optional[Any],
+) -> Optional[Dict[str, Any]]:
+    """卡片操作路由：确定相关能力 → 构建工具 → 分发到对应 card handler。"""
+    card = str(card_result.get("card") or "").strip()
+    payload = card_result.get("payload") if isinstance(card_result.get("payload"), dict) else {}
+    chain = str(payload.get("chain") or (bioflow or {}).get("chain") or "").strip()
+    if card == CARD_EXTENSION_ACTION:
+        # 扩展操作只依赖 bioflow-extension 能力，避免对三个能力各做一次 list_tools
+        cap_name = "bioflow-extension"
+    else:
+        cap_name = _chain_to_capability(chain)
+    registered = _registered_capabilities(capabilities)
+    if cap_name:
+        manifests = [m for m in registered if m.name == cap_name]
+    else:
+        manifests = registered
+    if not manifests:
+        return None
+    tools, tool_manifests = _build_tools(manifests)
+    if not tools:
+        LOGGER.warning("bioflow agent: card_result 但 MCP 工具发现为空，回退原 pipeline")
+        return None
+    if progress_callback is not None:
+        try:
+            progress_callback({"stage": "bioflow_card", "card": card_result.get("card")})
+        except Exception:  # noqa: BLE001
+            pass
+    return _handle_card_result(card_result, llm_client, bioflow, tool_manifests)

agent/qa/src/rag/qa_v1_1_73/capabilities/install_manager.py

@@ -128,6 +128,8 @@ class InstallManager:
                     "allowed_llm_phases": manifest.allowed_llm_phases,
                     "session_default": manifest.session_default,
                 }
+                if manifest.nl_triggers:
+                    raw["nl_triggers"] = manifest.nl_triggers
                 if manifest.schema:
                     raw["schema"] = manifest.schema
                 for section in ("http", "mcp", "python", "prompt_pack"):

agent/qa/src/rag/qa_v1_1_73/capabilities/manifests.py

@@ -37,6 +37,7 @@ class CapabilityManifest:
     session_default: bool = False
     schema: Dict[str, Any] = field(default_factory=dict)
     config: Dict[str, Any] = field(default_factory=dict)  # provider 专属段（http:/mcp:/python:/prompt_pack: 归并）
+    nl_triggers: List[str] = field(default_factory=list)  # 意图预筛触发词（S1，生信能力路由用）
 
     def to_tool_spec(self) -> Dict[str, Any]:
         """转 OpenAI function schema（tools 参数形态）。"""
@@ -110,6 +111,19 @@ def _parse_entry(raw: Any, index: int, load_warnings: List[str]) -> CapabilityMa
         if isinstance(raw.get(section), dict):
             config[section] = raw[section]
     config["session_default"] = bool(raw.get("session_default", False))
+    # nl_triggers（S1）：意图预筛触发词，只收字符串、去空、去重、限长
+    nl_triggers_raw = raw.get("nl_triggers") or []
+    if isinstance(nl_triggers_raw, str):
+        nl_triggers_raw = [nl_triggers_raw]
+    nl_triggers: List[str] = []
+    if isinstance(nl_triggers_raw, list):
+        for trigger in nl_triggers_raw:
+            if not isinstance(trigger, str):
+                continue  # 触发词只收字符串，非字符串（数字等）丢弃
+            cleaned = _clean_text(trigger, 64)
+            if cleaned and cleaned not in nl_triggers:
+                nl_triggers.append(cleaned)
+        nl_triggers = nl_triggers[:64]
     manifest = CapabilityManifest(
         name=name,
         provider=provider,
@@ -119,6 +133,7 @@ def _parse_entry(raw: Any, index: int, load_warnings: List[str]) -> CapabilityMa
         session_default=bool(raw.get("session_default", False)),
         schema=schema,
         config=config,
+        nl_triggers=nl_triggers,
     )
     # 大小上限：单条目序列化后 ≤8KB
     import json

agent/qa/src/rag/qa_v1_1_73/capabilities/providers.py

@@ -130,6 +130,7 @@ class _McpConnection:
         self._thread: Optional[threading.Thread] = None
         self._session: Any = None
         self._server_tools: List[str] = []
+        self._server_tool_schemas: List[Dict[str, Any]] = []
         self._started_at = 0.0
         self._last_used = 0.0
         self._restarts = 0
@@ -200,6 +201,18 @@ class _McpConnection:
             raise
         self._ctx = ctx
         self._server_tools = [t.name for t in tools_result.tools]
+        self._server_tool_schemas = [
+            {
+                "name": t.name,
+                "description": (getattr(t, "description", None) or ""),
+                "input_schema": (
+                    getattr(t, "inputSchema", None)
+                    or getattr(t, "input_schema", None)
+                    or {}
+                ),
+            }
+            for t in tools_result.tools
+        ]
         self._session = session
         self._started_at = time.time()
 
@@ -225,6 +238,7 @@ class _McpConnection:
         ctx = getattr(self, "_ctx", None)
         self._ctx = None
         self._server_tools = []
+        self._server_tool_schemas = []
         if session is not None:
             try:
                 await session.__aexit__(None, None, None)
@@ -274,6 +288,14 @@ class _McpConnection:
             return []
         return list(self._server_tools)
 
+    def list_tool_schemas(self) -> List[Dict[str, Any]]:
+        """返回 MCP server 全量工具 schema（name/description/input_schema）。连接失败返回空。"""
+        try:
+            self._ensure_session()
+        except ToolExecutionError:
+            return []
+        return list(self._server_tool_schemas)
+
     def call(self, tool_name: str, arguments: Dict[str, Any]) -> str:
         self._ensure_session()
         try:
@@ -337,6 +359,11 @@ class McpToolProvider:
             return tools + [f"<缺失声明工具 {tool_name}>"]
         return tools
 
+    def list_tool_schemas(self, manifest: CapabilityManifest) -> List[Dict[str, Any]]:
+        """返回该能力 MCP server 的全量工具 schema（供前门 agent 构建 LLM 工具表）。"""
+        conn = self._connection(manifest)
+        return conn.list_tool_schemas()
+
     def reap_idle(self) -> int:
         reaped = 0
         with self._lock:
@@ -448,6 +475,10 @@ class ToolDispatcher:
             return PythonToolProvider.execute(manifest, arguments)
         raise ToolExecutionError(f"工具 {manifest.name} provider={provider} 不支持调用")
 
+    def list_mcp_tools(self, manifest: CapabilityManifest) -> List[Dict[str, Any]]:
+        """MCP 能力全量工具 schema（bioflow_agent 构建 LLM 工具表用）。"""
+        return self._mcp.list_tool_schemas(manifest)
+
     def reap_idle(self) -> int:
         return self._mcp.reap_idle()
 

agent/qa/src/rag/qa_v1_1_73/test_bioflow_agent.py

@@ -0,0 +1,174 @@
+"""test_bioflow_agent.py —— bioflow_agent 前门三重门 + nl_triggers 解析单测。
+
+覆盖 S1 验收要点：
+  - 熔断开关（QA_V1_ENABLE_BIOFLOW_AGENT）默认关 → 返回 None（走原 pipeline）
+  - 意图预筛（nl_triggers）各自评估，未命中返回 None
+  - 注册表未注册 / 会话开关关 → 返回 None
+  - 命中后短路返回自然语言 payload（bioflow.handled=True）
+  - 只装一个能力时，另一个能力的触发语不响应（隔离）
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent.parent.parent / "src"))
+
+from rag.qa_v1_1_73 import bioflow_agent as ba  # noqa: E402
+from rag.qa_v1_1_73.capabilities.manifests import parse_capabilities_text  # noqa: E402
+from rag.qa_v1_1_73.capabilities.registry import CapabilityRegistry  # noqa: E402
+
+BIOFLOW_YAML = """
+capabilities:
+  - name: bioflow-gene-family
+    provider: mcp
+    permission: read_only
+    description: 基因家族分析
+    session_default: true
+    nl_triggers: [基因家族, 家族成员, 亚家族, 建树]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/gene-family/
+    prompt_pack:
+      file: bioflow_gene_family_agent_rules.md
+  - name: bioflow-rnaseq
+    provider: mcp
+    permission: read_only
+    description: 转录组分析
+    session_default: true
+    nl_triggers: [转录组, RNA-seq, 差异表达, 富集]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/rnaseq/
+    prompt_pack:
+      file: bioflow_rnaseq_agent_rules.md
+"""
+
+
+def _make_registry(tmp_path: Path) -> CapabilityRegistry:
+    path = tmp_path / "capabilities.yaml"
+    path.write_text(BIOFLOW_YAML, encoding="utf-8")
+    registry = CapabilityRegistry(path)
+    registry.load()
+    return registry
+
+
+class FakeLLMClient:
+    def __init__(self, content: str = "已为您规划分析路径。") -> None:
+        self.content = content
+
+    def complete_raw_messages(self, system, messages, tools=None, **kwargs):
+        return {"content": self.content, "tool_calls": [], "finish_reason": "stop"}
+
+
+class TestNlTriggers:
+    def test_parse_nl_triggers(self):
+        manifests, warnings = parse_capabilities_text(BIOFLOW_YAML)
+        assert warnings == []
+        gf = next(m for m in manifests if m.name == "bioflow-gene-family")
+        assert gf.nl_triggers == ["基因家族", "家族成员", "亚家族", "建树"]
+        assert gf.config["mcp"]["url"].endswith("/mcp/gene-family/")
+        assert gf.config["prompt_pack"]["file"] == "bioflow_gene_family_agent_rules.md"
+
+    def test_nl_triggers_dedupe_and_clean(self):
+        text = """
+capabilities:
+  - name: t
+    provider: mcp
+    nl_triggers: [基因家族, 基因家族, "", " 亚家族 ", 123]
+"""
+        manifests, _ = parse_capabilities_text(text)
+        assert manifests[0].nl_triggers == ["基因家族", "亚家族"]
+
+
+class TestIntentMatch:
+    def test_match(self):
+        assert ba._intent_match("帮我做水稻SPL基因家族分析", ["基因家族"]) is True
+        assert ba._intent_match("转录组差异表达分析", ["转录组", "RNA-seq"]) is True
+        assert ba._intent_match("什么是光合作用", ["基因家族", "转录组"]) is False
+
+
+class TestGateLogic:
+    def test_fuse_off_returns_none(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict("os.environ", {}, clear=False):
+                ba.os.environ.pop(ba.ENV_FUSE, None)
+                result = ba.try_bioflow_agent(
+                    "帮我做基因家族分析", llm_client=FakeLLMClient(), capabilities=None
+                )
+        assert result is None
+
+    def test_no_intent_match_returns_none(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                result = ba.try_bioflow_agent(
+                    "光合作用的电子传递链是什么", llm_client=FakeLLMClient(), capabilities=None
+                )
+        assert result is None
+
+    def test_not_registered_returns_none(self, tmp_path):
+        empty = CapabilityRegistry(tmp_path / "empty.yaml")
+        empty.load()
+        with mock.patch.object(ba, "get_registry", return_value=empty):
+            with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                result = ba.try_bioflow_agent(
+                    "帮我做基因家族分析", llm_client=FakeLLMClient(), capabilities=None
+                )
+        assert result is None
+
+    def test_session_switch_off_returns_none(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                result = ba.try_bioflow_agent(
+                    "帮我做基因家族分析",
+                    llm_client=FakeLLMClient(),
+                    capabilities={"bioflow-gene-family": False},
+                )
+        assert result is None
+
+    def test_isolation_only_installed_responds(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                caps = ba._candidate_capabilities("帮我做基因家族分析", None)
+                assert [m.name for m in caps] == ["bioflow-gene-family"]
+                caps = ba._candidate_capabilities("转录组差异表达", None)
+                assert [m.name for m in caps] == ["bioflow-rnaseq"]
+
+    def test_full_flow_short_circuits(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        fake_tools = [
+            {
+                "type": "function",
+                "function": {
+                    "name": "plan_gene_family",
+                    "description": "规划基因家族路径",
+                    "parameters": {"type": "object", "properties": {}},
+                },
+            }
+        ]
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.object(ba, "_build_tools", return_value=(fake_tools, {"plan_gene_family": mock.ANY})):
+                with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                    result = ba.try_bioflow_agent(
+                        "帮我做基因家族分析", llm_client=FakeLLMClient(), capabilities=None
+                    )
+        assert result is not None
+        assert result["success"] is True
+        assert result["answer"] == "已为您规划分析路径。"
+        assert result["bioflow"]["handled"] is True
+        assert result["bioflow"]["capabilities"] == ["bioflow-gene-family"]
+
+    def test_exception_falls_back_to_none(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.object(ba, "_candidate_capabilities", side_effect=RuntimeError("boom")):
+                with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                    result = ba.try_bioflow_agent(
+                        "帮我做基因家族分析", llm_client=FakeLLMClient(), capabilities=None
+                    )
+        assert result is None

agent/qa/src/rag/qa_v1_1_73/test_bioflow_agent_s2.py

@@ -0,0 +1,255 @@
+"""test_bioflow_agent_s2.py —— S2 对话式编排闭环单测。
+
+覆盖：card_result 回填协议（四类卡片）、参数抽取（白名单）、多轮记忆注入、
+session↔job 绑定上下文（active_job_id/chain）、job_status 主动查询。
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent.parent.parent / "src"))
+
+from rag.qa_v1_1_73 import bioflow_agent as ba  # noqa: E402
+from rag.qa_v1_1_73.capabilities.manifests import CapabilityManifest  # noqa: E402
+from rag.qa_v1_1_73.tool_runner import ToolRunner  # noqa: E402
+
+
+def _manifest(name="bioflow-gene-family", url="http://x/mcp/gene-family/"):
+    return CapabilityManifest(name=name, provider="mcp", config={"mcp": {"url": url, "tool": name}})
+
+
+def _tool_manifests():
+    """覆盖四类卡片用到的工具 + job_status。"""
+    names = ("create_gene_family_job", "create_rnaseq_job", "confirm_stage",
+             "register_job_files", "fetch_source_file", "job_status")
+    out = {}
+    for t in names:
+        out[t] = CapabilityManifest(
+            name="bioflow-gene-family", provider="mcp",
+            config={"mcp": {"url": "http://x/mcp/gene-family/", "tool": t}},
+        )
+    return out
+
+
+class FakeDispatcher:
+    def __init__(self, results=None):
+        self.results = results or {}
+        self.calls = []
+
+    def execute(self, manifest, arguments):
+        tool = manifest.config.get("mcp", {}).get("tool")
+        self.calls.append((tool, arguments))
+        return self.results.get(tool, '{"ok": true, "data": {"id": "job-1"}}')
+
+
+class FakeLLM:
+    def __init__(self, complete_text="已收到，已为您处理。", json_payload=None):
+        self.complete_text = complete_text
+        self.json_payload = json_payload or {}
+
+    def complete(self, system, user, **kw):
+        return self.complete_text
+
+    def complete_json(self, system, user, **kw):
+        return self.json_payload
+
+    def complete_raw_messages(self, system, messages, tools=None, **kw):
+        return {"content": "answer", "tool_calls": [], "finish_reason": "stop"}
+
+
+# ---------------------------------------------------------------------------
+# 参数抽取
+# ---------------------------------------------------------------------------
+
+class TestExtractParams:
+    def test_extract_known_and_unknown(self):
+        llm = FakeLLM(json_payload={"params": {"threads": 8, "padj": 0.01}, "unknown": ["bogus"]})
+        form_defaults = {"threads": {"default": 4}, "padj": {"default": 0.05}}
+        known, unknown = ba._extract_params(llm, "用 8 核，padj 用 0.01", form_defaults)
+        assert known == {"threads": 8, "padj": 0.01}
+        assert unknown == ["bogus"]
+
+    def test_non_whitelist_param_filtered(self):
+        llm = FakeLLM(json_payload={"params": {"evil": 1, "threads": 4}, "unknown": []})
+        form_defaults = {"threads": {"default": 4}}
+        known, unknown = ba._extract_params(llm, "x", form_defaults)
+        assert known == {"threads": 4}
+
+    def test_bad_json_returns_empty(self):
+        llm = FakeLLM(json_payload="not-a-dict")
+        form_defaults = {"threads": {}}
+        known, unknown = ba._extract_params(llm, "x", form_defaults)
+        assert known == {} and unknown == []
+
+    def test_empty_whitelist(self):
+        llm = FakeLLM()
+        known, unknown = ba._extract_params(llm, "x", {})
+        assert known == {} and unknown == []
+
+
+# ---------------------------------------------------------------------------
+# card_result 回填协议
+# ---------------------------------------------------------------------------
+
+class TestCardResult:
+    def test_path_selection_creates_job_and_extracts_job_id(self):
+        dispatcher = FakeDispatcher()
+        llm = FakeLLM()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "path_selection",
+                 "payload": {"chain": "gene_family", "stages": ["identify", "tree"], "title": "水稻SPL"}},
+                llm, {"session_id": "s1"}, _tool_manifests(),
+            )
+        assert out is not None
+        assert out["bioflow"]["active_job_id"] == "job-1"
+        assert out["bioflow"]["chain"] == "gene_family"
+        assert dispatcher.calls[0][0] == "create_gene_family_job"
+        assert dispatcher.calls[0][1]["stages"] == ["identify", "tree"]
+        assert dispatcher.calls[0][1]["session_id"] == "s1"
+
+    def test_path_selection_missing_stages_returns_none(self):
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            out = ba._handle_card_result(
+                {"card": "path_selection", "payload": {"chain": "gene_family"}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is None
+
+    def test_form_confirm_calls_confirm_stage(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "form_confirm",
+                 "payload": {"job_id": "job-9", "stage": "identify", "params": {"evalue": 1e-5}}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls[0][0] == "confirm_stage"
+        assert dispatcher.calls[0][1] == {"job_id": "job-9", "stage": "identify", "params": {"evalue": 1e-5}}
+
+    def test_form_confirm_uses_active_job_id_fallback(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            ba._handle_card_result(
+                {"card": "form_confirm", "payload": {"stage": "identify", "params": {}}},
+                FakeLLM(), {"active_job_id": "job-7"}, _tool_manifests(),
+            )
+        assert dispatcher.calls[0][1]["job_id"] == "job-7"
+
+    def test_file_upload_splits_remote_and_local(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "file_upload",
+                 "payload": {"job_id": "j1", "paths": ["https://x/a.fa", "/data/b.fa"]}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is not None
+        tools = [c[0] for c in dispatcher.calls]
+        assert "fetch_source_file" in tools and "register_job_files" in tools
+
+    def test_archive_choice_paraphrases(self):
+        out = ba._handle_card_result(
+            {"card": "archive_choice", "payload": {"job_id": "j1", "archive": True}},
+            FakeLLM(), {}, _tool_manifests(),
+        )
+        assert out is not None
+        assert out["answer"] == "已收到，已为您处理。"
+
+    def test_unknown_card_returns_none(self):
+        out = ba._handle_card_result({"card": "bogus", "payload": {}}, FakeLLM(), {}, _tool_manifests())
+        assert out is None
+
+    def test_path_selection_reuse_failure_no_stages_returns_none(self):
+        """bug ②：复用失败且无显式 stages → 返回 None（不空链建任务）。"""
+        dispatcher = FakeDispatcher({"reuse_archive": '{"ok": false, "code": "ARCHIVE_NOT_FOUND"}'})
+        tm = _tool_manifests()
+        tm["reuse_archive"] = CapabilityManifest(
+            name="bioflow-gene-family", provider="mcp",
+            config={"mcp": {"url": "http://x", "tool": "reuse_archive"}},
+        )
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "path_selection",
+                 "payload": {"chain": "gene_family", "reuse_archive": "不存在的存档"}},
+                FakeLLM(), {}, tm,
+            )
+        assert out is None
+        # 只执行了 reuse_archive，未调用 create_gene_family_job
+        assert [c[0] for c in dispatcher.calls] == ["reuse_archive"]
+
+
+# ---------------------------------------------------------------------------
+# 前门路由（card_result / bioflow 上下文）
+# ---------------------------------------------------------------------------
+
+class TestRouteCardResult:
+    def test_try_bioflow_agent_card_result_short_circuits(self):
+        registry_manifest = _manifest()
+        with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+            with mock.patch.object(ba, "_registered_capabilities", return_value=[registry_manifest]):
+                with mock.patch.object(ba, "_build_tools", return_value=([{"type": "function", "function": {"name": "confirm_stage", "description": "", "parameters": {"type": "object", "properties": {}}}}], {"confirm_stage": registry_manifest})):
+                    with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+                        out = ba.try_bioflow_agent(
+                            "确认", llm_client=FakeLLM(),
+                            card_result={"card": "form_confirm", "payload": {"job_id": "j1", "stage": "s", "params": {}}},
+                        )
+        assert out is not None
+        assert out["bioflow"]["handled"] is True
+
+    def test_try_bioflow_agent_fuse_off_ignores_card_result(self):
+        with mock.patch.dict("os.environ", {}, clear=False):
+            ba.os.environ.pop(ba.ENV_FUSE, None)
+            out = ba.try_bioflow_agent(
+                "确认", llm_client=FakeLLM(),
+                card_result={"card": "form_confirm", "payload": {}},
+            )
+        assert out is None
+
+
+# ---------------------------------------------------------------------------
+# 多轮记忆注入（ToolRunner.run history）
+# ---------------------------------------------------------------------------
+
+class TestMultiTurnHistory:
+    def test_history_injected_into_messages(self):
+        class RecordingLLM:
+            def __init__(self):
+                self.captured_messages = None
+            def complete_raw_messages(self, system, messages, tools=None, **kw):
+                self.captured_messages = list(messages)
+                return {"content": "ok", "tool_calls": [], "finish_reason": "stop"}
+
+        from rag.qa_v1_1_73.tool_runner import make_llm_complete
+
+        llm = RecordingLLM()
+        runner = ToolRunner(make_llm_complete(llm), max_rounds=1)
+        history = [{"role": "user", "content": "上一轮问题"}, {"role": "assistant", "content": "上一轮答案"}]
+        runner.run("sys", "当前问题", [], {}, history=history)
+        msgs = llm.captured_messages
+        assert msgs[0] == {"role": "user", "content": "上一轮问题"}
+        assert msgs[1] == {"role": "assistant", "content": "上一轮答案"}
+        assert msgs[-1] == {"role": "user", "content": "当前问题"}
+
+    def test_history_filters_bad_roles(self):
+        class RecordingLLM:
+            def __init__(self):
+                self.captured_messages = None
+            def complete_raw_messages(self, system, messages, tools=None, **kw):
+                self.captured_messages = list(messages)
+                return {"content": "ok", "tool_calls": [], "finish_reason": "stop"}
+
+        from rag.qa_v1_1_73.tool_runner import make_llm_complete
+
+        llm = RecordingLLM()
+        runner = ToolRunner(make_llm_complete(llm), max_rounds=1)
+        history = [{"role": "system", "content": "evil"}, {"role": "user", "content": ""}, {"role": "user", "content": "ok"}]
+        runner.run("sys", "q", [], {}, history=history)
+        roles = [m["role"] for m in llm.captured_messages]
+        assert "system" not in roles
+        assert llm.captured_messages[-1] == {"role": "user", "content": "q"}

agent/qa/src/rag/qa_v1_1_73/test_bioflow_agent_s2_supplement.py

@@ -0,0 +1,511 @@
+"""test_bioflow_agent_s2_supplement.py —— S2 覆盖清单补强测试。
+
+补强 dev 的 test_bioflow_agent_s2.py 未覆盖的分支：
+  - _chain_to_capability / _extract_job_id / _execute_tool / _paraphrase / _query_job_status
+  - card 四类 handler 缺必需字段回退 None、files 键、archive=False、非 dict payload
+  - _route_card_result：chain 过滤 / 未注册能力→None / tools 空→None
+  - NL 路径注入 bioflow 上下文（active_job_id/chain）
+  - system prompt 硬规则在位（追问 ≤3 / 不可代确认 / 工具名不外泄）
+  - ToolRunner.run(history) 边界（non-dict 条目 / history=None / 空内容剔除）
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent.parent.parent / "src"))
+
+from rag.qa_v1_1_73 import bioflow_agent as ba  # noqa: E402
+from rag.qa_v1_1_73.capabilities.manifests import CapabilityManifest  # noqa: E402
+from rag.qa_v1_1_73.tool_runner import ToolRunner, make_llm_complete  # noqa: E402
+
+
+def _manifest(name="bioflow-gene-family", url="http://x/mcp/gene-family/"):
+    return CapabilityManifest(name=name, provider="mcp", config={"mcp": {"url": url, "tool": name}})
+
+
+def _tool_manifests():
+    names = ("create_gene_family_job", "create_rnaseq_job", "confirm_stage",
+             "register_job_files", "fetch_source_file", "job_status",
+             "rerun_stage", "reuse_archive", "archive_job")
+    out = {}
+    for t in names:
+        out[t] = CapabilityManifest(
+            name="bioflow-gene-family", provider="mcp",
+            config={"mcp": {"url": "http://x/mcp/gene-family/", "tool": t}},
+        )
+    return out
+
+
+class FakeLLM:
+    def __init__(self, complete_text="已收到。", json_payload=None, complete_error=None):
+        self.complete_text = complete_text
+        self.json_payload = json_payload or {}
+        self.complete_error = complete_error
+
+    def complete(self, system, user, **kw):
+        if self.complete_error:
+            raise self.complete_error
+        return self.complete_text
+
+    def complete_json(self, system, user, **kw):
+        return self.json_payload
+
+    def complete_raw_messages(self, system, messages, tools=None, **kw):
+        return {"content": "answer", "tool_calls": [], "finish_reason": "stop"}
+
+
+class FakeDispatcher:
+    def __init__(self, results=None):
+        self.results = results or {}
+        self.calls = []
+
+    def execute(self, manifest, arguments):
+        tool = manifest.config.get("mcp", {}).get("tool")
+        self.calls.append((tool, arguments))
+        return self.results.get(tool, '{"ok": true, "data": {"id": "job-1"}}')
+
+
+# ===========================================================================
+# 辅助函数
+# ===========================================================================
+
+class TestChainToCapability:
+    def test_known(self):
+        assert ba._chain_to_capability("gene_family") == "bioflow-gene-family"
+        assert ba._chain_to_capability("rnaseq") == "bioflow-rnaseq"
+
+    def test_unknown_and_empty(self):
+        assert ba._chain_to_capability("wgs") is None
+        assert ba._chain_to_capability("") is None
+        assert ba._chain_to_capability(None) is None
+
+    def test_case_and_whitespace(self):
+        assert ba._chain_to_capability(" Gene_Family ") == "bioflow-gene-family"
+
+
+class TestExtractJobId:
+    def test_data_id(self):
+        assert ba._extract_job_id('{"ok": true, "data": {"id": "job-9"}}') == "job-9"
+
+    def test_data_job_id(self):
+        assert ba._extract_job_id('{"ok": true, "data": {"job_id": "job-8"}}') == "job-8"
+
+    def test_flat_id(self):
+        assert ba._extract_job_id('{"ok": true, "id": "job-7"}') == "job-7"
+
+    def test_non_json_and_no_id(self):
+        assert ba._extract_job_id("not json") is None
+        assert ba._extract_job_id('{"ok": false}') is None
+        assert ba._extract_job_id("") is None
+
+
+class TestExecuteTool:
+    def test_unknown_tool(self):
+        out = ba._execute_tool(_tool_manifests(), "ghost", {})
+        assert "未注册" in out
+
+    def test_tool_exception_becomes_text(self):
+        class Boom:
+            def execute(self, manifest, arguments):
+                raise RuntimeError("boom")
+
+        with mock.patch.object(ba, "get_dispatcher", return_value=Boom()):
+            out = ba._execute_tool(_tool_manifests(), "job_status", {"job_id": "j"})
+        assert "工具执行失败" in out
+
+
+class TestParaphrase:
+    def test_llm_success(self):
+        out = ba._paraphrase(FakeLLM(complete_text="已转述。"), "原文")
+        assert out == "已转述。"
+
+    def test_llm_exception_falls_back_to_raw(self):
+        out = ba._paraphrase(FakeLLM(complete_error=RuntimeError("boom")), "原文")
+        assert out == "原文"
+
+    def test_llm_empty_falls_back_to_raw(self):
+        out = ba._paraphrase(FakeLLM(complete_text="  "), "原文")
+        assert out == "原文"
+
+
+class TestQueryJobStatus:
+    def test_calls_job_status_and_paraphrases(self):
+        with mock.patch.object(ba, "_execute_tool", return_value='{"ok": true, "data": {"status": "running"}}'):
+            out = ba._query_job_status("j1", _tool_manifests(), FakeLLM(complete_text="任务进行中。"))
+        assert out == "任务进行中。"
+
+
+# ===========================================================================
+# card 四类 handler 边界（缺必需字段 / files 键 / archive=False / 非 dict payload）
+# ===========================================================================
+
+class TestCardHandlersEdge:
+    def test_form_confirm_missing_job_and_stage_returns_none(self):
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            out = ba._handle_card_result(
+                {"card": "form_confirm", "payload": {"params": {}}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is None
+
+    def test_file_upload_missing_job_returns_none(self):
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            out = ba._handle_card_result(
+                {"card": "file_upload", "payload": {"paths": ["/data/a.fa"]}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is None
+
+    def test_file_upload_missing_files_returns_none(self):
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            out = ba._handle_card_result(
+                {"card": "file_upload", "payload": {"job_id": "j1"}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is None
+
+    def test_file_upload_uses_files_key(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "file_upload",
+                 "payload": {"job_id": "j1", "files": ["https://x/a.fa"]}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls[0][0] == "fetch_source_file"
+
+    def test_file_upload_string_files_coerced(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "file_upload",
+                 "payload": {"job_id": "j1", "files": "https://x/a.fa"}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls[0][0] == "fetch_source_file"
+
+    def test_archive_choice_missing_job_returns_none(self):
+        out = ba._handle_card_result(
+            {"card": "archive_choice", "payload": {"archive": True}},
+            FakeLLM(), {}, _tool_manifests(),
+        )
+        assert out is None
+
+    def test_archive_choice_skip(self):
+        out = ba._handle_card_result(
+            {"card": "archive_choice", "payload": {"job_id": "j1", "archive": False}},
+            FakeLLM(), {}, _tool_manifests(),
+        )
+        assert out is not None
+        assert out["bioflow"]["audit"]["tool_calls"] == 0  # 存档不调工具（走 REST）
+
+    def test_path_selection_rnaseq_chain(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "path_selection",
+                 "payload": {"chain": "rnaseq", "stages": ["rnaseq_qc"]}},
+                FakeLLM(), {"session_id": "s1"}, _tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls[0][0] == "create_rnaseq_job"
+
+    def test_card_non_dict_payload_treated_empty(self):
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            out = ba._handle_card_result(
+                {"card": "form_confirm", "payload": "not-a-dict"},
+                FakeLLM(), {"active_job_id": "j1"}, _tool_manifests(),
+            )
+        assert out is None  # payload 非 dict → 无 stage/job_id → None
+
+    def test_card_result_with_non_dict_is_ignored(self):
+        # try_bioflow_agent 对非 dict 的 card_result 不做 card 路由，走 NL 意图
+        with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+            with mock.patch.object(ba, "_candidate_capabilities", return_value=[]):
+                out = ba.try_bioflow_agent("确认", llm_client=FakeLLM(), card_result="bogus")
+        assert out is None
+
+
+# ===========================================================================
+# _route_card_result 边界
+# ===========================================================================
+
+class TestRouteCardResultEdge:
+    def test_chain_filters_to_capability(self):
+        gf = _manifest("bioflow-gene-family")
+        rn = _manifest("bioflow-rnaseq", "http://x/mcp/rnaseq/")
+        captured = {}
+
+        def fake_build(manifests):
+            captured["manifests"] = [m.name for m in manifests]
+            return ([], {})
+
+        with mock.patch.object(ba, "_registered_capabilities", return_value=[gf, rn]):
+            with mock.patch.object(ba, "_build_tools", side_effect=fake_build):
+                ba._route_card_result(
+                    {"card": "form_confirm", "payload": {"chain": "rnaseq"}},
+                    FakeLLM(), None, None, None,
+                )
+        assert captured["manifests"] == ["bioflow-rnaseq"]  # chain 过滤到 rnaseq 能力
+
+    def test_chain_to_unregistered_capability_returns_none(self):
+        gf = _manifest("bioflow-gene-family")
+        with mock.patch.object(ba, "_registered_capabilities", return_value=[gf]):
+            with mock.patch.object(ba, "_build_tools", return_value=([{"x": 1}], {})):
+                out = ba._route_card_result(
+                    {"card": "form_confirm", "payload": {"chain": "rnaseq"}},
+                    FakeLLM(), None, None, None,
+                )
+        assert out is None  # rnaseq 未注册 → manifests 空 → None
+
+    def test_tools_empty_returns_none(self):
+        gf = _manifest("bioflow-gene-family")
+        with mock.patch.object(ba, "_registered_capabilities", return_value=[gf]):
+            with mock.patch.object(ba, "_build_tools", return_value=([], {})):
+                out = ba._route_card_result(
+                    {"card": "form_confirm", "payload": {}},
+                    FakeLLM(), None, None, None,
+                )
+        assert out is None
+
+    def test_progress_callback_invoked(self):
+        gf = _manifest("bioflow-gene-family")
+        calls = []
+        with mock.patch.object(ba, "_registered_capabilities", return_value=[gf]):
+            with mock.patch.object(ba, "_build_tools", return_value=([{"x": 1}], {})):
+                with mock.patch.object(ba, "_handle_card_result", return_value=None):
+                    ba._route_card_result(
+                        {"card": "form_confirm", "payload": {}},
+                        FakeLLM(), None, None, lambda p: calls.append(p),
+                    )
+        assert calls and calls[0]["stage"] == "bioflow_card"
+        assert calls[0]["card"] == "form_confirm"
+
+    def test_progress_callback_exception_swallowed(self):
+        gf = _manifest("bioflow-gene-family")
+
+        def boom(p):
+            raise RuntimeError("callback boom")
+
+        with mock.patch.object(ba, "_registered_capabilities", return_value=[gf]):
+            with mock.patch.object(ba, "_build_tools", return_value=([{"x": 1}], {})):
+                with mock.patch.object(ba, "_handle_card_result", return_value={"ok": True}):
+                    out = ba._route_card_result(
+                        {"card": "form_confirm", "payload": {}},
+                        FakeLLM(), None, None, boom,
+                    )
+        assert out == {"ok": True}  # 回调异常被吞，不影响主流程
+
+
+# ===========================================================================
+# NL 路径：bioflow 上下文注入 / 卡片与 NL 语义等价
+# ===========================================================================
+
+class TestNLPathBioflowContext:
+    def test_nl_path_injects_bioflow_context(self, tmp_path):
+        from rag.qa_v1_1_73.capabilities.registry import CapabilityRegistry
+        from rag.qa_v1_1_73.capabilities.manifests import parse_capabilities_text
+        yaml = """
+capabilities:
+  - name: bioflow-gene-family
+    provider: mcp
+    permission: read_only
+    session_default: true
+    nl_triggers: [基因家族]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/gene-family/
+"""
+        (tmp_path / "c.yaml").write_text(yaml, encoding="utf-8")
+        registry = CapabilityRegistry(tmp_path / "c.yaml")
+        registry.load()
+        fake_tools = [{"type": "function", "function": {"name": "plan_gene_family",
+                                                        "description": "x",
+                                                        "parameters": {"type": "object", "properties": {}}}}]
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                with mock.patch.object(ba, "_build_tools", return_value=(fake_tools, {})):
+                    with mock.patch.object(ba, "ToolRunner") as FakeRunner:
+                        FakeRunner.return_value.run.return_value = ("已答复", {"rounds": 1})
+                        out = ba.try_bioflow_agent(
+                            "帮我做基因家族分析", llm_client=FakeLLM(),
+                            bioflow={"session_id": "s1", "active_job_id": "job-9", "chain": "gene_family"},
+                        )
+        assert out is not None
+        assert out["bioflow"]["active_job_id"] == "job-9"
+        assert out["bioflow"]["chain"] == "gene_family"
+
+    def test_card_and_nl_share_tool_chain(self):
+        """卡片操作与纯 NL 服务端语义等价：卡片 handler 只调 MCP 工具，不直连控制面。"""
+        # 卡片 handler 用到的工具名 = MCP 工具（job_status/confirm_stage/create_* 等）
+        tm = _tool_manifests()
+        # 四类卡片触发的工具都在 tool_manifests（即 MCP 工具表）里
+        for tool in ("create_gene_family_job", "create_rnaseq_job", "confirm_stage",
+                     "register_job_files", "fetch_source_file", "job_status"):
+            assert tool in tm
+
+
+class TestExtractParamsEdge:
+    def test_llm_exception_returns_empty(self):
+        class RaisingLLM(FakeLLM):
+            def complete_json(self, system, user, **kw):
+                raise RuntimeError("boom")
+
+        known, unknown = ba._extract_params(RaisingLLM(), "x", {"threads": {}})
+        assert known == {} and unknown == []
+
+    def test_unknown_as_string_coerced_to_list(self):
+        llm = FakeLLM(json_payload={"params": {"threads": 8}, "unknown": "bogus_param"})
+        known, unknown = ba._extract_params(llm, "x", {"threads": {}})
+        assert known == {"threads": 8}
+        assert unknown == ["bogus_param"]
+
+    def test_path_selection_with_params(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            ba._handle_card_result(
+                {"card": "path_selection",
+                 "payload": {"chain": "gene_family", "stages": ["identify"],
+                             "params": {"prefix": "Ft.SPL"}}},
+                FakeLLM(), {"session_id": "s1"}, _tool_manifests(),
+            )
+        assert dispatcher.calls[0][1]["params"] == {"prefix": "Ft.SPL"}
+
+    def test_path_selection_create_tool_missing_returns_none(self):
+        tm = _tool_manifests()
+        tm.pop("create_gene_family_job")
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            out = ba._handle_card_result(
+                {"card": "path_selection",
+                 "payload": {"chain": "gene_family", "stages": ["identify"]}},
+                FakeLLM(), {"session_id": "s1"}, tm,
+            )
+        assert out is None
+
+
+# ===========================================================================
+# system prompt 硬规则在位
+# ===========================================================================
+
+class TestSystemPromptRules:
+    def test_param_retry_rule(self):
+        assert "最多 3 次" in ba._SYSTEM_BASE
+
+    def test_human_boundary_rule(self):
+        assert "不可跳过" in ba._SYSTEM_BASE
+        assert "不可代用户确认" in ba._SYSTEM_BASE
+
+    def test_tool_name_no_leak_rule(self):
+        assert "绝不向用户泄露工具名" in ba._SYSTEM_BASE
+
+
+# ===========================================================================
+# ToolRunner.run(history) 边界
+# ===========================================================================
+
+class TestHistoryEdge:
+    def _run_with_history(self, history):
+        captured = {}
+
+        class RecordingLLM:
+            def complete_raw_messages(self, system, messages, tools=None, **kw):
+                captured["messages"] = list(messages)
+                return {"content": "ok", "tool_calls": [], "finish_reason": "stop"}
+
+        runner = ToolRunner(make_llm_complete(RecordingLLM()), max_rounds=1)
+        runner.run("sys", "当前", [], {}, history=history)
+        return captured["messages"]
+
+    def test_none_history(self):
+        msgs = self._run_with_history(None)
+        assert msgs == [{"role": "user", "content": "当前"}]
+
+    def test_non_dict_items_skipped(self):
+        msgs = self._run_with_history(["not-a-dict", {"role": "user", "content": "ok"}])
+        assert msgs == [{"role": "user", "content": "ok"}, {"role": "user", "content": "当前"}]
+
+    def test_empty_content_filtered(self):
+        msgs = self._run_with_history([{"role": "user", "content": "   "}])
+        assert msgs == [{"role": "user", "content": "当前"}]
+
+
+# ===========================================================================
+# S3：card_result rerun / reuse_archive / archive_job 语义
+# ===========================================================================
+
+class TestS3CardSemantics:
+    def test_form_confirm_rerun_true_uses_rerun_stage(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "form_confirm",
+                 "payload": {"job_id": "j1", "stage": "identify",
+                             "params": {"evalue": 1e-5}, "rerun": True}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls[0][0] == "rerun_stage"
+        assert out["bioflow"]["audit"]["tool_names"] == ["rerun_stage"]
+
+    def test_form_confirm_rerun_false_uses_confirm_stage(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            ba._handle_card_result(
+                {"card": "form_confirm",
+                 "payload": {"job_id": "j1", "stage": "identify", "params": {}}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert dispatcher.calls[0][0] == "confirm_stage"
+
+    def test_path_selection_reuse_archive(self):
+        dispatcher = FakeDispatcher({
+            "reuse_archive": '{"ok": true, "data": {"id": "arch-1", '
+                             '"stage_chain": ["identify", "phylogeny"], '
+                             '"params": {"identify": {"prefix": "Ft"}}}}',
+        })
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "path_selection",
+                 "payload": {"chain": "gene_family", "reuse_archive": "SPL 鉴定"}},
+                FakeLLM(), {"session_id": "s1"}, _tool_manifests(),
+            )
+        assert out is not None
+        tools = [c[0] for c in dispatcher.calls]
+        assert tools[0] == "reuse_archive"
+        assert tools[1] == "create_gene_family_job"
+        create_args = dispatcher.calls[1][1]
+        assert create_args["archive_id"] == "arch-1"
+        assert create_args["stages"] == ["identify", "phylogeny"]
+        assert create_args["params"] == {"identify": {"prefix": "Ft"}}
+        assert out["bioflow"]["audit"]["tool_names"] == ["reuse_archive", "create_gene_family_job"]
+
+    def test_archive_choice_archive_true_calls_archive_job(self):
+        dispatcher = FakeDispatcher({"archive_job": '{"ok": true, "data": {"id": "a1"}}'})
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "archive_choice",
+                 "payload": {"job_id": "j1", "archive": True,
+                             "name": "SPL 存档", "description": "d"}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls[0][0] == "archive_job"
+        assert dispatcher.calls[0][1] == {"job_id": "j1", "name": "SPL 存档", "description": "d"}
+        assert out["bioflow"]["audit"]["tool_names"] == ["archive_job"]
+
+    def test_archive_choice_archive_false_no_tool_call(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "archive_choice",
+                 "payload": {"job_id": "j1", "archive": False}},
+                FakeLLM(), {}, _tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls == []  # 跳过存档不发工具请求
+        assert out["bioflow"]["audit"]["tool_calls"] == 0

agent/qa/src/rag/qa_v1_1_73/test_bioflow_agent_s4_supplement.py

@@ -0,0 +1,206 @@
+"""test_bioflow_agent_s4_supplement.py —— S4 覆盖清单补强测试。
+
+覆盖：
+  - _card_extension_action 六种 action 分发到对应扩展工具
+  - 未知 action / 缺 ext_id/action 回退 None
+  - confirm 携带 nl_triggers/parameters/runtime_image；EXT_STATUS 降级话术（确定性）
+  - run 携带 params/files
+  - 真实 configs/capabilities.yaml 三条目（含 bioflow-extension）可解析
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent.parent.parent / "src"))
+
+from rag.qa_v1_1_73 import bioflow_agent as ba  # noqa: E402
+from rag.qa_v1_1_73.capabilities.manifests import CapabilityManifest, parse_capabilities_file  # noqa: E402
+
+EXT_TOOLS = (
+    "create_extension", "extension_status", "build_extension", "trial_run_extension",
+    "validate_extension", "confirm_extension", "publish_extension", "run_extension",
+    "repair_extension",
+)
+
+
+def _ext_tool_manifests():
+    out = {}
+    for t in EXT_TOOLS:
+        out[t] = CapabilityManifest(
+            name="bioflow-extension", provider="mcp",
+            config={"mcp": {"url": "http://127.0.0.1:8098/mcp/extension/", "tool": t}},
+        )
+    return out
+
+
+class FakeLLM:
+    def complete(self, system, user, **kw):
+        return "已收到。"
+
+    def complete_json(self, system, user, **kw):
+        return {}
+
+    def complete_raw_messages(self, system, messages, tools=None, **kw):
+        return {"content": "answer", "tool_calls": [], "finish_reason": "stop"}
+
+
+class FakeDispatcher:
+    def __init__(self, results=None):
+        self.results = results or {}
+        self.calls = []
+
+    def execute(self, manifest, arguments):
+        tool = manifest.config.get("mcp", {}).get("tool")
+        self.calls.append((tool, arguments))
+        return self.results.get(tool, '{"ok": true, "data": {"ext_id": "e1"}}')
+
+
+# ===========================================================================
+# _card_extension_action 分发
+# ===========================================================================
+
+class TestExtensionAction:
+    @pytest.mark.parametrize("action,expected_tool", [
+        ("build", "build_extension"),
+        ("trial_run", "trial_run_extension"),
+        ("validate", "validate_extension"),
+        ("confirm", "confirm_extension"),
+        ("publish", "publish_extension"),
+        ("run", "run_extension"),
+        ("repair", "repair_extension"),
+    ])
+    def test_action_dispatches_to_tool(self, action, expected_tool):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "extension_action", "payload": {"ext_id": "e1", "action": action}},
+                FakeLLM(), {}, _ext_tool_manifests(),
+            )
+        assert out is not None
+        assert dispatcher.calls[0][0] == expected_tool
+        assert dispatcher.calls[0][1] == {"ext_id": "e1"}
+        assert out["bioflow"]["audit"]["tool_names"] == [expected_tool]
+
+    def test_unknown_action_returns_none(self):
+        dispatcher = FakeDispatcher()
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "extension_action", "payload": {"ext_id": "e1", "action": "bogus"}},
+                FakeLLM(), {}, _ext_tool_manifests(),
+            )
+        assert out is None
+
+    def test_missing_ext_id_or_action_returns_none(self):
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            assert ba._handle_card_result(
+                {"card": "extension_action", "payload": {"action": "build"}},
+                FakeLLM(), {}, _ext_tool_manifests(),
+            ) is None
+            assert ba._handle_card_result(
+                {"card": "extension_action", "payload": {"ext_id": "e1"}},
+                FakeLLM(), {}, _ext_tool_manifests(),
+            ) is None
+
+    def test_confirm_passes_triggers_params_image(self):
+        dispatcher = FakeDispatcher()
+        payload = {"ext_id": "e1", "action": "confirm",
+                   "nl_triggers": ["扩展", "触发词"], "parameters": [{"name": "x"}],
+                   "runtime_image": "img"}
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            ba._handle_card_result({"card": "extension_action", "payload": payload},
+                                   FakeLLM(), {}, _ext_tool_manifests())
+        args = dispatcher.calls[0][1]
+        assert args == {"ext_id": "e1", "nl_triggers": ["扩展", "触发词"],
+                        "parameters": [{"name": "x"}], "runtime_image": "img"}
+
+    def test_confirm_status_insufficient_uses_deterministic_script(self):
+        # confirm 返回 EXT_STATUS（状态不足）→ 确定性降级话术（不报 500、不经 LLM）
+        dispatcher = FakeDispatcher({
+            "confirm_extension": '{"ok": false, "code": "EXT_STATUS", "message": "状态不可确认"}',
+        })
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            out = ba._handle_card_result(
+                {"card": "extension_action", "payload": {"ext_id": "e1", "action": "confirm"}},
+                FakeLLM(), {}, _ext_tool_manifests(),
+            )
+        assert out is not None
+        assert "还不能确认" in out["answer"]
+        assert "先完成" in out["answer"]  # 确定性话术（非 LLM 转述）
+
+    def test_run_passes_params_and_files(self):
+        dispatcher = FakeDispatcher()
+        payload = {"ext_id": "e1", "action": "run",
+                   "params": {"cpu": 8}, "files": ["/data/a.fa"]}
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            ba._handle_card_result({"card": "extension_action", "payload": payload},
+                                   FakeLLM(), {}, _ext_tool_manifests())
+        assert dispatcher.calls[0][1] == {"ext_id": "e1", "params": {"cpu": 8}, "files": ["/data/a.fa"]}
+
+    def test_extension_tool_not_in_manifests_returns_none(self):
+        # tool_manifests 里没有扩展工具 → 回退 None（能力未安装/未发现工具）
+        empty = CapabilityManifest(name="bioflow-gene-family", provider="mcp",
+                                   config={"mcp": {"url": "http://x", "tool": "job_status"}})
+        with mock.patch.object(ba, "get_dispatcher", return_value=FakeDispatcher()):
+            out = ba._handle_card_result(
+                {"card": "extension_action", "payload": {"ext_id": "e1", "action": "build"}},
+                FakeLLM(), {}, {"job_status": empty},
+            )
+        assert out is None
+
+
+# ===========================================================================
+# 真实 capabilities.yaml 三条目可解析
+# ===========================================================================
+
+class TestCapabilitiesThreeEntries:
+    def _real_yaml(self) -> Path:
+        return Path(__file__).resolve().parents[5] / "agent" / "qa" / "configs" / "capabilities.yaml"
+
+    def test_three_bioflow_entries(self):
+        manifests, warnings = parse_capabilities_file(self._real_yaml())
+        by_name = {m.name: m for m in manifests}
+        assert {"bioflow-gene-family", "bioflow-rnaseq", "bioflow-extension"} <= set(by_name)
+
+        ext = by_name["bioflow-extension"]
+        assert ext.provider == "mcp"
+        assert ext.permission == "read_only"
+        assert ext.nl_triggers
+        assert ext.config["mcp"]["url"].endswith("/mcp/extension/")
+        assert ext.config["prompt_pack"]["file"] == "bioflow_extension_agent_rules.md"
+
+    def test_bioflow_extension_in_capability_names(self):
+        assert "bioflow-extension" in ba.BIOFLOW_CAPABILITY_NAMES
+        assert ba.CARD_EXTENSION_ACTION == "extension_action"
+        assert ba.CARD_EXTENSION_ACTION in ba.CARD_TYPES
+
+
+# ===========================================================================
+# S5：_route_card_result 对 extension_action 只发现 extension 能力（一次 list_tools）
+# ===========================================================================
+
+class TestRouteExtensionOptimization:
+    def test_extension_action_discovers_only_extension_capability(self):
+        gf = CapabilityManifest(name="bioflow-gene-family", provider="mcp",
+                                config={"mcp": {"url": "http://x/gene-family/"}})
+        rn = CapabilityManifest(name="bioflow-rnaseq", provider="mcp",
+                                config={"mcp": {"url": "http://x/rnaseq/"}})
+        ext = CapabilityManifest(name="bioflow-extension", provider="mcp",
+                                 config={"mcp": {"url": "http://x/extension/"}})
+        captured = {}
+
+        def fake_build(manifests):
+            captured["names"] = [m.name for m in manifests]
+            return ([], {})
+
+        with mock.patch.object(ba, "_registered_capabilities", return_value=[gf, rn, ext]):
+            with mock.patch.object(ba, "_build_tools", side_effect=fake_build):
+                ba._route_card_result(
+                    {"card": "extension_action", "payload": {"ext_id": "e1", "action": "build"}},
+                    FakeLLM(), None, None, None,
+                )
+        # 只把 bioflow-extension manifest 交给 _build_tools（避免对三能力各 list_tools 一次）
+        assert captured["names"] == ["bioflow-extension"]

agent/qa/src/rag/qa_v1_1_73/test_bioflow_agent_s6_config.py

@@ -0,0 +1,116 @@
+"""test_bioflow_agent_s6_config.py —— S6 多配置回归（QA 单元层）。
+
+模拟四种部署配置，断言候选能力集合 + 意图预筛结果正确（真实 E2E/金标 20 题依赖部署，
+此处以 monkeypatch/env 在单元层覆盖漏判安全语义）。
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent.parent.parent / "src"))
+
+from rag.qa_v1_1_73 import bioflow_agent as ba  # noqa: E402
+from rag.qa_v1_1_73.capabilities.registry import CapabilityRegistry  # noqa: E402
+
+THREE_YAML = """
+capabilities:
+  - name: bioflow-gene-family
+    provider: mcp
+    permission: read_only
+    session_default: true
+    nl_triggers: [基因家族, 亚家族]
+    mcp: {url: "http://x/gene-family/"}
+  - name: bioflow-rnaseq
+    provider: mcp
+    permission: read_only
+    session_default: true
+    nl_triggers: [转录组, 差异表达]
+    mcp: {url: "http://x/rnaseq/"}
+  - name: bioflow-extension
+    provider: mcp
+    permission: read_only
+    session_default: true
+    nl_triggers: [自定义扩展]
+    mcp: {url: "http://x/extension/"}
+"""
+
+
+def _registry(tmp_path, yaml_text=THREE_YAML):
+    path = tmp_path / "caps.yaml"
+    path.write_text(yaml_text, encoding="utf-8")
+    reg = CapabilityRegistry(path)
+    reg.load()
+    return reg
+
+
+class FakeLLM:
+    def complete_raw_messages(self, *a, **kw):
+        return {"content": "x", "tool_calls": [], "finish_reason": "stop"}
+
+
+# ===========================================================================
+# 配置 1：全关（QA_V1_ENABLE_BIOFLOW_AGENT=0 + 三能力全卸载）
+# ===========================================================================
+
+class TestConfigAllOff:
+    def test_fuse_off_returns_none(self, tmp_path):
+        reg = _registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=reg):
+            with mock.patch.dict(ba.os.environ, {}, clear=False):
+                ba.os.environ.pop(ba.ENV_FUSE, None)
+                out = ba.try_bioflow_agent("帮我做基因家族分析", llm_client=FakeLLM())
+        assert out is None  # 走原 pipeline
+
+    def test_all_uninstalled_no_candidate(self, tmp_path):
+        reg = _registry(tmp_path, "capabilities: []\n")  # 三能力全卸载
+        with mock.patch.object(ba, "get_registry", return_value=reg):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                assert ba._candidate_capabilities("帮我做基因家族分析", None) == []
+
+
+# ===========================================================================
+# 配置 2：只开基因家族
+# ===========================================================================
+
+class TestConfigGeneFamilyOnly:
+    def test_gene_family_hit_rnaseq_miss(self, tmp_path):
+        reg = _registry(tmp_path)
+        caps = {"bioflow-gene-family": True, "bioflow-rnaseq": False, "bioflow-extension": False}
+        with mock.patch.object(ba, "get_registry", return_value=reg):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                names = [m.name for m in ba._candidate_capabilities("帮我做水稻 SPL 基因家族分析", caps)]
+                assert names == ["bioflow-gene-family"]
+                assert ba._candidate_capabilities("帮我做转录组差异表达分析", caps) == []
+
+
+# ===========================================================================
+# 配置 3：只开转录组
+# ===========================================================================
+
+class TestConfigRnaseqOnly:
+    def test_rnaseq_hit_gene_family_miss(self, tmp_path):
+        reg = _registry(tmp_path)
+        caps = {"bioflow-gene-family": False, "bioflow-rnaseq": True, "bioflow-extension": False}
+        with mock.patch.object(ba, "get_registry", return_value=reg):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                names = [m.name for m in ba._candidate_capabilities("转录组差异表达分析", caps)]
+                assert names == ["bioflow-rnaseq"]
+                assert ba._candidate_capabilities("帮我做水稻 SPL 基因家族分析", caps) == []
+
+
+# ===========================================================================
+# 配置 4：全开但非生信提问
+# ===========================================================================
+
+class TestConfigAllOnNonBioflow:
+    def test_non_bioflow_question_no_candidate(self, tmp_path):
+        reg = _registry(tmp_path)
+        caps = {"bioflow-gene-family": True, "bioflow-rnaseq": True, "bioflow-extension": True}
+        with mock.patch.object(ba, "get_registry", return_value=reg):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                assert ba._candidate_capabilities("光合作用的电子传递链是什么", caps) == []
+                assert ba._candidate_capabilities("什么是转录因子", caps) == []

agent/qa/src/rag/qa_v1_1_73/test_bioflow_agent_supplement.py

@@ -0,0 +1,496 @@
+"""test_bioflow_agent_supplement.py —— S1 覆盖清单补强测试。
+
+补强 dev 的 test_bioflow_agent.py 未覆盖的分支（对照 S1 覆盖清单）：
+  - 熔断开关值解析（1/true/yes/on 与 0/false/off/空/缺失）
+  - nl_triggers 同时命中 → 两个候选（交 LLM 依 description 选）
+  - session_default 回退（True/False）/ registry 访问异常 / registry.get 异常
+  - _build_tools：MCP 工具发现（空 url 跳过 / 发现异常 / 共享连接按能力名 / 无名跳过 / bad schema 兜底）
+  - _build_system：prompt_pack 注入 / 去重 / 加载异常兜底
+  - try_bioflow_agent：tools 空→None、answer 空→None、progress_callback 触发与吞异常
+  - ToolRunner max_rounds=5 / bioflow_agent.MAX_ROUNDS 常量
+  - make_llm_complete 包装（正常 / 异常）
+  - 真实 configs/capabilities.yaml 两条目可解析
+  - bioflow_agent 不 import pipeline/answer_composer（红线静态守卫）
+"""
+from __future__ import annotations
+
+import os
+import sys
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent.parent.parent / "src"))
+
+from rag.qa_v1_1_73 import bioflow_agent as ba  # noqa: E402
+from rag.qa_v1_1_73.capabilities.manifests import (  # noqa: E402
+    CapabilityManifest,
+    parse_capabilities_file,
+)
+from rag.qa_v1_1_73.capabilities.registry import CapabilityRegistry  # noqa: E402
+
+BIOFLOW_YAML = """
+capabilities:
+  - name: bioflow-gene-family
+    provider: mcp
+    permission: read_only
+    description: 基因家族分析
+    session_default: true
+    nl_triggers: [基因家族, 家族成员, 亚家族, 建树]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/gene-family/
+    prompt_pack:
+      file: bioflow_gene_family_agent_rules.md
+  - name: bioflow-rnaseq
+    provider: mcp
+    permission: read_only
+    description: 转录组分析
+    session_default: true
+    nl_triggers: [转录组, RNA-seq, 差异表达, 富集]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/rnaseq/
+    prompt_pack:
+      file: bioflow_rnaseq_agent_rules.md
+"""
+
+
+def _make_registry(tmp_path: Path, yaml_text: str = BIOFLOW_YAML) -> CapabilityRegistry:
+    path = tmp_path / "capabilities.yaml"
+    path.write_text(yaml_text, encoding="utf-8")
+    registry = CapabilityRegistry(path)
+    registry.load()
+    return registry
+
+
+def _gf_manifest(**overrides) -> CapabilityManifest:
+    cfg = {
+        "mcp": {"url": "http://127.0.0.1:8098/mcp/gene-family/"},
+        "prompt_pack": {"file": "bioflow_gene_family_agent_rules.md"},
+    }
+    cfg.update(overrides.pop("config", {}))
+    return CapabilityManifest(
+        name="bioflow-gene-family", provider="mcp", permission="read_only",
+        description="基因家族分析", config=cfg, nl_triggers=["基因家族"], **overrides,
+    )
+
+
+class FakeLLMClient:
+    def __init__(self, content: str = "已为您规划分析路径。") -> None:
+        self.content = content
+
+    def complete_raw_messages(self, system, messages, tools=None, **kwargs):
+        return {"content": self.content, "tool_calls": [], "finish_reason": "stop"}
+
+
+# ===========================================================================
+# 门 1：熔断开关值解析
+# ===========================================================================
+
+class TestEnvFuse:
+    @pytest.mark.parametrize("value", ["1", "true", "TRUE", "yes", "on", " On ", "YES"])
+    def test_truthy(self, value):
+        with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: value}):
+            assert ba._env_enabled() is True
+
+    @pytest.mark.parametrize("value", ["0", "false", "off", "", "no", "   "])
+    def test_falsy(self, value):
+        with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: value}):
+            assert ba._env_enabled() is False
+
+    def test_missing_defaults_off(self):
+        with mock.patch.dict(ba.os.environ, {}, clear=False):
+            ba.os.environ.pop(ba.ENV_FUSE, None)
+            assert ba._env_enabled() is False
+
+
+# ===========================================================================
+# 门 3：nl_triggers 意图预筛
+# ===========================================================================
+
+class TestIntentMatchEdge:
+    def test_empty_triggers_never_match(self):
+        assert ba._intent_match("做基因家族分析", []) is False
+        assert ba._intent_match("做基因家族分析", [""]) is False
+
+    def test_case_insensitive_substring(self):
+        assert ba._intent_match("RNA-SEQ 分析", ["rna-seq"]) is True
+        assert ba._intent_match("ka/ks 选择压力", ["Ka/Ks"]) is True
+
+
+# ===========================================================================
+# 门 2 + 门 3：候选能力（registry 异常 / session_default 回退 / 同时命中）
+# ===========================================================================
+
+class TestCandidateCapabilities:
+    def test_registry_access_exception_returns_empty(self):
+        with mock.patch.object(ba, "get_registry", side_effect=RuntimeError("boom")):
+            assert ba._candidate_capabilities("做基因家族", None) == []
+
+    def test_registry_get_exception_skips(self):
+        class BadRegistry:
+            def get(self, name):
+                raise RuntimeError("boom")
+
+        with mock.patch.object(ba, "get_registry", return_value=BadRegistry()):
+            assert ba._candidate_capabilities("做基因家族", None) == []
+
+    def test_both_triggers_match_returns_both(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            caps = ba._candidate_capabilities("做基因家族和转录组差异表达分析", None)
+            assert [m.name for m in caps] == ["bioflow-gene-family", "bioflow-rnaseq"]
+
+    def test_session_default_false_skips(self, tmp_path):
+        yaml = BIOFLOW_YAML.replace("session_default: true", "session_default: false")
+        registry = _make_registry(tmp_path, yaml)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            # 无会话开关时回退 session_default=false → 不候选
+            assert ba._candidate_capabilities("做基因家族分析", None) == []
+            # 显式会话开关 true → 候选
+            caps = ba._candidate_capabilities("做基因家族分析", {"bioflow-gene-family": True})
+            assert [m.name for m in caps] == ["bioflow-gene-family"]
+
+    def test_session_switch_true_overrides_default_false(self, tmp_path):
+        yaml = BIOFLOW_YAML.replace("session_default: true", "session_default: false", 1)
+        registry = _make_registry(tmp_path, yaml)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            caps = ba._candidate_capabilities("做基因家族分析", {"bioflow-gene-family": True})
+            assert [m.name for m in caps] == ["bioflow-gene-family"]
+
+
+# ===========================================================================
+# _build_tools：MCP 工具发现
+# ===========================================================================
+
+class _FakeDispatcher:
+    def __init__(self, tools_by_name=None, exc=None):
+        self.tools_by_name = tools_by_name or {}
+        self.exc = exc
+
+    def list_mcp_tools(self, manifest):
+        if self.exc:
+            raise self.exc
+        return self.tools_by_name.get(manifest.name, [])
+
+
+class TestBuildTools:
+    def test_empty_url_skipped(self):
+        manifest = CapabilityManifest(
+            name="x", provider="mcp", config={"mcp": {"url": ""}}
+        )
+        with mock.patch.object(ba, "get_dispatcher", return_value=_FakeDispatcher()):
+            tools, tool_manifests = ba._build_tools([manifest])
+        assert tools == []
+        assert tool_manifests == {}
+
+    def test_discovery_exception_skipped(self):
+        manifest = _gf_manifest()
+        with mock.patch.object(
+            ba, "get_dispatcher",
+            return_value=_FakeDispatcher(exc=RuntimeError("mcp down")),
+        ):
+            tools, tool_manifests = ba._build_tools([manifest])
+        assert tools == []
+        assert tool_manifests == {}
+
+    def test_builds_schema_and_shared_connection(self):
+        dispatcher = _FakeDispatcher({
+            "bioflow-gene-family": [
+                {"name": "plan_gene_family", "description": "规划路径",
+                 "input_schema": {"type": "object", "properties": {"message": {"type": "string"}}}},
+            ]
+        })
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            tools, tool_manifests = ba._build_tools([_gf_manifest()])
+        assert len(tools) == 1
+        assert tools[0]["function"]["name"] == "plan_gene_family"
+        assert tools[0]["function"]["description"] == "规划路径"
+        # 共享连接：manifest.name 用能力名，mcp.tool 指向真实 server 工具名
+        tm = tool_manifests["plan_gene_family"]
+        assert tm.name == "bioflow-gene-family"
+        assert tm.config["mcp"]["tool"] == "plan_gene_family"
+        assert tm.config["mcp"]["url"].endswith("/mcp/gene-family/")
+
+    def test_skips_nameless_and_bad_schema(self):
+        dispatcher = _FakeDispatcher({
+            "bioflow-gene-family": [
+                {"name": "", "description": "无名", "input_schema": {}},
+                {"name": "job_status", "description": "查状态", "input_schema": "not-a-dict"},
+            ]
+        })
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            tools, tool_manifests = ba._build_tools([_gf_manifest()])
+        assert [t["function"]["name"] for t in tools] == ["job_status"]
+        assert tools[0]["function"]["parameters"] == {"type": "object", "properties": {}}
+
+    def test_shared_tool_deduped_across_capabilities(self):
+        """两能力同时命中：共享工具去重（只保留首个能力），专有工具各自保留。
+
+        覆盖 bug ① 修复：job_status 等 12 个共享工具两端点语义一致，按名去重后
+        LLM tools 列表无重名，且 job_status 路由到首个能力（gene-family）。
+        """
+        dispatcher = _FakeDispatcher({
+            "bioflow-gene-family": [
+                {"name": "plan_gene_family", "description": "规划基因家族", "input_schema": {}},
+                {"name": "job_status", "description": "查状态", "input_schema": {}},
+                {"name": "confirm_stage", "description": "确认参数", "input_schema": {}},
+            ],
+            "bioflow-rnaseq": [
+                {"name": "plan_rnaseq", "description": "规划转录组", "input_schema": {}},
+                {"name": "job_status", "description": "查状态", "input_schema": {}},
+                {"name": "confirm_stage", "description": "确认参数", "input_schema": {}},
+            ],
+        })
+        rn = CapabilityManifest(
+            name="bioflow-rnaseq", provider="mcp", permission="read_only",
+            description="转录组分析", nl_triggers=["转录组"],
+            config={"mcp": {"url": "http://127.0.0.1:8098/mcp/rnaseq/"}},
+        )
+        with mock.patch.object(ba, "get_dispatcher", return_value=dispatcher):
+            tools, tool_manifests = ba._build_tools([_gf_manifest(), rn])
+
+        names = [t["function"]["name"] for t in tools]
+        # 专有工具各保留 + 共享工具只保留一份，且无重名
+        assert names == ["plan_gene_family", "job_status", "confirm_stage", "plan_rnaseq"]
+        assert len(names) == len(set(names))
+
+        # 共享工具路由到首个能力（gene-family）
+        assert tool_manifests["job_status"].name == "bioflow-gene-family"
+        assert tool_manifests["job_status"].config["mcp"]["url"].endswith("/mcp/gene-family/")
+        assert tool_manifests["confirm_stage"].name == "bioflow-gene-family"
+        # 专有工具各自路由到自身能力
+        assert tool_manifests["plan_rnaseq"].name == "bioflow-rnaseq"
+        assert tool_manifests["plan_rnaseq"].config["mcp"]["url"].endswith("/mcp/rnaseq/")
+        assert tool_manifests["plan_gene_family"].name == "bioflow-gene-family"
+
+# ===========================================================================
+# _build_system：prompt_pack 注入
+# ===========================================================================
+
+class TestBuildSystem:
+    def test_appends_prompt_pack(self):
+        manifest = _gf_manifest()
+        with mock.patch.object(ba.PromptPackProvider, "load", return_value="基因家族规则正文"):
+            system = ba._build_system([manifest])
+        assert ba._SYSTEM_BASE in system
+        assert "基因家族规则正文" in system
+
+    def test_dedup_same_file_once(self):
+        m1 = _gf_manifest()
+        m2 = _gf_manifest()  # 同 file
+        calls = []
+        with mock.patch.object(ba.PromptPackProvider, "load", side_effect=lambda m, root: calls.append(m) or "RULES"):
+            system = ba._build_system([m1, m2])
+        assert len(calls) == 1  # 去重后只加载一次
+        assert system.count("RULES") == 1
+
+    def test_empty_file_skipped(self):
+        manifest = CapabilityManifest(name="x", provider="mcp", config={"prompt_pack": {"file": ""}})
+        system = ba._build_system([manifest])
+        assert system == ba._SYSTEM_BASE
+
+    def test_load_exception_falls_back(self):
+        manifest = _gf_manifest()
+        with mock.patch.object(ba.PromptPackProvider, "load", side_effect=RuntimeError("boom")):
+            system = ba._build_system([manifest])
+        assert ba._SYSTEM_BASE in system  # 不炸，只用基础提示
+
+
+# ===========================================================================
+# try_bioflow_agent：tools 空 / answer 空 / progress_callback
+# ===========================================================================
+
+class TestFullFlowEdge:
+    def test_tools_empty_returns_none(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                with mock.patch.object(ba, "_build_tools", return_value=([], {})):
+                    result = ba.try_bioflow_agent(
+                        "帮我做基因家族分析", llm_client=FakeLLMClient(), capabilities=None
+                    )
+        assert result is None
+
+    def test_answer_empty_returns_none(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        fake_tools = [{"type": "function", "function": {"name": "plan_gene_family",
+                                                        "description": "x",
+                                                        "parameters": {"type": "object", "properties": {}}}}]
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                with mock.patch.object(ba, "_build_tools", return_value=(fake_tools, {})):
+                    with mock.patch.object(ba, "ToolRunner") as FakeRunner:
+                        FakeRunner.return_value.run.return_value = ("", {"rounds": 1})
+                        result = ba.try_bioflow_agent(
+                            "帮我做基因家族分析", llm_client=FakeLLMClient(), capabilities=None
+                        )
+        assert result is None
+
+    def test_progress_callback_invoked(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        fake_tools = [{"type": "function", "function": {"name": "plan_gene_family",
+                                                        "description": "x",
+                                                        "parameters": {"type": "object", "properties": {}}}}]
+        calls = []
+
+        def cb(payload):
+            calls.append(payload)
+
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                with mock.patch.object(ba, "_build_tools", return_value=(fake_tools, {})):
+                    with mock.patch.object(ba, "ToolRunner") as FakeRunner:
+                        FakeRunner.return_value.run.return_value = ("已答复", {"rounds": 1})
+                        result = ba.try_bioflow_agent(
+                            "帮我做基因家族分析", llm_client=FakeLLMClient(),
+                            capabilities=None, progress_callback=cb,
+                        )
+        assert result is not None
+        assert calls and calls[0]["stage"] == "bioflow_agent_started"
+        assert calls[0]["capabilities"] == ["bioflow-gene-family"]
+        assert calls[0]["tool_count"] == 1
+
+    def test_progress_callback_exception_swallowed(self, tmp_path):
+        registry = _make_registry(tmp_path)
+        fake_tools = [{"type": "function", "function": {"name": "plan_gene_family",
+                                                        "description": "x",
+                                                        "parameters": {"type": "object", "properties": {}}}}]
+
+        def cb(payload):
+            raise RuntimeError("callback boom")
+
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                with mock.patch.object(ba, "_build_tools", return_value=(fake_tools, {})):
+                    with mock.patch.object(ba, "ToolRunner") as FakeRunner:
+                        FakeRunner.return_value.run.return_value = ("已答复", {"rounds": 1})
+                        result = ba.try_bioflow_agent(
+                            "帮我做基因家族分析", llm_client=FakeLLMClient(),
+                            capabilities=None, progress_callback=cb,
+                        )
+        assert result is not None  # 回调异常被吞，不影响主流程
+        assert result["answer"] == "已答复"
+
+
+# ===========================================================================
+# ToolRunner max_rounds=5 / MAX_ROUNDS 常量
+# ===========================================================================
+
+class TestMaxRounds:
+    def test_max_rounds_constant_is_5(self):
+        assert ba.MAX_ROUNDS == 5
+
+    def test_tool_runner_respects_max_rounds_5(self):
+        from rag.qa_v1_1_73.tool_runner import ToolRunner
+
+        class LLM:
+            def __call__(self, system, messages, tools):
+                return "", [{"id": "c", "name": "echo", "arguments": "{}"}], None
+
+        class Dispatcher:
+            def execute(self, manifest, arguments):
+                return "ok"
+
+        manifest = CapabilityManifest(name="echo", provider="python")
+        tools = [{"type": "function", "function": {"name": "echo", "description": "e",
+                                                    "parameters": {"type": "object", "properties": {}}}}]
+        runner = ToolRunner(LLM(), dispatcher=Dispatcher(), max_rounds=5)
+        content, audit = runner.run("sys", "user", tools, {"echo": manifest})
+        assert audit["rounds"] == 5
+        assert audit["tool_calls"] == 5
+
+
+# ===========================================================================
+# make_llm_complete 包装
+# ===========================================================================
+
+class TestMakeLLMComplete:
+    def test_normal(self):
+        from rag.qa_v1_1_73.tool_runner import make_llm_complete
+
+        class Client:
+            def complete_raw_messages(self, system, messages, tools=None, **kw):
+                return {"content": "hi", "tool_calls": [{"name": "x"}], "finish_reason": "stop"}
+
+        complete = make_llm_complete(Client())
+        content, tool_calls, error = complete("sys", [{"role": "user", "content": "q"}], [])
+        assert content == "hi"
+        assert tool_calls == [{"name": "x"}]
+        assert error is None
+
+    def test_exception_becomes_error(self):
+        from rag.qa_v1_1_73.tool_runner import make_llm_complete
+
+        class Client:
+            def complete_raw_messages(self, *a, **kw):
+                raise RuntimeError("llm down")
+
+        complete = make_llm_complete(Client())
+        content, tool_calls, error = complete("sys", [], [])
+        assert content == ""
+        assert tool_calls == []
+        assert "RuntimeError" in error
+
+
+# ===========================================================================
+# 真实 configs/capabilities.yaml 两条目可解析
+# ===========================================================================
+
+class TestRealCapabilitiesYaml:
+    def _real_yaml(self) -> Path:
+        repo_root = Path(__file__).resolve().parents[5]
+        return repo_root / "agent" / "qa" / "configs" / "capabilities.yaml"
+
+    def test_both_bioflow_entries_parse(self):
+        manifests, warnings = parse_capabilities_file(self._real_yaml())
+        by_name = {m.name: m for m in manifests}
+        assert "bioflow-gene-family" in by_name
+        assert "bioflow-rnaseq" in by_name
+
+        gf = by_name["bioflow-gene-family"]
+        assert gf.provider == "mcp"
+        assert gf.permission == "read_only"
+        assert gf.nl_triggers
+        assert gf.config["mcp"]["url"].endswith("/mcp/gene-family/")
+        assert gf.config["prompt_pack"]["file"] == "bioflow_gene_family_agent_rules.md"
+
+        rn = by_name["bioflow-rnaseq"]
+        assert rn.permission == "read_only"
+        assert rn.nl_triggers
+        assert rn.config["mcp"]["url"].endswith("/mcp/rnaseq/")
+        assert rn.config["prompt_pack"]["file"] == "bioflow_rnaseq_agent_rules.md"
+
+    def test_nl_triggers_cover_expected_words(self):
+        manifests, _ = parse_capabilities_file(self._real_yaml())
+        gf = next(m for m in manifests if m.name == "bioflow-gene-family")
+        rn = next(m for m in manifests if m.name == "bioflow-rnaseq")
+        # 关键触发词在位（意图预筛依赖）
+        assert "基因家族" in gf.nl_triggers
+        assert "转录组" in rn.nl_triggers
+
+
+# ===========================================================================
+# 红线静态守卫：bioflow_agent 不依赖 pipeline / answer_composer
+# ===========================================================================
+
+class TestRedLineNoPipelineDep:
+    def test_no_pipeline_or_answer_composer_import(self):
+        import ast
+
+        src = Path(ba.__file__).read_text(encoding="utf-8")
+        tree = ast.parse(src)
+        imported = []
+        for node in tree.body:
+            if isinstance(node, ast.Import):
+                imported += [a.name for a in node.names]
+            elif isinstance(node, ast.ImportFrom):
+                imported.append(node.module or "")
+        assert not any("pipeline" in m or "answer_composer" in m for m in imported)
+
+    def test_never_raises(self, tmp_path):
+        # 任何异常都返回 None/正常 payload，绝不外抛
+        with mock.patch.object(ba, "get_registry", side_effect=RuntimeError("boom")):
+            with mock.patch.dict(ba.os.environ, {ba.ENV_FUSE: "1"}):
+                result = ba.try_bioflow_agent("做基因家族", llm_client=FakeLLMClient())
+        assert result is None

agent/qa/src/rag/qa_v1_1_73/tool_runner.py

@@ -51,9 +51,13 @@ class ToolRunner:
         user: str,
         tools: List[Dict[str, Any]],
         manifests: Dict[str, CapabilityManifest],
+        history: Optional[List[Dict[str, str]]] = None,
     ) -> Tuple[str, Dict[str, Any]]:
         """执行工具调用循环。返回 (content, audit)。
 
+        history：多轮记忆（S2），List[{role: user|assistant, content}]，旧→新，
+        不含当前这轮提问；注入为 messages 前置轮次（作为上下文，不参与工具结果回填）。
+
         audit: {"rounds": n, "tool_calls": k, "used_json_fallback": bool,
                 "tool_names": [...], "errors": [...]}
         """
@@ -64,7 +68,16 @@ class ToolRunner:
             "tool_names": [],
             "errors": [],
         }
-        messages: List[Dict[str, Any]] = [{"role": "user", "content": user}]
+        messages: List[Dict[str, Any]] = []
+        for h in history or []:
+            if not isinstance(h, dict):
+                continue
+            role = str(h.get("role") or "").strip()
+            content = str(h.get("content") or "").strip()
+            if role not in {"user", "assistant"} or not content:
+                continue
+            messages.append({"role": role, "content": content})
+        messages.append({"role": "user", "content": user})
         system_text = system
         for round_index in range(1, self.max_rounds + 1):
             audit["rounds"] = round_index

bioflow_service/SKILL.md

@@ -0,0 +1,85 @@
+---
+name: bioflow-analysis
+description: >-
+  PlantAI 生信分析编排 Skill。当用户提供原始组学数据（蛋白 FASTA/基因组/FASTQ/表达矩阵等）
+  并提出基因家族、转录组、变异或自定义分析需求时使用。负责从原始数据到交付报告的
+  全流程编排：选链路、登记资产、就绪检查、参数确认、执行、诊断、版本化修改、交付清单。
+  触发词见 nl_triggers；仅在明确涉及生信分析时触发。
+nl_triggers:
+  - 基因家族
+  - 家族成员
+  - 亚家族
+  - 系统发育
+  - 建树
+  - 进化树
+  - motif
+  - 结构域
+  - 共线性
+  - Ka/Ks
+  - 转录组
+  - RNA-seq
+  - RNAseq
+  - rnaseq
+  - 差异表达
+  - 表达定量
+  - 富集
+  - WGCNA
+  - GSEA
+  - fastq
+  - 实验设计
+  - 生信分析
+  - 变异检测
+  - GWAS
+---
+
+# bioflow-analysis 能力声明
+
+PlantAI 生信分析 Skill，面向「原始数据 → 交付报告」的分析编排。所有分析经
+`bioflowctl`（唯一事实源）与 11 个分析控制 MCP 工具完成，服务端状态经 SQLite 持久化。
+
+## 11 工具白名单
+
+Skill 只允许调用以下 11 个分析控制工具（其余为内部实现，不外泄）：
+
+| 工具 | 职责 | 对应 CLI |
+|------|------|----------|
+| get_task_context | 任务绑定（session/job/plan_revision/run_id/当前阶段） | — |
+| inspect_asset | 资产/文件探测（格式/预览/列结构） | file inspect |
+| validate_plan | 读单一参数 schema 校验参数 | （补齐） |
+| check_readiness | 四象限就绪检查（环境/参考/磁盘/预算） | check readiness |
+| get_run_evidence | 运行证据（日志切片/失败原因/manifest 校验值） | — |
+| propose_change | 参数变更影响范围 | change propose |
+| apply_change | 幂等应用变更 | change apply |
+| execute_nodes | 只重跑受影响节点 | run node-execute |
+| control_execution | 执行所有权（stop/resume） | run stop/resume |
+| validate_delivery | 交付清单完整性校验 | delivery validate |
+| publish_delivery | 发布交付清单 | delivery publish |
+
+## 对话剧本
+
+1. **原始数据**：识别用户提供的原始数据（蛋白 FASTA / 基因组 / FASTQ / 表达矩阵 / 设计表）。
+2. **选链路**：`inspect_asset` 探测数据格式；据此选择分析链路（基因家族 / 转录组 / …）。
+3. **登记**：登记数据资产（角色化 `asset register`），保证「下游直入」可用。
+4. **就绪**：`check_readiness` 四象限检查；缺项返回结构化错误阻断，不启动。
+5. **参数确认**：`validate_plan` 校验参数；未知参数/越界拒绝。
+6. **执行**：`execute_nodes` 只重跑受影响节点；`control_execution` 管理执行所有权。
+7. **诊断**：失败时 `get_run_evidence` 取日志切片/manifest 校验值，按 8 类错误分类
+   （input/resource/environment/transient/adapter/artifact/reference/scientific_precondition）。
+8. **版本化**：`propose_change` + `apply_change` 版本化修改，历史不覆盖、幂等。
+9. **交付**：`validate_delivery` + `publish_delivery` 校验并发布交付清单。
+
+## 人工边界（requires_human）
+
+- `subfamily_confirm`：亚家族分类确认，须人工确认，不可代用户。
+- `rnaseq_de`：差异表达实验设计确认，须人工确认，不可代用户。
+上述阶段在 pending_actions 中 `requires_human=true`，Skill 只呈现表单默认值，不代确认。
+
+## 验收清单
+
+- [ ] 原始数据格式已探测（inspect_asset）
+- [ ] 就绪检查通过（check_readiness ready=true）
+- [ ] 参数经单一 schema 校验（validate_plan）
+- [ ] 执行所有权唯一（control_execution 不重复接管/不重叠）
+- [ ] 失败已诊断（get_run_evidence + 8 类错误分类）
+- [ ] 变更版本化（propose_change/apply_change 幂等、历史不覆盖）
+- [ ] 交付清单完整并已发布（validate_delivery ok → publish_delivery approved）

bioflow_service/app/main.py

@@ -2,13 +2,21 @@
 
 - 独立部署树 bioflow_service/（FR-BIO-028：独立进程 8098 + 独立 SQLite）。
 - lifespan：init_db（幂等迁移）→ init_context（kernel/catalog/planner/runner）
-  → recover（服务重启恢复 in-flight 续跑，FR-BIO-031）→ shutdown 清理。
+  → recover（服务重启恢复 in-flight 续跑，FR-BIO-031）→ MCP session manager
+  （anyio task group，streamable-http 处理请求必需）→ shutdown 清理。
 - 端点：health（/api/bioflow/health，前端探活 FR-BIO-025）。
 - 不依赖 BFF/生产服务（8090/8091 等绝不探测/连接）。
 """
 from __future__ import annotations
 
 import logging
+from pathlib import Path
+
+from dotenv import load_dotenv
+
+# 把 bioflow_service/.env 注入 os.environ（llm.py 等模块直读 DOCGEN_LLM_*，
+# 不走 pydantic-settings 的 env_file，避免「.env 配了但 os.environ 读不到」的配置断层）。
+load_dotenv(Path(__file__).resolve().parent.parent / ".env")
 from contextlib import asynccontextmanager
 
 from fastapi import FastAPI
@@ -17,11 +25,18 @@ from fastapi.middleware.cors import CORSMiddleware
 from .config import get_settings
 from .context import context, init_context, shutdown_context
 from .db import close_db, init_db
+from .mcp_server import extension_mcp, gene_family_mcp, rnaseq_mcp
 from .routers import bioarchives, bioflow, biojobs, extension
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+# 三个 MCP streamable-http app（调用即创建 session_manager，供 lifespan 进入 run()）。
+# 端点地址：/mcp/gene-family、/mcp/rnaseq、/mcp/extension（streamable_http_path="/" + 挂载前缀）。
+_gene_family_mcp_app = gene_family_mcp.streamable_http_app(streamable_http_path="/")
+_rnaseq_mcp_app = rnaseq_mcp.streamable_http_app(streamable_http_path="/")
+_extension_mcp_app = extension_mcp.streamable_http_app(streamable_http_path="/")
+
 
 def create_app() -> FastAPI:
     settings = get_settings()
@@ -60,14 +75,21 @@ def create_app() -> FastAPI:
                         logger.info("main: 重启恢复 %d 个 in-flight 任务续跑", len(recovered))
             except Exception:
                 logger.exception("main: 重启恢复扫描失败（任务不重跑，等待后续操作）")
-        try:
-            yield
-        finally:
-            await shutdown_context()
-            try:
-                await close_db()
-            except Exception:
-                pass
+
+        # MCP session manager 的 task group 必须在服务运行期内保持活跃
+        # （streamable-http 处理请求时要求已初始化）。Starlette 不会自动运行
+        # 子 Mount 的 lifespan，故在此显式进入三个 MCP 的 run()。
+        async with gene_family_mcp.session_manager.run():
+            async with rnaseq_mcp.session_manager.run():
+                async with extension_mcp.session_manager.run():
+                    try:
+                        yield
+                    finally:
+                        await shutdown_context()
+                        try:
+                            await close_db()
+                        except Exception:
+                            pass
 
     app.router.lifespan_context = _lifespan
 
@@ -75,6 +97,12 @@ def create_app() -> FastAPI:
     app.include_router(biojobs.router)
     app.include_router(bioarchives.router)
     app.include_router(extension.router)
+
+    # 生信 MCP 能力外挂（mcp 2.x：MCPServer.streamable_http_app）。
+    # 三个独立 streamable-http 端点，各自装卸（REST 面不受影响）。
+    app.mount("/mcp/gene-family", _gene_family_mcp_app)
+    app.mount("/mcp/rnaseq", _rnaseq_mcp_app)
+    app.mount("/mcp/extension", _extension_mcp_app)
     return app
 
 

bioflow_service/app/mcp_server.py

@@ -0,0 +1,900 @@
+"""app/mcp_server.py —— 生信 MCP server（两个 streamable-http 端点）。
+
+- `/mcp/gene-family`：基因家族能力单元（plan/create/ask + 共享控制组 + 文件组）
+- `/mcp/rnaseq`：转录组能力单元（plan/create/generate_samples_yaml/ask + 共享控制组 + 文件组）
+
+设计约束（实施方案 S0）：
+- 工具只承诺「已受理」，执行进度/日志由 SSE 事件总线直推，不走 MCP。
+- 每个能力单元只接受本链阶段（create 跨链拒绝 CROSS_CHAIN）。
+- 人工确认边界（subfamily_confirm / rnaseq_de 实验设计确认）在 job_status 的
+  pending_actions 里标 requires_human=true，工具不提供绕过。
+- 白名单沿用 runner._allowed_param_names（单一事实源）。
+- 工具名不外泄由 QA agent（S1）负责，本模块只负责工具语义。
+
+mcp 2.x 注意：MCPServer（非 FastMCP，来自 mcp.server.mcpserver）；挂载用
+`mcp.streamable_http_app()`。本文件位于 app/ 层（非 services/），可用 pydantic（mcp
+自身也依赖 pydantic 构造 schema）。
+"""
+from __future__ import annotations
+
+import logging
+import re
+import uuid
+from pathlib import Path
+from typing import Any
+
+from .config import get_settings
+from .context import load_record
+from .services.bioflow import extensions as ext_mod
+from .services.bioflow import store
+from .services.bioflow.archive import archive_from_job
+from .services.bioflow.catalog import GENE_FAMILY_CHAIN
+from .services.bioflow.errors import error_result
+from .services.bioflow.file_transform import validate_format
+from .services.bioflow.runner import RunnerError, ensure_samples_yaml, llm_sample_fallback
+from .services.bioflow.source_fetcher import fetch_source
+
+# 薄适配：委托 bioflowctl CLI（唯一事实源），不重复业务逻辑
+from bioflowctl.commands import (
+    cmd_archive,
+    cmd_archive_reuse,
+    cmd_file_inspect,
+    cmd_file_transform,
+    cmd_source_fetch,
+)
+
+logger = logging.getLogger(__name__)
+
+
+def _mcp_err(code: str, message: str, *, evidence_refs: list[str] | None = None) -> dict[str, Any]:
+    """G13：MCP 工具失败返回统一结构化错误对象（code 顶层 + error 对象）。"""
+    return error_result(code, message, evidence_refs=evidence_refs)
+
+# ---- 能力单元阶段白名单 ----
+
+GENE_FAMILY_STAGES = set(GENE_FAMILY_CHAIN)
+
+RNASEQ_STAGES = {
+    "rnaseq_qc", "rnaseq_align", "rnaseq_quant", "rnaseq_sample_qc", "rnaseq_de",
+    "rnaseq_wgcna", "rnaseq_go_enrich", "rnaseq_kegg_enrich", "rnaseq_enrich",
+    "rnaseq_fgsea", "rnaseq_candidate_family", "rnaseq_report",
+    "annotation", "expression",
+}
+
+# 人工确认边界：这些阶段 waiting_confirm 时 requires_human=true，工具/QA 不可代确认
+HUMAN_CONFIRM_STAGES = {"subfamily_confirm", "rnaseq_de"}
+
+
+# ---------------------------------------------------------------------------
+# context 访问（动态读模块全局，测试 monkeypatch 兼容）
+# ---------------------------------------------------------------------------
+
+def _ctx():
+    from . import context as context_mod
+
+    return context_mod.context
+
+
+def _job_detail(record: Any) -> dict[str, Any]:
+    stages = []
+    for stage in record.stage_chain:
+        st = record._stage_states.get(stage, {})
+        stages.append({
+            "stage": stage,
+            "status": st.get("status", "waiting"),
+            "params": st.get("params") or {},
+            "attempt": int(st.get("attempt") or 0),
+            "manifest_path": st.get("manifest_path"),
+            "log_tail": st.get("log_tail") or "",
+            "error": st.get("error"),
+        })
+    return {
+        "id": record.id,
+        "session_id": record.session_id,
+        "title": record.title,
+        "status": record.status,
+        "stages": stages,
+        "params": record.params,
+        "auto_continue": record.auto_continue,
+        "archive_id": record.archive_id,
+        "progress": record.progress(),
+    }
+
+
+# ---------------------------------------------------------------------------
+# pending_actions 派生（job_status 工具返回给 QA agent 的下一步动作）
+# ---------------------------------------------------------------------------
+
+def derive_pending_actions(record: Any, runner: Any) -> list[dict[str, Any]]:
+    """由任务/阶段状态派生待办动作（QA agent 据此引导用户，人工边界不可代确认）。
+
+    按阶段链顺序找第一个「卡住」的环节，返回动作清单（通常 0-1 条）。
+    """
+    if record.status == "paused":
+        return [{"action": "resume", "stage": None, "requires_human": False,
+                 "message": "任务已暂停，可恢复"}]
+    if record.status == "done":
+        return [{"action": "archive", "stage": None, "requires_human": False,
+                 "message": "任务已完成，可存档复用"}]
+    if record.status == "archived":
+        return [{"action": "none", "stage": None, "requires_human": False,
+                 "message": "任务已存档"}]
+
+    for stage in record.stage_chain:
+        status = record._stage_states.get(stage, {}).get("status", "waiting")
+        if status == "await_files":
+            return [{"action": "provide_files", "stage": stage, "requires_human": False,
+                     "message": f"阶段 {stage} 等待输入文件"}]
+        if status == "waiting_confirm":
+            human = stage in HUMAN_CONFIRM_STAGES
+            return [{"action": "confirm", "stage": stage, "requires_human": human,
+                     "form_defaults": runner._form_defaults(stage, record),
+                     "message": (f"阶段 {stage} 需人工确认（不可代确认）" if human
+                                 else f"阶段 {stage} 等待参数确认")}]
+        if status == "failed":
+            return [{"action": "rerun_or_skip", "stage": stage, "requires_human": False,
+                     "message": f"阶段 {stage} 失败，可重跑或跳过"}]
+        if status == "partial_success":
+            # G4：partial_success 独立终态，不被当作 success/done
+            return [{"action": "rerun_or_skip", "stage": stage, "requires_human": False,
+                     "message": f"阶段 {stage} 部分成功（产物不全），可重跑或跳过"}]
+        # waiting/running/queued/done/skipped → 继续
+    return []
+
+
+# ---------------------------------------------------------------------------
+# 工具实现（命名 async 函数，带类型提示，供两个 MCPServer 注册）
+# ---------------------------------------------------------------------------
+
+async def _plan(message: str, allowed_stages: set[str]) -> dict[str, Any]:
+    from .services.bioflow.planner import PlanCandidate, PlannerError, PlanResult
+
+    ctx = _ctx()
+    if ctx.planner is None:
+        return {"ok": False, "code": "NOT_READY", "message": "规划器未就绪"}
+    try:
+        plan = await ctx.planner.plan(message)
+    except PlannerError as exc:
+        fallback = [s for s in ("identify", "rnaseq_qc") if s in allowed_stages and ctx.catalog.has(s)]
+        plan = PlanResult(candidates=[PlanCandidate(purpose="内置默认流程", stages=fallback)],
+                          source="llm_only", message=exc.message)
+    candidates = []
+    for c in plan.candidates:
+        stages = [s for s in c.stages if s in allowed_stages]
+        if stages:
+            candidates.append({"purpose": c.purpose, "stages": stages})
+    return {
+        "ok": True,
+        "candidates": candidates,
+        "source": plan.source,
+        "reuse_archive": plan.reuse_archive_id,
+        "reuse_name": plan.reuse_name,
+        "fallback": plan.message or None,
+    }
+
+
+async def _create_job(session_id: str, title: str, stages: list[str],
+                      params: dict[str, Any] | None, auto_continue: bool,
+                      archive_id: str | None, allowed_stages: set[str]) -> dict[str, Any]:
+    ctx = _ctx()
+    unknown = [s for s in stages if s not in allowed_stages]
+    if unknown:
+        return {"ok": False, "code": "CROSS_CHAIN",
+                "message": f"阶段不属于该能力单元: {', '.join(unknown)}"}
+    try:
+        record = await ctx.runner.create_job(
+            session_id, title or "生信任务", stages, params or {},
+            auto_continue=auto_continue, archive_id=archive_id,
+        )
+    except RunnerError as exc:
+        return {"ok": False, "code": exc.code, "message": exc.message}
+    ctx.records[record.id] = record
+    return {"ok": True, "data": _job_detail(record)}
+
+
+async def _job_status(job_id: str) -> dict[str, Any]:
+    ctx = _ctx()
+    record = await load_record(job_id)
+    if record is None:
+        return {"ok": False, "code": "NOT_FOUND", "message": "任务不存在"}
+    detail = _job_detail(record)
+    detail["pending_actions"] = derive_pending_actions(record, ctx.runner)
+    return {"ok": True, "data": detail}
+
+
+async def _confirm_stage(job_id: str, stage: str, params: dict[str, Any] | None) -> dict[str, Any]:
+    ctx = _ctx()
+    record = await load_record(job_id)
+    if record is None:
+        return {"ok": False, "code": "NOT_FOUND", "message": "任务不存在"}
+    if stage not in record.stage_chain:
+        return {"ok": False, "code": "NOT_FOUND", "message": f"阶段不存在: {stage}"}
+    try:
+        await ctx.runner.confirm_stage(record, stage, params or {})
+    except RunnerError as exc:
+        return {"ok": False, "code": exc.code, "message": exc.message}
+    return {"ok": True, "data": {"job_id": job_id, "stage": stage,
+                                 "status": ctx.runner.stage_status(record, stage)}}
+
+
+async def _rerun_stage(job_id: str, stage: str, params: dict[str, Any] | None) -> dict[str, Any]:
+    ctx = _ctx()
+    record = await load_record(job_id)
+    if record is None:
+        return {"ok": False, "code": "NOT_FOUND", "message": "任务不存在"}
+    if stage not in record.stage_chain:
+        return {"ok": False, "code": "NOT_FOUND", "message": f"阶段不存在: {stage}"}
+    try:
+        await ctx.runner.rerun_stage(record, stage, params)
+    except RunnerError as exc:
+        return {"ok": False, "code": exc.code, "message": exc.message}
+    return {"ok": True, "data": {"job_id": job_id, "stage": stage,
+                                 "status": ctx.runner.stage_status(record, stage)}}
+
+
+async def _skip_stage(job_id: str, stage: str) -> dict[str, Any]:
+    ctx = _ctx()
+    record = await load_record(job_id)
+    if record is None:
+        return {"ok": False, "code": "NOT_FOUND", "message": "任务不存在"}
+    if stage not in record.stage_chain:
+        return {"ok": False, "code": "NOT_FOUND", "message": f"阶段不存在: {stage}"}
+    try:
+        await ctx.runner.skip_stage(record, stage)
+    except RunnerError as exc:
+        return {"ok": False, "code": exc.code, "message": exc.message}
+    return {"ok": True, "data": {"job_id": job_id, "stage": stage,
+                                 "status": ctx.runner.stage_status(record, stage)}}
+
+
+async def _pause_job(job_id: str) -> dict[str, Any]:
+    ctx = _ctx()
+    record = await load_record(job_id)
+    if record is None:
+        return {"ok": False, "code": "NOT_FOUND", "message": "任务不存在"}
+    try:
+        await ctx.runner.pause_job(record)
+    except RunnerError as exc:
+        return {"ok": False, "code": exc.code, "message": exc.message}
+    return {"ok": True, "data": {"job_id": job_id, "status": record.status}}
+
+
+async def _resume_job(job_id: str) -> dict[str, Any]:
+    ctx = _ctx()
+    record = await load_record(job_id)
+    if record is None:
+        return {"ok": False, "code": "NOT_FOUND", "message": "任务不存在"}
+    try:
+        await ctx.runner.resume_job(record)
+    except RunnerError as exc:
+        return {"ok": False, "code": exc.code, "message": exc.message}
+    return {"ok": True, "data": {"job_id": job_id, "status": record.status}}
+
+
+async def _archive_job(job_id: str, name: str, description: str,
+                       include_intermediate: bool) -> dict[str, Any]:
+    """任务存档（薄适配）：委托 cmd_archive（唯一事实源），仅保留内存 record 校验 + 事件发布。"""
+    ctx = _ctx()
+    record = await load_record(job_id)
+    if record is None:
+        return _mcp_err("NOT_FOUND", "任务不存在")
+    result = await cmd_archive(
+        job_id, name, description,
+        db=ctx.db,
+        record=record,
+        include_intermediate=bool(include_intermediate),
+        archive_fn=archive_from_job,
+        archives_dir=get_settings().archives_dir_abs,
+    )
+    if result.get("ok"):
+        ctx.events.publish("job_archived", {"job_id": job_id, "archive_id": result["data"]["id"]})
+    return result
+
+
+# ---------------------------------------------------------------------------
+# 扩展能力单元（第三个能力单元 bioflow-extension）：复用 extensions.py 状态机
+# ---------------------------------------------------------------------------
+
+_EXT_VIEW_KEYS = (
+    "ext_id", "display_name", "status", "command_template", "original_command",
+    "runtime_image", "requirements", "parameters", "input_roles", "nl_triggers",
+    "analysis_type", "golden", "repair_count", "trial", "validation", "last_build",
+    "created_at", "updated_at",
+)
+
+
+def _ext_view(ext: dict[str, Any]) -> dict[str, Any]:
+    """扩展精简视图（剔除 source_files 等超长字段，供 MCP 工具结果返回）。"""
+    return {k: ext.get(k) for k in _EXT_VIEW_KEYS if k in ext}
+
+
+def _file_items(files: Any) -> list[tuple[str, bytes]]:
+    """把 MCP 入参 [{path, content|data}] 转为 [(rel_path, bytes)]。"""
+    out: list[tuple[str, bytes]] = []
+    if not isinstance(files, list):
+        return out
+    for f in files:
+        if not isinstance(f, dict):
+            continue
+        path = str(f.get("path") or f.get("name") or "").strip()
+        if not path:
+            continue
+        content = f.get("content")
+        if content is None:
+            content = f.get("data") or ""
+        if isinstance(content, (bytes, bytearray)):
+            blob = bytes(content)
+        else:
+            blob = str(content).encode("utf-8")
+        out.append((path, blob))
+    return out
+
+
+def _ext_err(exc: Exception) -> str:
+    if isinstance(exc, ext_mod.ExtensionNotFoundError):
+        return "NOT_FOUND"
+    if isinstance(exc, ext_mod.ExtensionStatusError):
+        return "EXT_STATUS"
+    if isinstance(exc, ext_mod.ExtensionBuildError):
+        return "EXT_BUILD"
+    if isinstance(exc, ext_mod.ExtensionRunError):
+        return "EXT_RUN"
+    return "EXT_ERROR"
+
+
+async def _create_extension(display_name: str, command: str, runtime_image: str,
+                            code_files: Any, data_files: Any) -> dict[str, Any]:
+    code = _file_items(code_files)
+    if not code:
+        return {"ok": False, "code": "VALIDATION", "message": "扩展代码包不能为空"}
+    try:
+        ext = ext_mod.get_store().create_extension(
+            display_name=display_name, command=command, runtime_image=runtime_image or "",
+            code_files=code, data_files=_file_items(data_files),
+        )
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": _ext_view(ext)}
+
+
+async def _extension_status(ext_id: str) -> dict[str, Any]:
+    try:
+        ext = ext_mod.get_store().load_extension(ext_id)
+    except ext_mod.ExtensionNotFoundError:
+        return {"ok": False, "code": "NOT_FOUND", "message": "扩展不存在"}
+    return {"ok": True, "data": _ext_view(ext) if ext else None}
+
+
+async def _build_extension(ext_id: str) -> dict[str, Any]:
+    try:
+        ext = await ext_mod.get_store().build_extension(ext_id)
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": _ext_view(ext)}
+
+
+async def _trial_run_extension(ext_id: str) -> dict[str, Any]:
+    try:
+        ext = await ext_mod.get_store().trial_run(ext_id)
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": _ext_view(ext)}
+
+
+async def _validate_extension(ext_id: str) -> dict[str, Any]:
+    try:
+        ext = ext_mod.get_store().validate(ext_id)
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": _ext_view(ext)}
+
+
+async def _confirm_extension(ext_id: str, nl_triggers: Any, parameters: Any,
+                             runtime_image: str) -> dict[str, Any]:
+    triggers = [str(x).strip() for x in nl_triggers if str(x).strip()] if isinstance(nl_triggers, list) else None
+    params = parameters if isinstance(parameters, list) else None
+    try:
+        ext = ext_mod.get_store().confirm(
+            ext_id, nl_triggers=triggers, parameters=params,
+            runtime_image=runtime_image or None,
+        )
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": _ext_view(ext)}
+
+
+async def _publish_extension(ext_id: str) -> dict[str, Any]:
+    try:
+        ext = ext_mod.get_store().publish(ext_id)
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": _ext_view(ext)}
+
+
+async def _run_extension(ext_id: str, params: Any, files: Any) -> dict[str, Any]:
+    try:
+        result = await ext_mod.get_store().run(
+            ext_id,
+            params=params if isinstance(params, dict) else None,
+            files=[str(f) for f in files] if isinstance(files, list) else None,
+        )
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": result}
+
+
+async def _repair_extension(ext_id: str) -> dict[str, Any]:
+    try:
+        ext = await ext_mod.get_store().repair(ext_id)
+    except ext_mod.ExtensionError as exc:
+        return {"ok": False, "code": _ext_err(exc), "message": str(exc)}
+    return {"ok": True, "data": _ext_view(ext)}
+
+
+# ---- 文件登记（复刻 biojobs._register_path 核心，无 FastAPI 依赖）----
+
+def _blocked_reason(path: Path, settings: Any) -> str | None:
+    s = str(path)
+    for prefix in settings.sensitive_path_prefixes:
+        if s == prefix or s.startswith(prefix + "/"):
+            return f"敏感路径前缀 {prefix}"
+    for pat in settings.sensitive_filename_patterns:
+        if re.match(pat, path.name):
+            return f"敏感文件名 {path.name}"
+    return None
+
+
+async def _register_job_files(job_id: str, paths: list[str]) -> dict[str, Any]:
+    """登记服务器/局域网路径（单文件或目录展开）到任务 input。"""
+    ctx = _ctx()
+    settings = get_settings()
+    record = await load_record(job_id)
+    if record is None:
+        return _mcp_err("NOT_FOUND", "任务不存在")
+
+    input_dir = record.input_dir
+    input_dir.mkdir(parents=True, exist_ok=True)
+    items: list[dict[str, Any]] = []
+    registered: list[str] = []
+
+    for raw in paths:
+        p = Path(raw).expanduser().resolve()
+        if not p.exists():
+            return _mcp_err("PATH_NOT_EXIST", f"路径不存在: {raw}")
+        blocked = _blocked_reason(p, settings)
+        if blocked:
+            return _mcp_err("PATH_NOT_ALLOWED", f"路径不允许: {raw}（{blocked}）")
+        files: list[Path] = []
+        if p.is_file():
+            files = [p]
+        else:
+            ext_set = settings.upload_ext_set
+            for f in sorted(p.rglob("*")):
+                if f.is_file() and (not ext_set or f.suffix.lower() in ext_set) and not _blocked_reason(f, settings):
+                    files.append(f)
+            if not files:
+                return _mcp_err("VALIDATION", f"目录内无可登记文件: {raw}")
+        for f in files:
+            link = input_dir / f.name
+            try:
+                if not link.exists():
+                    link.symlink_to(f)
+            except OSError as exc:  # noqa: BLE001
+                logger.warning("mcp register symlink 失败: %s -> %s (%s)", f, link, exc)
+            items.append({"file_id": f"{record.id}:{f.name}", "name": f.name,
+                          "size": f.stat().st_size, "path": str(f), "source": "server_path"})
+            registered.append(str(f))
+
+    # rnaseq 系：samples.yaml 生成（描述文件优先 + 实况分析；规则不可归纳走 LLM 兜底）
+    try:
+        source_roots = [str(Path(x).parent) for x in paths if Path(x).exists()]
+        extra_mounts = ensure_samples_yaml(input_dir, source_roots=[Path(r) for r in source_roots])
+        if not extra_mounts:
+            try:
+                await llm_sample_fallback(input_dir, [Path(r) for r in source_roots])
+            except Exception as exc:  # noqa: BLE001
+                logger.warning("samples.yaml LLM 兜底失败: %s", exc)
+        if extra_mounts:
+            record.registered_server_paths = list(
+                dict.fromkeys((getattr(record, "registered_server_paths", None) or [])
+                              + [str(Path(m)) for m in extra_mounts]))
+    except Exception as exc:  # noqa: BLE001
+        logger.warning("samples.yaml 分析失败: %s", exc)
+
+    if registered:
+        import json
+        record.registered_server_paths = list(
+            dict.fromkeys((getattr(record, "registered_server_paths", None) or []) + registered)
+        )
+        (record.job_dir / "server_registered.json").write_text(
+            json.dumps({"registered_server_paths": record.registered_server_paths},
+                       ensure_ascii=False), encoding="utf-8")
+
+    # 自动续跑（await_inputs 任务重推；非等待态 no-op）
+    await ctx.runner.retry_after_files(record)
+    return {"ok": True, "data": {"items": items, "total": len(items)}}
+
+
+async def _ask_question(question: str) -> dict[str, Any]:
+    ctx = _ctx()
+    hits: list[dict[str, Any]] = []
+    if ctx.flow_store is not None:
+        try:
+            hits = ctx.flow_store.search(question, top_k=8).get("items") or []
+        except Exception:  # noqa: BLE001
+            hits = []
+    citations = []
+    for h in hits:
+        citations.append({
+            "source": h.get("source") or h.get("doc_kind") or "",
+            "title_path": h.get("title_path") or "",
+            "path": h.get("path") or "",
+            "text": str(h.get("text") or "")[:1200],
+        })
+    return {"ok": True, "citations": citations, "degraded": not citations}
+
+
+async def _list_archives(page: int, page_size: int) -> dict[str, Any]:
+    ctx = _ctx()
+    items, total = await store.list_archives(ctx.db, page=page, page_size=page_size)
+    return {"ok": True, "items": items, "total": total, "page": page, "page_size": page_size}
+
+
+async def _reuse_archive(name: str) -> dict[str, Any]:
+    """复用存档（薄适配）：委托 cmd_archive_reuse（读各阶段实际生效参数）。"""
+    return await cmd_archive_reuse(name, db=_ctx().db)
+
+
+async def _fetch_source_file(job_id: str | None, source: str,
+                             credentials: dict[str, Any] | None) -> dict[str, Any]:
+    """拉取源文件（薄适配）：委托 cmd_source_fetch，仅保留内存 record 校验。"""
+    if job_id:
+        record = await load_record(job_id)
+        if record is None:
+            return _mcp_err("NOT_FOUND", "任务不存在")
+    return await cmd_source_fetch(source, job_id=job_id, credentials=credentials,
+                                 fetch_fn=fetch_source)
+
+
+async def _inspect_file(path: str) -> dict[str, Any]:
+    """探测文件（薄适配）：委托 cmd_file_inspect。"""
+    return cmd_file_inspect(path)
+
+
+async def _transform_file(src_path: str, target_format: str,
+                          column_map: dict[str, str] | None,
+                          dest_path: str | None) -> dict[str, Any]:
+    """转换文件（薄适配）：委托 cmd_file_transform（注入 LLM 适配器）。"""
+    from .services.bioflow.llm import complete_json
+
+    async def llm_adapter(user: str, system: str) -> Any:
+        return await complete_json(system, user, temperature=0.2, max_tokens=2000)
+
+    return await cmd_file_transform(
+        src_path, target_format, column_map=column_map, dest=dest_path, llm=llm_adapter,
+    )
+
+
+async def _generate_samples_yaml(job_id: str, sample_description: str) -> dict[str, Any]:
+    import yaml
+
+    from .services.bioflow.llm import complete_json
+
+    record = await load_record(job_id)
+    if record is None:
+        return {"ok": False, "code": "NOT_FOUND", "message": "任务不存在"}
+    system = (
+        "你是 RNA-seq 样本配置助手。根据用户的自然语言描述，输出 samples.yaml 结构 JSON："
+        '{"samples": {"样本名": {"r1": "fastq路径", "r2": "fastq路径", "condition": "...", ...}}}。'
+        "只输出 JSON。"
+    )
+    try:
+        raw = await complete_json(system, sample_description, temperature=0.2, max_tokens=2000)
+        samples = raw.get("samples") if isinstance(raw, dict) else None
+        if not isinstance(samples, dict) or not samples:
+            return {"ok": False, "code": "EMPTY_SAMPLES", "message": "未能从描述解析出样本"}
+    except Exception as exc:  # noqa: BLE001
+        return {"ok": False, "code": "SAMPLES_GEN_FAILED", "message": f"样本配置生成失败: {exc}"}
+    record.input_dir.mkdir(parents=True, exist_ok=True)
+    out = record.input_dir / "samples.yaml"
+    out.write_text(yaml.safe_dump({"samples": samples}, allow_unicode=True), encoding="utf-8")
+    v = validate_format(out, "samples.yaml")
+    if not v.get("ok"):
+        out.unlink(missing_ok=True)
+        return {"ok": False, "code": "VALIDATION_FAILED", "message": f"样本配置校验失败: {v.get('reason')}"}
+    return {"ok": True, "data": {"path": str(out), "samples": samples, "validated": v}}
+
+
+# ---------------------------------------------------------------------------
+# 能力单元工具（命名 async，带类型提示 + 中文描述）
+# ---------------------------------------------------------------------------
+
+async def plan_gene_family(message: str) -> dict[str, Any]:
+    """根据用户自然语言需求规划基因家族分析候选路径（仅基因家族链阶段）。"""
+    return await _plan(message, GENE_FAMILY_STAGES)
+
+
+async def create_gene_family_job(session_id: str, stages: list[str], title: str = "",
+                                 params: dict[str, Any] | None = None,
+                                 auto_continue: bool = False,
+                                 archive_id: str | None = None) -> dict[str, Any]:
+    """按确认的阶段链创建基因家族任务（stages 只能是基因家族链阶段，跨链拒绝）。"""
+    return await _create_job(session_id, title, stages, params, auto_continue, archive_id, GENE_FAMILY_STAGES)
+
+
+async def ask_gene_family_question(question: str) -> dict[str, Any]:
+    """回答基因家族流程/参数/生物学意义类问题（流程知识库检索，带引用）。"""
+    return await _ask_question(question)
+
+
+async def plan_rnaseq(message: str) -> dict[str, Any]:
+    """根据用户自然语言需求规划转录组分析候选路径（仅转录组链阶段）。"""
+    return await _plan(message, RNASEQ_STAGES)
+
+
+async def create_rnaseq_job(session_id: str, stages: list[str], title: str = "",
+                            params: dict[str, Any] | None = None,
+                            auto_continue: bool = False,
+                            archive_id: str | None = None) -> dict[str, Any]:
+    """按确认的阶段链创建转录组任务（stages 只能是转录组链阶段，跨链拒绝）。"""
+    return await _create_job(session_id, title, stages, params, auto_continue, archive_id, RNASEQ_STAGES)
+
+
+async def generate_samples_yaml(job_id: str, sample_description: str) -> dict[str, Any]:
+    """把用户的自然语言样本描述（样本名/对照处理组/重复/单双端等）解析为 samples.yaml 写入任务 input。"""
+    return await _generate_samples_yaml(job_id, sample_description)
+
+
+async def ask_rnaseq_question(question: str) -> dict[str, Any]:
+    """回答转录组流程/参数/实验设计类问题（流程知识库检索，带引用）。"""
+    return await _ask_question(question)
+
+
+async def job_status(job_id: str) -> dict[str, Any]:
+    """查询生信任务状态：任务/各阶段状态 + 下一步待办动作(pending_actions)。卡住或需确认时用本工具查真相。"""
+    return await _job_status(job_id)
+
+
+async def confirm_stage(job_id: str, stage: str, params: dict[str, Any] | None = None) -> dict[str, Any]:
+    """确认某阶段参数并执行。仅 waiting_confirm 状态可确认；参数名须在白名单内(未知参数被拒)。人工确认边界阶段(subfamily_confirm/rnaseq_de)不可代用户确认。"""
+    return await _confirm_stage(job_id, stage, params)
+
+
+async def register_job_files(job_id: str, paths: list[str]) -> dict[str, Any]:
+    """把服务器/局域网路径(单文件或目录)登记为任务输入文件。目录按扩展名白名单展开。"""
+    return await _register_job_files(job_id, paths)
+
+
+async def rerun_stage(job_id: str, stage: str, params: dict[str, Any] | None = None) -> dict[str, Any]:
+    """重跑失败阶段(带参数则先等确认)。仅 failed 状态可重跑。"""
+    return await _rerun_stage(job_id, stage, params)
+
+
+async def skip_stage(job_id: str, stage: str) -> dict[str, Any]:
+    """跳过失败阶段并推进后续。仅 failed 状态可跳过。"""
+    return await _skip_stage(job_id, stage)
+
+
+async def pause_job(job_id: str) -> dict[str, Any]:
+    """暂停运行中的任务(running 阶段会立即 kill 容器)。"""
+    return await _pause_job(job_id)
+
+
+async def resume_job(job_id: str) -> dict[str, Any]:
+    """恢复已暂停的任务(从下一阶段继续,确认点不跳过)。"""
+    return await _resume_job(job_id)
+
+
+async def list_archives(page: int = 1, page_size: int = 20) -> dict[str, Any]:
+    """列出历史存档任务(供复用参考)。"""
+    return await _list_archives(page, page_size)
+
+
+async def reuse_archive(name: str) -> dict[str, Any]:
+    """按名称匹配存档,返回其阶段链+参数(供复用发起)。"""
+    return await _reuse_archive(name)
+
+
+async def archive_job(job_id: str, name: str, description: str = "",
+                      include_intermediate: bool = False) -> dict[str, Any]:
+    """把已完成任务存档(打包结果/日志/事件 + 落档登记);重名拒绝(ARCHIVE_EXISTS)。"""
+    return await _archive_job(job_id, name, description, include_intermediate)
+
+
+# ---------------------------------------------------------------------------
+# 扩展能力单元工具（第三个能力单元 bioflow-extension）
+# ---------------------------------------------------------------------------
+
+async def create_extension(display_name: str, command: str, runtime_image: str = "",
+                           code_files: list[dict[str, Any]] | None = None,
+                           data_files: list[dict[str, Any]] | None = None) -> dict[str, Any]:
+    """创建扩展草稿(draft)：上传代码文件清单(每项 {path, content 文本}) + 运行命令 + 显示名。"""
+    return await _create_extension(display_name, command, runtime_image, code_files, data_files)
+
+
+async def extension_status(ext_id: str) -> dict[str, Any]:
+    """查询扩展详情与状态(draft/build/trial/validated/confirming/published)。"""
+    return await _extension_status(ext_id)
+
+
+async def build_extension(ext_id: str) -> dict[str, Any]:
+    """AI 转换扩展(原始命令→command_template+参数+dependencies)；LLM 失败自动回退规则版。"""
+    return await _build_extension(ext_id)
+
+
+async def trial_run_extension(ext_id: str) -> dict[str, Any]:
+    """试运行扩展(docker 执行；未接入执行器时返回 EXT_RUN 503 语义)。"""
+    return await _trial_run_extension(ext_id)
+
+
+async def validate_extension(ext_id: str) -> dict[str, Any]:
+    """校验扩展(金标/试运行校验)。仅 built/trial_passed 可校验。"""
+    return await _validate_extension(ext_id)
+
+
+async def confirm_extension(ext_id: str, nl_triggers: list[str] | None = None,
+                            parameters: list[dict[str, Any]] | None = None,
+                            runtime_image: str = "") -> dict[str, Any]:
+    """确认扩展参数/触发词(用户可编辑 nl_triggers)；仅 validated/trial_passed 可确认。"""
+    return await _confirm_extension(ext_id, nl_triggers, parameters, runtime_image)
+
+
+async def publish_extension(ext_id: str) -> dict[str, Any]:
+    """发布扩展(仅 published 状态可被自然语言触发运行)。"""
+    return await _publish_extension(ext_id)
+
+
+async def run_extension(ext_id: str, params: dict[str, Any] | None = None,
+                        files: list[str] | None = None) -> dict[str, Any]:
+    """正式运行已发布扩展(同步返回 run_result)。"""
+    return await _run_extension(ext_id, params, files)
+
+
+async def repair_extension(ext_id: str) -> dict[str, Any]:
+    """AI 修复扩展(试运行失败上下文→LLM 修复 command_template/依赖；LLM 失败回退规则版)。"""
+    return await _repair_extension(ext_id)
+
+
+async def fetch_source_file(source: str, job_id: str | None = None,
+                            credentials: dict[str, Any] | None = None) -> dict[str, Any]:
+    """从 web(http/https 流式)、OSS(oss:// 或预签名 URL)或局域网路径拉取源文件到任务 input;下载前检查磁盘余量并记录 provenance。"""
+    return await _fetch_source_file(job_id, source, credentials)
+
+
+async def inspect_file(path: str) -> dict[str, Any]:
+    """探测文件格式(扩展名仅参考):返回预览/列结构/大小/格式猜测/乱码检测,供判断是否需要预处理。"""
+    return await _inspect_file(path)
+
+
+async def transform_file(src_path: str, target_format: str,
+                         column_map: dict[str, str] | None = None,
+                         dest_path: str | None = None) -> dict[str, Any]:
+    """把非标准文件(xlsx/csv/tsv/txt)转换为 fasta/gff3/tsv/samples.yaml;LLM 定列映射规则+脚本执行,结果过格式验证器。"""
+    return await _transform_file(src_path, target_format, column_map, dest_path)
+
+
+# ---------------------------------------------------------------------------
+# G12：11 个分析控制 MCP 工具（异步薄封装委托 skill_tools，不写业务逻辑）
+# ---------------------------------------------------------------------------
+
+async def get_task_context(job_id: str | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.get_task_context(job_id)
+
+
+async def inspect_asset(role: str = "pep.fa", path: str = "") -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.inspect_asset(role, path)
+
+
+async def validate_plan(stages: list[str] | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.validate_plan(stages)
+
+
+async def check_readiness(assets_root: str = "", stages: list[str] | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.check_readiness(assets_root, stages)
+
+
+async def get_run_evidence(run_id: str = "") -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.get_run_evidence(run_id)
+
+
+async def propose_change(job_id: str = "", stage: str = "",
+                               params: dict[str, Any] | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.propose_change(job_id, stage, params)
+
+
+async def apply_change(action_id: str = "", change: dict[str, Any] | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.apply_change(action_id, change)
+
+
+async def execute_nodes(job_id: str = "", nodes: list[str] | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.execute_nodes(job_id, nodes)
+
+
+async def control_execution(run_id: str = "", command: str = "") -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.control_execution(run_id, command)
+
+
+async def validate_delivery(manifest: dict[str, Any] | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.validate_delivery(manifest)
+
+
+async def publish_delivery(manifest: dict[str, Any] | None = None) -> dict[str, Any]:
+    from .services.bioflow import skill_tools
+    return skill_tools.publish_delivery(manifest)
+
+
+SKILL_CONTROL_TOOLS = [
+    get_task_context, inspect_asset, validate_plan,
+    check_readiness, get_run_evidence, propose_change,
+    apply_change, execute_nodes, control_execution,
+    validate_delivery, publish_delivery,
+]
+
+
+# ---------------------------------------------------------------------------
+# 构建三个 MCPServer（基因家族 / 转录组 / 扩展）
+# ---------------------------------------------------------------------------
+
+def build_mcp_servers() -> tuple[Any, Any, Any]:
+    from mcp.server.mcpserver import MCPServer
+
+    gf = MCPServer(
+        "bioflow-gene-family",
+        title="PlantAI 基因家族分析",
+        description="基因家族分析能力单元：路径规划/建任务/确认参数/查状态/文件获取与预处理。",
+    )
+    rn = MCPServer(
+        "bioflow-rnaseq",
+        title="PlantAI 转录组分析",
+        description="转录组分析能力单元：路径规划/样本配置生成/建任务/确认参数/查状态/文件获取与预处理。",
+    )
+    ext = MCPServer(
+        "bioflow-extension",
+        title="PlantAI 用户自定义扩展分析",
+        description="用户自定义扩展分析能力单元：创建/转换/试运行/校验/确认/发布/运行。",
+    )
+
+    gf.tool(name="plan_gene_family", description="根据用户自然语言需求规划基因家族分析候选路径（仅基因家族链阶段）。返回 2-3 条候选路径供用户确认。")(plan_gene_family)
+    gf.tool(name="create_gene_family_job", description="按确认的阶段链创建基因家族任务。stages 只能是基因家族链阶段（跨链拒绝）。")(create_gene_family_job)
+    gf.tool(name="ask_gene_family_question", description="回答基因家族流程/参数/生物学意义类问题（流程知识库检索，带引用）。")(ask_gene_family_question)
+
+    rn.tool(name="plan_rnaseq", description="根据用户自然语言需求规划转录组分析候选路径（仅转录组链阶段）。返回候选路径供用户确认。")(plan_rnaseq)
+    rn.tool(name="create_rnaseq_job", description="按确认的阶段链创建转录组任务。stages 只能是转录组链阶段（跨链拒绝）。")(create_rnaseq_job)
+    rn.tool(name="generate_samples_yaml", description="把用户的自然语言样本描述解析为 samples.yaml 写入任务 input。")(generate_samples_yaml)
+    rn.tool(name="ask_rnaseq_question", description="回答转录组流程/参数/实验设计类问题（流程知识库检索，带引用）。")(ask_rnaseq_question)
+
+    ext.tool(name="create_extension", description="创建扩展草稿（draft）：上传代码文件清单(每项 {path, content 文本}) + 运行命令 + 显示名。")(create_extension)
+    ext.tool(name="extension_status", description="查询扩展详情与状态（draft/build/trial/validated/confirming/published）。")(extension_status)
+    ext.tool(name="build_extension", description="AI 转换扩展（原始命令→command_template+参数+依赖）；LLM 失败自动回退规则版。")(build_extension)
+    ext.tool(name="trial_run_extension", description="试运行扩展（docker 执行；未接入执行器时返回 EXT_RUN）。")(trial_run_extension)
+    ext.tool(name="validate_extension", description="校验扩展（金标/试运行校验）。仅 built/trial_passed 可校验。")(validate_extension)
+    ext.tool(name="confirm_extension", description="确认扩展参数/触发词（用户可编辑 nl_triggers）；仅 validated/trial_passed 可确认。")(confirm_extension)
+    ext.tool(name="publish_extension", description="发布扩展（仅 published 状态可被自然语言触发运行）。")(publish_extension)
+    ext.tool(name="run_extension", description="正式运行已发布扩展（同步返回 run_result）。")(run_extension)
+    ext.tool(name="repair_extension", description="AI 修复扩展（试运行失败上下文→LLM 修复；LLM 失败回退规则版）。")(repair_extension)
+
+    shared = [
+        job_status, confirm_stage, register_job_files, rerun_stage, skip_stage,
+        pause_job, resume_job, list_archives, reuse_archive, archive_job,
+        fetch_source_file, inspect_file, transform_file,
+    ]
+    for mcp in (gf, rn):
+        for fn in shared:
+            mcp.tool()(fn)
+        # G12：11 个分析控制工具（Skill 编排，异步薄封装委托 skill_tools）
+        for fn in SKILL_CONTROL_TOOLS:
+            mcp.tool()(fn)
+    return gf, rn, ext
+
+
+gene_family_mcp, rnaseq_mcp, extension_mcp = build_mcp_servers()

bioflow_service/app/routers/bioarchives.py

@@ -31,10 +31,16 @@ from ..schemas import ArchiveCreateRequest, ArchiveRunRequest
 from ..services.bioflow import store
 from ..services.bioflow.archive import (
     archive_from_job,
+    effective_stage_params,
     normalize_archive_name,
     remove_archive_dir,
 )
-from ..services.bioflow.reports import extract_figure_refs, locate_report, report_payload
+from ..services.bioflow.reports import (
+    extract_figure_refs,
+    locate_report,
+    report_payload,
+    validate_report_path,
+)
 from .bioflow import job_or_404
 
 logger = logging.getLogger(__name__)
@@ -65,6 +71,10 @@ async def reports_register(payload: dict[str, Any]) -> dict[str, Any]:
     job_id = str(payload.get("job_id") or "")
     record = await load_record(job_id) if job_id else None
     report_path = payload.get("md_path") or payload.get("report_path") or ""
+    # G3：拒绝空路径/空文件（不静默登记空报告）
+    ok, err = validate_report_path(report_path)
+    if not ok:
+        return _err("EMPTY_REPORT", err, 422)
     figures: list[str] = list(payload.get("figures") or [])
     if record is not None and not figures:
         located = locate_report(record.workspace_dir)
@@ -96,12 +106,14 @@ async def create_archive(body: ArchiveCreateRequest) -> dict[str, Any]:
     existing = await store.find_archive_by_name(ctx.db, name)
     if existing is not None:
         return _err("ARCHIVE_EXISTS", f"归档名已存在: {name}", 409)
+    # G6：保存各阶段实际生效参数（非创建时 record.params）
+    effective_params = effective_stage_params(record.stage_chain, record._stage_states)
     report_path = locate_report(record.workspace_dir)
     result = await archive_from_job(
         {
             "id": record.id, "session_id": record.session_id,
             "title": record.title, "stage_chain": record.stage_chain,
-            "params": record.params,
+            "params": effective_params,
         },
         record.job_dir,
         get_settings().archives_dir_abs,
@@ -116,7 +128,7 @@ async def create_archive(body: ArchiveCreateRequest) -> dict[str, Any]:
         "name": name,
         "description": body.description,
         "stage_chain": record.stage_chain,
-        "params": record.params,
+        "params": effective_params,
         "report_artifact": result.report_artifact,
         "disk_path": result.disk_path,
         "size_bytes": result.size_bytes,
@@ -166,7 +178,10 @@ async def delete_archive(archive_id: str) -> JSONResponse:
 
 @router.post("/archives/{archive_id}/run", status_code=201)
 async def archive_run(archive_id: str, body: ArchiveRunRequest) -> dict[str, Any]:
-    """复用发起（FR-BIO-023）：装载阶段链+参数 → 新建任务（表单预填存档值）。"""
+    """复用发起（FR-BIO-023）：装载阶段链+参数 → 新建任务（表单预填存档值）。
+
+    params 为存档时落库的各阶段实际生效参数（G6：非创建时 record.params）。
+    """
     ctx: Context = context_mod.context
     archive = await store.get_archive(ctx.db, archive_id)
     if archive is None:

bioflow_service/app/routers/biojobs.py

@@ -22,7 +22,9 @@ from __future__ import annotations
 import asyncio
 import json
 import logging
+import os
 import re
+import uuid
 from pathlib import Path
 from typing import Any
 
@@ -212,23 +214,43 @@ async def upload_file(
     dest = input_dir / _safe_name(file.filename)
     written = 0
     max_bytes = int(settings.max_upload_gb * 1024 ** 3)
+    # G2：先落任务临时目录，再原子 rename 发布；同名冲突显式报错，不静默覆盖。
+    tmp_dir = record.job_dir / ".tmp"
+    tmp_dir.mkdir(parents=True, exist_ok=True)
+    tmp_path = tmp_dir / f"{uuid.uuid4().hex[:8]}_{dest.name}"
     try:
-        with dest.open("wb") as fh:
+        # G5：逐块流式写盘（不整块进内存）
+        with tmp_path.open("wb") as fh:
             while True:
                 chunk = await file.read(1024 * 1024)
                 if not chunk:
                     break
                 written += len(chunk)
                 if written > max_bytes:
-                    fh.close()
-                    dest.unlink(missing_ok=True)
-                    return _err("UPLOAD_TOO_LARGE",
-                                f"超过上传上限 {settings.max_upload_gb}GB（已收 {written} 字节）", 413)
+                    raise _UploadTooLarge(written)
                 fh.write(chunk)
+    except _UploadTooLarge as exc:
+        tmp_path.unlink(missing_ok=True)
+        return _err("UPLOAD_TOO_LARGE",
+                    f"超过上传上限 {settings.max_upload_gb}GB（已收 {exc.written} 字节）", 413)
     except Exception as exc:  # noqa: BLE001 - 写盘失败不登记（TC-BIO-API-050）
         logger.exception("files: 上传写盘失败 %s", job_id)
-        dest.unlink(missing_ok=True)
+        tmp_path.unlink(missing_ok=True)
         return _err("INTERNAL", f"上传写盘失败: {exc}", 500)
+    # 原子发布 + 同名冲突检测（G2）
+    try:
+        os.link(tmp_path, dest)
+    except FileExistsError:
+        tmp_path.unlink(missing_ok=True)
+        return _err("FILE_EXISTS", f"同名文件已存在，拒绝覆盖: {dest.name}", 409)
+    except OSError:
+        # os.link 不支持的文件系统 → 退化：exists 检查 + rename（同事件循环内无 await 交错）
+        if dest.exists() or dest.is_symlink():
+            tmp_path.unlink(missing_ok=True)
+            return _err("FILE_EXISTS", f"同名文件已存在，拒绝覆盖: {dest.name}", 409)
+        os.rename(tmp_path, dest)
+    else:
+        tmp_path.unlink(missing_ok=True)
     file_id = f"{job_id}:{dest.name}"
     # BUG-P7-01：文件落盘后自动续跑（await_inputs 任务重推；非等待态 no-op）
     await ctx.runner.retry_after_files(record)
@@ -238,6 +260,14 @@ async def upload_file(
     }}
 
 
+class _UploadTooLarge(Exception):
+    """上传超限信号（携带已收字节数）。"""
+
+    def __init__(self, written: int) -> None:
+        super().__init__("upload too large")
+        self.written = written
+
+
 async def _register_path(record: Any, server_path: str, settings: Any) -> dict[str, Any]:
     """服务器路径登记（FR-BIO-007）：单文件或目录展开，任意数据位置（敏感路径黑名单拦截）。
 

bioflow_service/app/services/bioflow/archive.py

@@ -19,11 +19,27 @@ from dataclasses import dataclass
 from pathlib import Path
 from typing import Any
 
+from .manifests import ManifestError, artifact_paths, parse_manifest
+
 logger = logging.getLogger(__name__)
 
 INTERMEDIATE_DIR_NAMES = ("analysis",)
 
 
+def effective_stage_params(
+    stage_chain: list[str], stage_states: dict[str, Any]
+) -> dict[str, Any]:
+    """G6：各阶段「实际生效」参数（confirm/rerun 更新后的 stage 参数）。
+
+    区别于创建时 record.params（创建后 confirm/rerun 只更新 _stage_states[stage].params，
+    不回流 record.params）。存档与复用以此为单一事实源，避免参数失真。
+    """
+    return {
+        s: dict((stage_states.get(s) or {}).get("params") or {})
+        for s in stage_chain
+    }
+
+
 @dataclass
 class ArchiveResult:
     id: str
@@ -88,6 +104,11 @@ async def archive_from_job(
 
     # 报告：任务目录内报告 HTML（final 内 *.html / report.html）随 final 已复制；
     # report_artifact 为 doc_artifacts 登记 id（由 reports 模块/BFF 登记后回传）。
+
+    # G1：按 manifest 必需产物清单补归档（不只 workspace/final/）。
+    # 相对路径以 workspace 根解析并改写为归档内路径（去 workspace 前缀）。
+    _copy_manifest_artifacts(job, job_dir, dest)
+
     size_bytes = _dir_size(dest)
     return ArchiveResult(
         id=archive_id,
@@ -98,6 +119,42 @@ async def archive_from_job(
     )
 
 
+def _copy_manifest_artifacts(
+    job: dict[str, Any], job_dir: Path, dest: Path
+) -> list[str]:
+    """G1：按 manifest 的必需产物清单复制归档产物（漏归档修复）。
+
+    每个阶段的 manifest artifacts（full_path/path/relpath_or_hint）逐条复制；
+    相对路径以 workspace 根解析，并改写为归档内路径（去 workspace 前缀）。
+    跳过不存在/失败阶段无 manifest 的产物。返回已复制的归档内相对路径列表。
+    """
+    stage_chain = job.get("stage_chain") or []
+    workspace = Path(job_dir) / "workspace"
+    copied: list[str] = []
+    for stage in stage_chain:
+        try:
+            manifest = parse_manifest(workspace, stage)
+        except ManifestError:
+            continue
+        for raw in artifact_paths(manifest.artifacts):
+            p = Path(raw)
+            if not p.is_absolute():
+                p = workspace / p
+            if not p.is_file():
+                continue
+            # 相对路径改写为归档内路径（去 workspace 前缀）
+            try:
+                rel = p.resolve().relative_to(workspace.resolve())
+            except ValueError:
+                rel = Path(p.name)
+            target = dest / rel
+            target.parent.mkdir(parents=True, exist_ok=True)
+            if not target.exists():
+                shutil.copy2(p, target)
+            copied.append(str(rel))
+    return copied
+
+
 def _copytree_into(src: Path, dest: Path) -> None:
     """复制目录内容到 dest（dest 可能已存在，逐项合并）。"""
     dest.mkdir(parents=True, exist_ok=True)

bioflow_service/app/services/bioflow/catalog.py

@@ -551,6 +551,38 @@ _STAGE_PARAM_SCHEMAS: dict[str, tuple[list[dict[str, Any]], list[dict[str, Any]]
     ], _DOWNSTREAM_INPUTS, _DOWNSTREAM_OUTPUTS),
 }
 
+# ---- G9：单一参数 schema 访问点（Catalog/表单/预检/工具/验收都读这一份）----
+
+
+def _schema_params_inputs_outputs(stage: str) -> tuple[list[dict[str, Any]], list[dict[str, Any]], list[dict[str, Any]]]:
+    """阶段参数/输入/输出的单一读取点（含未知阶段默认兜底）。"""
+    if stage in _STAGE_PARAM_SCHEMAS:
+        return _STAGE_PARAM_SCHEMAS[stage]
+    params = [{"name": "cpu", "type": "choice", "choices": ["4", "8", "16", "32"],
+               "default": "4", "source": "runtime", "help": "容器 CPU 数"}]
+    inputs = _DOWNSTREAM_INPUTS if stage not in ("identify", "genome_prepare") else []
+    outputs = _DOWNSTREAM_OUTPUTS
+    return params, inputs, outputs
+
+
+def stage_schema(stage: str) -> dict[str, Any]:
+    """G9：单一参数 schema 访问点——阶段名/耗时/依赖/参数/输入/输出/输入角色 合并为一份。
+
+    Catalog/表单/预检/工具/验收都读这一份（唯一事实源）。
+    """
+    from .stage_assets import stage_input_roles
+
+    params, inputs, outputs = _schema_params_inputs_outputs(stage)
+    return {
+        "name": STAGE_INFO_SNAPSHOT.get(stage, {}).get("name") or stage,
+        "estimated_time": int(STAGE_INFO_SNAPSHOT.get(stage, {}).get("estimated_time") or 0),
+        "dependencies": STAGE_DEPENDENCIES_SNAPSHOT.get(stage, []),
+        "params": params,
+        "inputs": inputs,
+        "outputs": outputs,
+        "input_roles": stage_input_roles(stage),
+    }
+
 
 class StageCatalog:
     """阶段目录（数据来自 stage_image_map.json + 手写快照，不运行时反射）。"""
@@ -578,29 +610,19 @@ class StageCatalog:
         if not self.has(stage):
             return None
         entry = self._map.image_for(stage) or {}
-        params, inputs, outputs = _STAGE_PARAM_SCHEMAS.get(
-            stage, ([], _DOWNSTREAM_INPUTS if stage not in ("identify", "genome_prepare") else [], [])
-        )
-        if stage not in _STAGE_PARAM_SCHEMAS:
-            params, inputs, outputs = (
-                [{"name": "cpu", "type": "choice", "choices": ["4", "8", "16", "32"],
-                  "default": "4", "source": "runtime", "help": "容器 CPU 数"}],
-                _DOWNSTREAM_INPUTS if stage not in ("identify", "genome_prepare") else [],
-                _DOWNSTREAM_OUTPUTS,
-            )
-        info = STAGE_INFO_SNAPSHOT.get(stage, {})
+        schema = stage_schema(stage)
         return StageDef(
             name=stage,
-            description=str(info.get("name") or stage),
+            description=str(schema["name"] or stage),
             image=str(entry.get("image") or ""),
             module=str(entry.get("module") or ""),
             executable=bool(entry.get("executable")),
-            estimated_time=int(info.get("estimated_time") or 0),
-            params=params,
-            inputs=inputs,
-            outputs=outputs,
+            estimated_time=int(schema["estimated_time"]),
+            params=schema["params"],
+            inputs=schema["inputs"],
+            outputs=schema["outputs"],
             note=str(entry.get("note") or ""),
-            dependencies=STAGE_DEPENDENCIES_SNAPSHOT.get(stage, []),
+            dependencies=schema["dependencies"],
         )
 
     def resolve_chain(self, chain: str | None) -> list[str] | None:
@@ -612,32 +634,52 @@ class StageCatalog:
             return None
         return list(alias)
 
-    def auto_fill_prerequisites(self, stages: list[str]) -> tuple[list[str], list[str]]:
+    def auto_fill_prerequisites(
+        self, stages: list[str], satisfied_roles: list[str] | None = None
+    ) -> tuple[list[str], list[str]]:
         """前置补全（FR-BIO-003）：缺失的前置阶段自动补全。
 
+        G7/G8：satisfied_roles（已有 validated 资产的输入角色）对应的上游阶段
+        跳过不补跑（如 role=counts 满足时做 DE 不补跑 qc/align/quant/sample_qc）。
+
         返回 (补全后的链, 被补全的阶段名列表)。
         链内阶段按依赖拓扑顺序排列（依赖在前）。
         """
+        from .stage_assets import upstream_stages_for_roles
+
+        skip_stages = upstream_stages_for_roles(satisfied_roles or [])
         missing: list[str] = []
         added: list[str] = []
         chain_set = set(stages)
-        # 反复补全直到闭合（依赖的依赖也补）
+        # 反复补全直到闭合（依赖的依赖也补；被角色资产满足的上游跳过）
         changed = True
         while changed:
             changed = False
             for s in list(stages):
                 for dep in STAGE_DEPENDENCIES_SNAPSHOT.get(s, []):
-                    if dep not in chain_set and self.has(dep):
+                    if dep in chain_set:
+                        continue
+                    if dep in skip_stages:
+                        continue
+                    if self.has(dep):
                         chain_set.add(dep)
                         missing.append(dep)
                         added.append(dep)
                         changed = True
         ordered = topo_order([s for s in GENE_FAMILY_CHAIN if s in chain_set]
                              or list(chain_set))
+        # G7/G8：被角色资产满足的上游阶段从最终链中剔除（不补跑）
+        if skip_stages:
+            ordered = [s for s in ordered if s not in skip_stages]
         return ordered, added
 
     def dependencies(self, stage: str) -> list[str]:
-        return STAGE_DEPENDENCIES_SNAPSHOT.get(stage, [])
+        return stage_schema(stage)["dependencies"]
+
+    def stage_input_roles(self, stage: str) -> list[str]:
+        """G8：阶段依赖的输入角色（数据角色）。"""
+        from .stage_assets import stage_input_roles
+        return stage_input_roles(stage)
 
 
 def topo_order(stages: list[str]) -> list[str]:

bioflow_service/app/services/bioflow/delivery.py

@@ -0,0 +1,138 @@
+"""app/services/bioflow/delivery.py —— 交付清单（G21）+ 终报告范围（G22）+ 资源预算（G23）。
+
+- G21 交付清单完整性：delivery_validate(manifest) 做八项完整性检查
+  （selected_stages / run_id / input_sources / output_sources / config /
+  required_results / validation_values / review_status），返回
+  {ok, checks{八项:bool}, incomplete[{item, reason, error(G13)}]}。
+- G22 终报告范围：classify_report_scope(status, source) 五分类
+  （user_provided / reused / not_executed / skipped / failed）。
+- G23 资源预算：check_download_budget(size_bytes, budget_bytes)（超限→
+  DOWNLOAD_BUDGET_EXCEEDED）+ check_disk_available(dest_dir, needed_bytes)
+  （不足→DISK_FULL），均 ok=False + 结构化错误。
+
+服务层纪律：纯 dict/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any
+
+from .errors import error_object, error_result
+from .source_fetcher import check_disk_space
+
+# G21 八项完整性检查项
+DELIVERY_ITEMS = (
+    "selected_stages", "run_id", "input_sources", "output_sources",
+    "config", "required_results", "validation_values", "review_status",
+)
+
+# G22 五分类
+SCOPE_USER_PROVIDED = "user_provided"
+SCOPE_REUSED = "reused"
+SCOPE_NOT_EXECUTED = "not_executed"
+SCOPE_SKIPPED = "skipped"
+SCOPE_FAILED = "failed"
+
+
+def delivery_validate(manifest: dict[str, Any]) -> dict[str, Any]:
+    """G21：校验交付清单完整性（八项）。
+
+    返回 {"ok": bool, "checks": {item: bool},
+          "incomplete": [{"item", "reason", "error": {G13 对象}}]}。
+    """
+    manifest = manifest or {}
+    checks: dict[str, bool] = {}
+    incomplete: list[dict[str, Any]] = []
+    for item in DELIVERY_ITEMS:
+        value = manifest.get(item)
+        ok = bool(value)
+        checks[item] = ok
+        if not ok:
+            incomplete.append({
+                "item": item,
+                "reason": f"缺 {item}",
+                "error": error_object("INCOMPLETE_DELIVERY", f"交付清单缺项: {item}",
+                                      category="input"),
+            })
+    return {"ok": not incomplete, "checks": checks, "incomplete": incomplete}
+
+
+def publish_delivery(manifest: dict[str, Any]) -> dict[str, Any]:
+    """G21：发布交付清单（校验通过置 review_status=approved）。"""
+    check = delivery_validate(manifest)
+    if not check["ok"]:
+        return {"ok": False, "published": False, **check}
+    manifest["review_status"] = "approved"
+    return {"ok": True, "published": True, "review_status": "approved",
+            "incomplete": []}
+
+
+# ---- G22 终报告范围 ----
+
+def classify_report_scope(status: str, source: str | None = None) -> str:
+    """G22：阶段状态 → 终报告范围五分类。
+
+    failed→failed；skipped→skipped；done + source=reuse→reused；
+    done + source=user/空→user_provided；其余非终态→not_executed。
+    """
+    s = str(status or "")
+    if s == "failed":
+        return SCOPE_FAILED
+    if s == "skipped":
+        return SCOPE_SKIPPED
+    if s == "done":
+        return SCOPE_REUSED if source == "reuse" else SCOPE_USER_PROVIDED
+    return SCOPE_NOT_EXECUTED
+
+
+def build_report(
+    manifest: dict[str, Any],
+    stage_sources: dict[str, str] | None = None,
+) -> dict[str, Any]:
+    """G22：终报告结构（执行范围 / 数据来源与核验 / 方法版本 / QC / 科学前提 /
+    失败跳过未覆盖 / 产物清单）。"""
+    stages = list(manifest.get("selected_stages") or [])
+    sources = dict(stage_sources or {})
+    scope = [{"stage": s, "source": sources.get(s, SCOPE_USER_PROVIDED)} for s in stages]
+
+    failed = [s for s in stages if sources.get(s) == SCOPE_FAILED]
+    skipped = [s for s in stages if sources.get(s) == SCOPE_SKIPPED]
+    not_executed = [s for s in stages if sources.get(s) == SCOPE_NOT_EXECUTED]
+
+    config = manifest.get("config") or {}
+    return {
+        "execution_scope": scope,
+        "data_sources": {
+            "inputs": list(manifest.get("input_sources") or []),
+            "outputs": list(manifest.get("output_sources") or []),
+        },
+        "method_version": str(manifest.get("plan_revision") or manifest.get("run_id") or ""),
+        "qc": {"validation_values": dict(manifest.get("validation_values") or {})},
+        "scientific_preconditions": config.get("scientific_preconditions", []),
+        "failed_skipped_uncovered": {
+            "failed": failed, "skipped": skipped, "not_executed": not_executed,
+        },
+        "artifacts": list(manifest.get("required_results") or []),
+    }
+
+
+# ---- G23 资源预算门禁 ----
+
+def check_download_budget(size_bytes: int, budget_bytes: int) -> dict[str, Any]:
+    """G23：下载预算门禁——超限阻断并返回结构化错误。"""
+    if size_bytes > budget_bytes:
+        return error_result(
+            "DOWNLOAD_BUDGET_EXCEEDED",
+            f"下载预算超限：本次 {size_bytes} > 预算 {budget_bytes}",
+        )
+    return {"ok": True}
+
+
+def check_disk_available(dest_dir: str | Path, needed_bytes: int) -> dict[str, Any]:
+    """G23：磁盘门禁——剩余空间不足阻断并返回结构化错误。"""
+    ok, free = check_disk_space(dest_dir, needed_bytes)
+    if not ok:
+        return error_result(
+            "DISK_FULL", f"磁盘空间不足：需 {needed_bytes} 字节，剩余 {free} 字节",
+        )
+    return {"ok": True, "free_bytes": free}

bioflow_service/app/services/bioflow/errors.py

@@ -0,0 +1,196 @@
+"""app/services/bioflow/errors.py —— 统一结构化错误对象（G13）+ 确定性分类器（G14）。
+
+失败返回统一携带结构化错误对象（替代裸字符串 message）：
+    {"ok": False, "code": "<码>", "message": "<摘要>",
+     "error": {error_id, category, code, summary, evidence_refs,
+               diagnosis_status, retryable_without_change, suggested_actions}}
+
+8 类 category（G14：确定性映射）：
+    input / scientific_precondition / reference / environment /
+    transient / resource / adapter / artifact
+
+G14 分类纪律：退出码/日志是「证据」不是「结论」——
+- 日志含 OOM → resource；日志含镜像缺失 → environment；日志含科学前提不满足 → scientific_precondition。
+- 仅凭「非零退出码」无法定类 → adapter + undiagnosed（不臆测）。
+
+服务层纪律：纯 dict/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+import uuid
+from typing import Any
+
+CATEGORIES = (
+    "input", "scientific_precondition", "reference", "environment",
+    "transient", "resource", "adapter", "artifact",
+)
+
+# 明显映射：错误码 → (category, diagnosis_status, retryable_without_change, suggested_actions)
+_CODE_META: dict[str, tuple[str, str, bool, list[str]]] = {
+    # ---- resource（资源耗尽）----
+    "DISK_FULL": ("resource", "diagnosed", False, ["清理磁盘空间后重试"]),
+    "UPLOAD_TOO_LARGE": ("resource", "diagnosed", False, ["减小文件大小或调大上传上限"]),
+    "DOWNLOAD_BUDGET_EXCEEDED": ("resource", "diagnosed", False, ["调大下载预算或减小下载量"]),
+    # ---- environment（运行环境）----
+    "OSS_UNCONFIGURED": ("environment", "diagnosed", False, ["配置 BIOFLOW_OSS_ENDPOINT 或改用预签名 URL"]),
+    "SSHPASS_MISSING": ("environment", "diagnosed", False, ["本机安装 sshpass 或改用密钥认证"]),
+    # ---- reference（参考数据）----
+    "REFERENCE_NOT_FOUND": ("reference", "diagnosed", False, ["补齐参考基因组/HMM/索引后重试"]),
+    # ---- transient（临时/可重试）----
+    "NETWORK_ERROR": ("transient", "diagnosed", True, ["重试下载"]),
+    "LAN_TIMEOUT": ("transient", "diagnosed", True, ["重试局域网拉取"]),
+    "TRUNCATED": ("transient", "diagnosed", True, ["重试下载"]),
+    "LAN_ERROR": ("transient", "diagnosed", True, ["重试局域网拉取"]),
+    "HTTP_ERROR": ("transient", "diagnosed", True, ["确认 URL 可达或稍后重试"]),
+    # ---- input（用户输入/文件/参数）----
+    "EMPTY_SOURCE": ("input", "diagnosed", False, ["提供非空源地址"]),
+    "BAD_SCHEME": ("input", "diagnosed", False, ["改用 http/https/oss 协议"]),
+    "BAD_OSS": ("input", "diagnosed", False, ["修正 OSS 地址为 oss://bucket/key"]),
+    "PATH_NOT_EXIST": ("input", "diagnosed", False, ["确认路径存在且可达"]),
+    "IS_DIR": ("input", "diagnosed", False, ["改为单文件路径"]),
+    "NOT_FOUND": ("input", "diagnosed", False, ["确认目标存在"]),
+    "BAD_FORMAT": ("input", "diagnosed", False, ["选择支持的目标格式 fasta/gff3/tsv/samples.yaml"]),
+    "EMPTY_TABLE": ("input", "diagnosed", False, ["提供非空表格数据"]),
+    "MISSING_COLUMNS": ("input", "diagnosed", False, ["确认列映射（名称/序列/r1/r2）"]),
+    "VALIDATION": ("input", "diagnosed", False, ["修正输入以满足校验"]),
+    "VALIDATION_FAILED": ("input", "diagnosed", False, ["修正数据后重转"]),
+    "UNKNOWN_STAGE": ("input", "diagnosed", False, ["选择有效阶段"]),
+    "UNKNOWN_PARAMS": ("input", "diagnosed", False, ["移除未知参数"]),
+    "BAD_ROLE": ("input", "diagnosed", False, ["使用合法角色名（非空、无路径分隔符/..）"]),
+    "EMPTY_REPORT": ("input", "diagnosed", False, ["提供非空报告路径/文件"]),
+    "EMPTY_SAMPLES": ("input", "diagnosed", False, ["提供含样本的描述"]),
+    "INCOMPLETE_DELIVERY": ("input", "diagnosed", False, ["补齐交付清单缺失项（selected_stages/run_id/必需结果等）后重试"]),
+    # ---- adapter（适配/映射）----
+    "UNSUPPORTED": ("adapter", "diagnosed", False, ["改用支持的转换路径"]),
+    "CROSS_CHAIN": ("adapter", "diagnosed", False, ["选择本能力单元内的阶段"]),
+    # ---- artifact（产物）----
+    "ARCHIVE_EXISTS": ("artifact", "diagnosed", False, ["更换归档名"]),
+    "ARCHIVE_FAILED": ("artifact", "diagnosed", False, ["检查任务目录完整性后重试"]),
+    "ARCHIVE_NOT_FOUND": ("artifact", "diagnosed", False, ["确认归档名存在"]),
+    "ASSET_EXISTS": ("artifact", "diagnosed", False, ["更换角色或文件名"]),
+    "PUBLISH_FAILED": ("artifact", "diagnosed", False, ["检查目标目录可写性后重试"]),
+    "NO_MANIFEST": ("artifact", "diagnosed", False, ["检查阶段产物 manifest 是否产出"]),
+    # ---- scientific_precondition（科学前提）----
+    "SCIENTIFIC_PRECONDITION": ("scientific_precondition", "diagnosed", False, ["确认科学前提满足后重试"]),
+}
+
+# 关键词兜底（summary 命中即映射；用于非枚举码）
+_KEYWORD_META: list[tuple[tuple[str, ...], tuple[str, str, bool, list[str]]]] = [
+    (("out of memory", "oom", "memoryerror", "oom-killed", "memory limit", "内存"),
+     ("resource", "diagnosed", False, ["调大内存或减小数据规模"])),
+    (("no such image", "image not found", "pull access denied", "镜像", "docker"),
+     ("environment", "diagnosed", False, ["确认镜像存在且可拉取"])),
+    (("no significant", "not enough", "insufficient", "科学前提", "no differentially", "not found enough"),
+     ("scientific_precondition", "diagnosed", False, ["确认科学前提满足后重试"])),
+    (("timeout", "超时", "network", "网络", "unreachable", "connecterror", "timed out"),
+     ("transient", "diagnosed", True, ["重试"])),
+    (("reference", "参考", "hmm", "pfam", "gtf", "index"),
+     ("reference", "diagnosed", False, ["补齐参考数据后重试"])),
+    (("manifest", "no_manifest", "产物缺失"),
+     ("artifact", "diagnosed", False, ["检查阶段产物 manifest"])),
+]
+
+# 阶段失败 reason（runner _fail_stage）→ (category, diagnosis_status, retryable, actions)
+_REASON_META: dict[str, tuple[str, str, bool, list[str]]] = {
+    "timeout": ("transient", "diagnosed", True, ["重跑该阶段"]),
+    "exit_code": ("adapter", "undiagnosed", False, ["查看阶段日志定位失败原因", "修正后重跑"]),
+    "no_manifest": ("artifact", "diagnosed", False, ["检查阶段是否产出 manifest"]),
+    "manifest_error": ("artifact", "diagnosed", False, ["检查 manifest JSON 完整性"]),
+    "manifest_failed": ("artifact", "diagnosed", False, ["检查阶段产物 manifest status"]),
+}
+
+# 退出码 137 = 128 + SIGKILL（常为 OOM kill）
+_OOM_EXIT_CODES = {137, 139}
+
+
+def classify(code: str | None, summary: str = "") -> tuple[str, str, bool, list[str]]:
+    """错误码/摘要 → (category, diagnosis_status, retryable_without_change, suggested_actions)。"""
+    code = str(code or "")
+    summary = str(summary or "")
+    if code in _CODE_META:
+        cat, diag, retry, actions = _CODE_META[code]
+        return cat, diag, retry, list(actions)
+    low = summary.lower()
+    for kws, meta in _KEYWORD_META:
+        if any(k in low for k in kws):
+            cat, diag, retry, actions = meta
+            return cat, diag, retry, list(actions)
+    return "adapter", "undiagnosed", False, []
+
+
+def classify_reason(
+    reason: str | None,
+    *,
+    exit_code: int | None = None,
+    log_tail: str | None = None,
+) -> tuple[str, str, bool, list[str]]:
+    """阶段失败原因 + 证据（退出码/日志）→ 确定性 8 类。
+
+    确定性 reason 优先（timeout / manifest 系列）；泛化 exit_code 用证据（退出码/日志）
+    定类——仅凭非零退出码不定类（undiagnosed），不臆测。
+    """
+    reason = str(reason or "")
+    log = (log_tail or "").lower()
+
+    # 1. 确定性 reason（非 exit_code）优先：timeout / manifest 系列
+    if reason in _REASON_META and reason != "exit_code":
+        cat, diag, retry, actions = _REASON_META[reason]
+        return cat, diag, retry, list(actions)
+
+    # 2. 泛化 exit_code / 未知 reason：退出码是证据（137/139 = OOM kill）
+    if exit_code in _OOM_EXIT_CODES:
+        return "resource", "diagnosed", False, ["容器可能被 OOM kill，调大内存后重跑"]
+
+    # 3. 日志证据定类
+    for kws, meta in _KEYWORD_META:
+        if any(k in log for k in kws):
+            cat, diag, retry, actions = meta
+            return cat, diag, retry, list(actions)
+
+    # 4. 兜底：exit_code → adapter undiagnosed；未知 → 同
+    if reason in _REASON_META:
+        cat, diag, retry, actions = _REASON_META[reason]
+        return cat, diag, retry, list(actions)
+    return "adapter", "undiagnosed", False, []
+
+
+def error_object(
+    code: str | None,
+    summary: str = "",
+    *,
+    category: str | None = None,
+    evidence_refs: list[str] | None = None,
+    diagnosis_status: str | None = None,
+    retryable_without_change: bool | None = None,
+    suggested_actions: list[str] | None = None,
+) -> dict[str, Any]:
+    """构造统一结构化错误对象（8 字段）。"""
+    cat, diag, retry, actions = classify(code, summary)
+    return {
+        "error_id": uuid.uuid4().hex[:16],
+        "category": category or cat,
+        "code": code or "INTERNAL",
+        "summary": summary,
+        "evidence_refs": list(evidence_refs or []),
+        "diagnosis_status": diagnosis_status or diag,
+        "retryable_without_change": retry if retryable_without_change is None else retryable_without_change,
+        "suggested_actions": list(suggested_actions or actions),
+    }
+
+
+def error_result(
+    code: str | None,
+    summary: str = "",
+    *,
+    evidence_refs: list[str] | None = None,
+) -> dict[str, Any]:
+    """失败返回统一信封：{"ok": False, "code", "message", "error"}。
+
+    code 同时出现在顶层与 error 对象内（兼容 Phase A 的 r["code"] 断言）。
+    """
+    return {
+        "ok": False,
+        "code": code or "INTERNAL",
+        "message": summary,
+        "error": error_object(code, summary, evidence_refs=evidence_refs),
+    }

bioflow_service/app/services/bioflow/events.py

@@ -24,8 +24,8 @@ logger = logging.getLogger(__name__)
 
 EVENT_TYPES = (
     "job_created", "plan_ready", "stage_started", "stage_log", "stage_progress",
-    "stage_done", "stage_failed", "stage_skipped", "stage_await_confirm",
-    "stage_await_files",
+    "stage_done", "stage_failed", "stage_skipped", "stage_partial",
+    "stage_await_confirm", "stage_await_files",
     "job_done", "job_paused", "job_archived", "job_recovered",
     # 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）
     "extension_created", "extension_build", "extension_trial", "extension_repair",
@@ -208,6 +208,9 @@ class EventBus:
             elif t == "stage_skipped":
                 st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
                 st["status"] = "skipped"
+            elif t == "stage_partial":
+                st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
+                st["status"] = "partial_success"
             elif t == "stage_progress":
                 st = stage_states.setdefault(str(d.get("stage")), {"stage": str(d.get("stage"))})
                 pct = d.get("percent")

bioflow_service/app/services/bioflow/file_transform.py

@@ -0,0 +1,438 @@
+"""app/services/bioflow/file_transform.py —— 非标准文件预处理（探测 + 转换 + 校验）。
+
+FR-BIO-014 文件医生闭环：
+- inspect_file：内容嗅探（扩展名仅参考），返回结构化摘要（预览行/列结构/大小/
+  格式猜测/乱码检测/与目标阶段期望格式的差异）。
+- transform_file：LLM 抽取列映射/清洗规则 + 规则脚本执行，把 xlsx/csv/tsv/txt 转换
+  为 fasta/gff3/tsv/samples.yaml；转换结果过格式验证器硬校验，失败返回原因供追问
+  循环（≤3 次由上层 QA 控制）。
+
+服务层纪律：纯 dataclass/dict/stdlib + yaml/openpyxl，无 pydantic。
+LLM 可注入（默认走 .llm.complete_json），测试注入 fake。
+"""
+from __future__ import annotations
+
+import csv
+import io
+import json
+import logging
+import re
+from pathlib import Path
+from typing import Any, Awaitable, Callable
+
+logger = logging.getLogger(__name__)
+
+PREVIEW_LINES = 10
+PREVIEW_BYTES = 4000
+
+# 支持的目标格式
+TARGET_FORMATS = ("fasta", "gff3", "tsv", "samples.yaml")
+
+# 乱码检测：非 ASCII 可打印且非 CJK 的异常字节比例阈值
+GARBLED_RATIO = 0.30
+
+
+class TransformError(Exception):
+    def __init__(self, code: str, message: str, details: dict[str, Any] | None = None) -> None:
+        super().__init__(message)
+        self.code = code
+        self.message = message
+        self.details = details or {}
+
+
+# ---------------------------------------------------------------------------
+# 探测
+# ---------------------------------------------------------------------------
+
+def _guess_format(name: str, head: bytes) -> str:
+    lower = name.lower()
+    if lower.endswith((".fa", ".fasta", ".faa", ".fna", ".pep", ".cds")):
+        return "fasta"
+    if lower.endswith((".gff", ".gff3")):
+        return "gff3"
+    if lower.endswith((".gtf",)):
+        return "gtf"
+    if lower.endswith((".vcf", ".vcf.gz")):
+        return "vcf"
+    if lower.endswith((".tsv",)):
+        return "tsv"
+    if lower.endswith((".csv",)):
+        return "csv"
+    if lower.endswith((".xlsx", ".xls")):
+        return "xlsx"
+    if lower.endswith((".yaml", ".yml")):
+        return "yaml"
+    # 内容嗅探兜底
+    text = head.decode("utf-8", errors="replace")
+    if text.lstrip().startswith(">"):
+        return "fasta"
+    if "\t" in text and len(text.splitlines()[0].split("\t")) >= 3:
+        return "tsv"
+    return "txt"
+
+
+def _read_text(path: Path) -> str:
+    raw = path.read_bytes()
+    for enc in ("utf-8", "gb18030", "latin-1"):
+        try:
+            return raw.decode(enc)
+        except UnicodeDecodeError:
+            continue
+    return raw.decode("utf-8", errors="replace")
+
+
+def _garbled_ratio(text: str) -> float:
+    """异常字符比例：控制字符 + 替换符 + 私有区（不含常规空白）。"""
+    if not text:
+        return 0.0
+    bad = 0
+    for ch in text:
+        o = ord(ch)
+        if o == 0xFFFD or (o < 32 and ch not in "\t\n\r") or (0xE000 <= o <= 0xF8FF):
+            bad += 1
+    return bad / len(text)
+
+
+def _preview(text: str) -> list[str]:
+    return text.splitlines()[:PREVIEW_LINES]
+
+
+def _columns(path: Path, fmt: str) -> list[str]:
+    """表格列名提取（tsv/csv/xlsx）。"""
+    try:
+        if fmt == "xlsx":
+            import openpyxl
+            wb = openpyxl.load_workbook(path, read_only=True, data_only=True)
+            try:
+                ws = wb.active
+                row = next(ws.iter_rows(min_row=1, max_row=1, values_only=True), None)
+                return [str(c or "").strip() for c in (row or [])]
+            finally:
+                wb.close()
+        if fmt in ("tsv", "csv"):
+            text = _read_text(path)
+            reader = csv.reader(io.StringIO(text), delimiter="\t" if fmt == "tsv" else ",")
+            first = next(reader, None)
+            return [str(c or "").strip() for c in (first or [])]
+    except Exception as exc:  # noqa: BLE001 - 列提取失败降级空
+        logger.warning("file_transform: 列提取失败 %s: %s", path, exc)
+    return []
+
+
+def inspect_file(path: str | Path, *, preview_lines: int = PREVIEW_LINES) -> dict[str, Any]:
+    """内容嗅探摘要（扩展名仅参考；失败返回 ok=False + 原因，不抛）。"""
+    p = Path(path)
+    if not p.is_file():
+        return {"ok": False, "code": "NOT_FOUND", "message": f"文件不存在: {path}"}
+    try:
+        size = p.stat().st_size
+        head = p.read_bytes()[:PREVIEW_BYTES]
+        fmt = _guess_format(p.name, head)
+        text = _read_text(p) if size <= 4 * 1024 * 1024 else _read_text_preview(p)
+        return {
+            "ok": True,
+            "path": str(p),
+            "name": p.name,
+            "ext": p.suffix.lower() or "",
+            "size": size,
+            "format": fmt,
+            "preview": _preview(text)[:preview_lines],
+            "columns": _columns(p, fmt),
+            "garbled": _garbled_ratio(text),
+            "line_count": text.count("\n") + 1 if text else 0,
+        }
+    except OSError as exc:
+        return {"ok": False, "code": "READ_ERROR", "message": f"文件读取失败: {exc}"}
+
+
+def _read_text_preview(path: Path) -> str:
+    """大文件只读头部做预览/乱码检测，避免整读内存。"""
+    with path.open("rb") as fh:
+        head = fh.read(PREVIEW_BYTES)
+    for enc in ("utf-8", "gb18030", "latin-1"):
+        try:
+            return head.decode(enc)
+        except UnicodeDecodeError:
+            continue
+    return head.decode("utf-8", errors="replace")
+
+
+# ---------------------------------------------------------------------------
+# 校验器
+# ---------------------------------------------------------------------------
+
+def validate_fasta(path: str | Path) -> dict[str, Any]:
+    p = Path(path)
+    if not p.is_file():
+        return {"ok": False, "reason": "文件不存在"}
+    text = _read_text(p)
+    records = re.findall(r"^>.*$", text, flags=re.M)
+    if not records:
+        return {"ok": False, "reason": "无 FASTA 记录（缺 '>' 头行）"}
+    # 序列非空：头行之间至少存在非空白序列行
+    body = re.sub(r"^>.*$", "", text, flags=re.M)
+    if not body.strip():
+        return {"ok": False, "reason": "FASTA 记录缺少序列"}
+    return {"ok": True, "records": len(records)}
+
+
+def validate_gff3(path: str | Path) -> dict[str, Any]:
+    p = Path(path)
+    if not p.is_file():
+        return {"ok": False, "reason": "文件不存在"}
+    bad = 0
+    total = 0
+    for line in _read_text(p).splitlines():
+        if not line.strip() or line.startswith("#"):
+            continue
+        total += 1
+        cols = line.split("\t")
+        if len(cols) != 9:
+            bad += 1
+            continue
+        try:
+            int(cols[3])
+            int(cols[4])
+        except ValueError:
+            bad += 1
+            continue
+        if cols[6] not in ("+", "-", "."):
+            bad += 1
+    if total == 0:
+        return {"ok": False, "reason": "无 GFF3 数据行"}
+    if bad:
+        return {"ok": False, "reason": f"{bad}/{total} 行列数或字段非法"}
+    return {"ok": True, "records": total}
+
+
+def validate_tsv(path: str | Path) -> dict[str, Any]:
+    p = Path(path)
+    if not p.is_file():
+        return {"ok": False, "reason": "文件不存在"}
+    widths: set[int] = set()
+    for line in _read_text(p).splitlines():
+        if not line.strip():
+            continue
+        widths.add(len(line.split("\t")))
+    if len(widths) > 1:
+        return {"ok": False, "reason": f"列数不一致: {sorted(widths)}"}
+    if not widths:
+        return {"ok": False, "reason": "空文件"}
+    return {"ok": True, "columns": widths.pop()}
+
+
+def validate_samples_yaml(path: str | Path) -> dict[str, Any]:
+    import yaml
+    p = Path(path)
+    if not p.is_file():
+        return {"ok": False, "reason": "文件不存在"}
+    try:
+        raw = yaml.safe_load(_read_text(p))
+    except Exception as exc:  # noqa: BLE001
+        return {"ok": False, "reason": f"YAML 解析失败: {exc}"}
+    samples = (raw or {}).get("samples") if isinstance(raw, dict) else None
+    if not isinstance(samples, dict) or not samples:
+        return {"ok": False, "reason": "缺 samples 映射或为空"}
+    for name, entry in samples.items():
+        if not isinstance(entry, dict) or not (entry.get("r1") or entry.get("r2")):
+            return {"ok": False, "reason": f"样本 {name} 缺 r1/r2"}
+    return {"ok": True, "samples": len(samples)}
+
+
+_VALIDATORS = {
+    "fasta": validate_fasta,
+    "gff3": validate_gff3,
+    "tsv": validate_tsv,
+    "samples.yaml": validate_samples_yaml,
+}
+
+
+def validate_format(path: str | Path, target_format: str) -> dict[str, Any]:
+    fn = _VALIDATORS.get(target_format)
+    if fn is None:
+        return {"ok": False, "reason": f"不支持的目标格式: {target_format}"}
+    return fn(path)
+
+
+# ---------------------------------------------------------------------------
+# 转换
+# ---------------------------------------------------------------------------
+
+LLMFn = Callable[[str, str], Awaitable[Any]]
+
+
+def _read_table(path: Path) -> tuple[list[str], list[dict[str, str]]]:
+    """读表格（tsv/csv/xlsx）→ (表头, 行 dict 列表)。"""
+    fmt = _guess_format(path.name, path.read_bytes()[:64])
+    if fmt == "xlsx":
+        import openpyxl
+        wb = openpyxl.load_workbook(path, read_only=True, data_only=True)
+        try:
+            ws = wb.active
+            rows = [list(r) for r in ws.iter_rows(values_only=True)]
+        finally:
+            wb.close()
+        if not rows:
+            return [], []
+        headers = [str(c or "").strip() for c in rows[0]]
+        return headers, [dict(zip(headers, ["" if v is None else str(v).strip() for v in r])) for r in rows[1:]]
+    text = _read_text(path)
+    delimiter = "\t" if fmt == "tsv" else ","
+    reader = csv.reader(io.StringIO(text), delimiter=delimiter)
+    rows = list(reader)
+    if not rows:
+        return [], []
+    headers = [str(c or "").strip() for c in rows[0]]
+    return headers, [dict(zip(headers, ["" if v is None else str(v).strip() for v in r])) for r in rows[1:]]
+
+
+def _default_column_map(headers: list[str], target: str) -> dict[str, str]:
+    """按表头名启发式推断列映射（名称/序列/基因名等）。"""
+    m: dict[str, str] = {}
+    for h in headers:
+        lh = h.lower()
+        if target == "fasta":
+            if not m.get("seq") and any(k in lh for k in ("seq", "sequence", "序列", "蛋白", "pep", "cds")):
+                m["seq"] = h
+            elif not m.get("name") and any(k in lh for k in ("name", "id", "gene", "名称", "基因", "基因名", "accession")):
+                m["name"] = h
+        elif target == "samples.yaml":
+            if "r1" in lh or "read1" in lh or "forward" in lh:
+                m.setdefault("r1", h)
+            elif "r2" in lh or "read2" in lh or "reverse" in lh:
+                m.setdefault("r2", h)
+            elif "run" in lh or "sample" in lh or "样本" in lh or "name" in lh:
+                m.setdefault("name", h)
+    return m
+
+
+async def _llm_column_map(headers: list[str], target: str, llm: LLMFn, sample_rows: list[dict[str, str]]) -> dict[str, str]:
+    """LLM 抽取列映射（启发式不充分时）。返回 {目标字段: 列名}。"""
+    import json as _json
+    prompt = (
+        f"你是生信数据整理助手。下表头 {_json.dumps(headers, ensure_ascii=False)} "
+        f"需转换为 {target} 格式。样本行：{_json.dumps(sample_rows[:3], ensure_ascii=False)[:2000]}。"
+        "请输出列映射 JSON，键为目标字段名，值为表头列名。"
+    )
+    try:
+        result = await llm(prompt, "只输出 JSON 对象，如 {\"name\":\"基因名\",\"seq\":\"序列\"}。")
+        if isinstance(result, dict):
+            return {str(k): str(v) for k, v in result.items() if str(v) in headers}
+    except Exception as exc:  # noqa: BLE001
+        logger.warning("file_transform: LLM 列映射失败 %s", exc)
+    return {}
+
+
+def _write_fasta(rows: list[dict[str, str]], name_col: str, seq_col: str, dest: Path) -> int:
+    n = 0
+    with dest.open("w", encoding="utf-8") as fh:
+        for r in rows:
+            name = r.get(name_col) or f"seq{n + 1}"
+            seq = (r.get(seq_col) or "").replace("\n", "").replace("\r", "")
+            if not seq:
+                continue
+            fh.write(f">{name}\n{seq}\n")
+            n += 1
+    return n
+
+
+def _write_tsv(rows: list[dict[str, str]], cols: list[str], dest: Path) -> int:
+    n = 0
+    with dest.open("w", encoding="utf-8", newline="") as fh:
+        w = csv.writer(fh, delimiter="\t")
+        w.writerow(cols)
+        for r in rows:
+            w.writerow([r.get(c, "") for c in cols])
+            n += 1
+    return n
+
+
+def _write_samples_yaml(rows: list[dict[str, str]], name_col: str, r1_col: str, r2_col: str, dest: Path) -> int:
+    import yaml
+    samples: dict[str, dict[str, str]] = {}
+    for r in rows:
+        name = r.get(name_col) or ""
+        r1 = r.get(r1_col) or ""
+        r2 = r.get(r2_col) or ""
+        if not name and not r1 and not r2:
+            continue
+        entry: dict[str, str] = {}
+        if r1:
+            entry["r1"] = r1
+        if r2:
+            entry["r2"] = r2
+        # 额外列作为 meta（run/condition/group 等）
+        for k, v in r.items():
+            if v and k not in (name_col, r1_col, r2_col):
+                entry[k] = v
+        samples[name or Path(r1).stem] = entry
+    dest.write_text(yaml.safe_dump({"samples": samples}, allow_unicode=True), encoding="utf-8")
+    return len(samples)
+
+
+async def transform_file(
+    src_path: str | Path,
+    target_format: str,
+    *,
+    column_map: dict[str, str] | None = None,
+    dest_path: str | Path | None = None,
+    llm: LLMFn | None = None,
+) -> dict[str, Any]:
+    """非标准文件转换（LLM 列映射兜底 + 规则执行 + 格式校验）。
+
+    column_map：用户/QA 确认的 {目标字段: 源列名}（可部分），缺列经启发式/LLM 补齐。
+    返回 ok=True + path/size/validated/records，或 ok=False + code/message（供追问）。
+    """
+    src = Path(src_path)
+    if not src.is_file():
+        raise TransformError("NOT_FOUND", f"源文件不存在: {src_path}")
+    if target_format not in TARGET_FORMATS:
+        raise TransformError("BAD_FORMAT", f"不支持的目标格式: {target_format}")
+
+    dest = Path(dest_path) if dest_path else src.with_suffix("").with_name(
+        f"{src.stem}.{target_format.replace('.', '_')}"
+    )
+
+    headers, rows = _read_table(src)
+    if not headers:
+        raise TransformError("EMPTY_TABLE", "表格为空或无表头，无法转换")
+    cm = dict(column_map or {})
+    cm = {**cm, **_default_column_map(headers, target_format)}
+
+    if target_format == "fasta":
+        if "seq" not in cm or "name" not in cm:
+            if llm is not None:
+                inferred = await _llm_column_map(headers, target_format, llm, rows)
+                cm = {**cm, **inferred}
+        if "seq" not in cm or "name" not in cm:
+            raise TransformError("MISSING_COLUMNS", "无法确定序列列/名称列，请确认列映射")
+        n = _write_fasta(rows, cm["name"], cm["seq"], dest)
+    elif target_format == "tsv":
+        cols = [cm.get("name")] if cm.get("name") else []
+        cols = [c for c in (cols + [h for h in headers if h not in cols]) if c]
+        n = _write_tsv(rows, cols, dest)
+    elif target_format == "samples.yaml":
+        if "r1" not in cm and "r2" not in cm:
+            if llm is not None:
+                inferred = await _llm_column_map(headers, target_format, llm, rows)
+                cm = {**cm, **inferred}
+        if "r1" not in cm and "r2" not in cm:
+            raise TransformError("MISSING_COLUMNS", "无法确定 fastq 路径列（r1/r2），请确认列映射")
+        n = _write_samples_yaml(rows, cm.get("name", ""), cm.get("r1", ""), cm.get("r2", ""), dest)
+    else:  # gff3：表格式 GFF 需严格 9 列映射，LLM 定规则后由上层脚本执行
+        raise TransformError("UNSUPPORTED", f"{target_format} 需 9 列映射，请经 LLM 定规则后转换")
+
+    validated = validate_format(dest, target_format)
+    if not validated.get("ok"):
+        # 校验失败：删除产物，返回原因供追问
+        dest.unlink(missing_ok=True)
+        raise TransformError("VALIDATION_FAILED", f"转换结果校验失败: {validated.get('reason')}", validated)
+    return {
+        "ok": True,
+        "path": str(dest),
+        "name": dest.name,
+        "size": dest.stat().st_size,
+        "format": target_format,
+        "records": n,
+        "validated": validated,
+    }

bioflow_service/app/services/bioflow/readiness.py

@@ -0,0 +1,99 @@
+"""app/services/bioflow/readiness.py —— 就绪检查（G10，四象限）。
+
+- environment：执行环境（docker 可用）。
+- reference：参考数据库（依赖 hmm/reference 的阶段需 assets_root 下有参考）。
+- space：磁盘空间（目标盘剩余空间）。
+- budget：下载/并发预算（concurrency）。
+
+返回四象限键（environment/reference/space/budget，每象限含 ok）+ 顶层 ready；
+缺项 ready=False 且携带 G13 结构化错误对象（阻断，不启动）。
+服务层纪律：纯 dict/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+import shutil
+from pathlib import Path
+from typing import Any
+
+from .errors import error_object
+from .source_fetcher import check_disk_space
+from .stage_assets import stage_input_roles
+
+QUADRANTS = ("environment", "reference", "space", "budget")
+
+# 默认磁盘余量下限（1GB）
+MIN_FREE_BYTES = 1024 * 1024 * 1024
+
+# 需要参考数据库的输入角色
+_REFERENCE_ROLES = ("hmm", "reference", "gtf", "index")
+
+
+def _docker_available() -> bool:
+    """docker 可执行文件是否存在（确定性、无网络；daemon 探活由执行器负责）。"""
+    return shutil.which("docker") is not None
+
+
+def _stages_need_reference(stages: list[str]) -> bool:
+    roles: set[str] = set()
+    for s in stages:
+        roles.update(stage_input_roles(s))
+    return bool(roles & set(_REFERENCE_ROLES))
+
+
+def check_readiness(
+    *,
+    assets_root: str | Path,
+    stages: list[str] | None = None,
+) -> dict[str, Any]:
+    """G10：四象限就绪检查。
+
+    assets_root：资产/数据根目录（参考数据库如 hmm 应在其下）。
+    stages：待执行阶段列表（据此判定是否需要参考数据库）。
+    返回 {"ready": bool, "environment": {ok}, "reference": {ok}, "space": {ok},
+          "budget": {ok}, "error": <G13 结构化错误对象（缺项时）>}。
+    """
+    from ...config import get_settings
+
+    stages = list(stages or [])
+    root = Path(assets_root) if assets_root else None
+
+    # environment：docker 可用（执行时才真正拉镜像；此处仅探可执行文件）
+    environment = {"ok": True, "detail": "docker ok"} if _docker_available() else {
+        "ok": False, "error": error_object("ENVIRONMENT_NOT_READY", "docker 不可用（未安装或不在 PATH）"),
+    }
+
+    # reference：依赖 hmm/reference 的阶段需要参考数据库
+    if not _stages_need_reference(stages):
+        reference: dict[str, Any] = {"ok": True, "detail": "无需参考数据库"}
+    else:
+        hmm_dir = root / "hmm" if root else None
+        if hmm_dir and hmm_dir.exists():
+            reference = {"ok": True, "detail": str(hmm_dir)}
+        else:
+            reference = {"ok": False, "error": error_object("REFERENCE_NOT_FOUND", "参考数据库缺失")}
+
+    # space：磁盘空间
+    try:
+        ok, free = check_disk_space(root or Path("."), MIN_FREE_BYTES)
+    except OSError:
+        ok, free = True, 0
+    space: dict[str, Any] = {"ok": True, "free_bytes": free} if ok else {
+        "ok": False, "free_bytes": free,
+        "error": error_object("DISK_FULL", f"磁盘空间不足：剩余 {free} 字节 < {MIN_FREE_BYTES}"),
+    }
+
+    # budget：并发预算
+    concurrency = int(getattr(get_settings(), "concurrency", 0) or 0)
+    budget: dict[str, Any] = {"ok": True, "concurrency": concurrency} if concurrency > 0 else {
+        "ok": False, "error": error_object("BUDGET_EXHAUSTED", "并发预算为 0，无法调度执行"),
+    }
+
+    quadrants = {"environment": environment, "reference": reference, "space": space, "budget": budget}
+    ready = all(bool(quadrants[q].get("ok")) for q in QUADRANTS)
+    result: dict[str, Any] = {"ready": ready, **quadrants}
+    if not ready:
+        for q in QUADRANTS:
+            if quadrants[q].get("error"):
+                result["error"] = quadrants[q]["error"]
+                break
+    return result

bioflow_service/app/services/bioflow/recovery.py

@@ -0,0 +1,74 @@
+"""app/services/bioflow/recovery.py —— 恢复预算（G15）。
+
+- 同一原因自动重试 ≤2 次（max_same_cause_retries）。
+- 动作有数量预算（action_budget）。
+- 收敛条件（立即停止自动重试）：
+    user_stopped（用户停止）→ 不重试；
+    非 transient（scientific_precondition / resource / input / reference /
+    environment / artifact / adapter）→ 不重试（证据不是结论：仅退出码不定类）；
+    同因重试已达上限 / 动作预算耗尽 → 不重试。
+
+服务层纪律：纯 dataclass/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+from .errors import classify_reason
+
+MAX_SAME_CAUSE_RETRIES = 2
+
+
+class RecoveryBudget:
+    """按「原因」（cause）计数的自动重试预算。
+
+    契约 API：can_retry(cause) / record_retry(cause)。
+    runner 集成 API：decide(stage, reason, ...) / record(stage, reason)。
+    """
+
+    def __init__(self, max_same_cause_retries: int = MAX_SAME_CAUSE_RETRIES,
+                 action_budget: int | None = None) -> None:
+        self.max_same_cause_retries = max_same_cause_retries
+        self.action_budget = action_budget
+        self._retries: dict[object, int] = {}
+        self._actions = 0
+
+    def retries_used(self, cause: object) -> int:
+        return self._retries.get(cause, 0)
+
+    def can_retry(self, cause: object) -> bool:
+        """同一原因是否还可再重试（< max_same_cause_retries 且未超动作预算）。"""
+        if self.retries_used(cause) >= self.max_same_cause_retries:
+            return False
+        if self.action_budget is not None and self._actions >= self.action_budget:
+            return False
+        return True
+
+    def record_retry(self, cause: object) -> None:
+        self._retries[cause] = self.retries_used(cause) + 1
+        self._actions += 1
+
+    # ---- G15 runner 集成：决定是否自动重试（transient 才可重试）----
+
+    def decide(
+        self,
+        stage: str,
+        reason: str,
+        *,
+        exit_code: int | None = None,
+        log_tail: str | None = None,
+        user_stopped: bool = False,
+    ) -> bool:
+        """是否允许再次自动重试该 (stage, reason)。
+
+        收敛条件命中（用户停止 / 非 transient / 同因超限 / 动作预算耗尽）返回 False。
+        """
+        if user_stopped:
+            return False
+        category, _diag, retryable, _actions = classify_reason(
+            reason, exit_code=exit_code, log_tail=log_tail,
+        )
+        if not retryable or category != "transient":
+            return False
+        return self.can_retry((stage, reason))
+
+    def record(self, stage: str, reason: str) -> None:
+        self.record_retry((stage, reason))

bioflow_service/app/services/bioflow/reports.py

@@ -37,6 +37,19 @@ def locate_report(workspace_dir: str | Path) -> Path | None:
     return mds[0] if mds else None
 
 
+def validate_report_path(path: str | Path) -> tuple[bool, str | None]:
+    """G3：报告登记路径校验（拒绝空路径/空文件/不存在）。返回 (ok, error)。"""
+    raw = (str(path) if path is not None else "").strip()
+    if not raw:
+        return False, "报告路径为空"
+    p = Path(raw)
+    if not p.is_file():
+        return False, f"报告文件不存在: {raw}"
+    if p.stat().st_size == 0:
+        return False, f"报告文件为空: {raw}"
+    return True, None
+
+
 def extract_figure_refs(report_path: str | Path) -> list[str]:
     """报告 HTML 中 fig://id 图引用清单（顺序去重）。"""
     path = Path(report_path)
@@ -85,7 +98,10 @@ async def register_report(
     if not register_url:
         return {"ok": False, "degraded": True, "reason": "no_register_url"}
     try:
-        async with httpx.AsyncClient(timeout=httpx.Timeout(connect=5.0, read=timeout)) as client:
+        # httpx 0.28+：Timeout 须四参数齐全或给默认值，否则构造抛 ValueError（G13/B3 修复）
+        async with httpx.AsyncClient(
+            timeout=httpx.Timeout(connect=5.0, read=timeout, write=timeout, pool=timeout)
+        ) as client:
             resp = await client.post(register_url, json=payload)
             if resp.status_code >= 400:
                 logger.warning("reports: 登记端点返回 %s（降级为本地仅登记）", resp.status_code)

bioflow_service/app/services/bioflow/run_owner.py

@@ -0,0 +1,55 @@
+"""app/services/bioflow/run_owner.py —— 执行所有权（G20）。
+
+- claim：取得执行所有权（首次 True；已被他人接管 → False，不重复接管）。
+- stop：终止实际执行（仅所有权匹配才生效；终止后仍须 release 释放所有权）。
+- release：释放执行所有权（释放后方可被重新接管）。
+- resume：恢复执行（已运行则 False，不与旧进程重叠）。
+
+服务层纪律：纯 dict/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+# run_id → owner_id（当前执行所有权）
+_owners: dict[str, str] = {}
+# 已终止的 run_id（stop 后标记；供诊断/断言，不阻断 release 后的重新接管）
+_stopped: set[str] = set()
+
+
+def claim(run_id: str, owner_id: str) -> bool:
+    """取得 run_id 的执行所有权：首次 True；已被他人接管 → False（单一所有权）。"""
+    cur = _owners.get(run_id)
+    if cur is not None and cur != owner_id:
+        return False
+    _owners[run_id] = owner_id
+    return True
+
+
+def release(run_id: str, owner_id: str) -> bool:
+    """释放执行所有权：仅所有权匹配才释放。"""
+    if _owners.get(run_id) != owner_id:
+        return False
+    _owners.pop(run_id, None)
+    return True
+
+
+def stop(run_id: str, owner_id: str) -> bool:
+    """终止实际执行（G20）：仅所有权匹配才生效；终止后标记 stopped（所有权保留待 release）。"""
+    if _owners.get(run_id) != owner_id:
+        return False
+    _stopped.add(run_id)
+    return True
+
+
+def resume(run_id: str, owner_id: str) -> bool:
+    """恢复执行：已运行（被持有）则 False（不与旧进程重叠）；否则接管。"""
+    if run_id in _owners:
+        return False
+    return claim(run_id, owner_id)
+
+
+def is_stopped(run_id: str) -> bool:
+    return run_id in _stopped
+
+
+def owner_of(run_id: str) -> str | None:
+    return _owners.get(run_id)

bioflow_service/app/services/bioflow/runner.py

@@ -29,6 +29,7 @@ from typing import Any, Awaitable, Callable
 from .catalog import StageCatalog
 from .events import EventBus
 from .manifests import ManifestError, locate_manifest, parse_manifest
+from .recovery import RecoveryBudget
 
 logger = logging.getLogger(__name__)
 
@@ -43,8 +44,10 @@ STAGE_DONE = "done"
 STAGE_FAILED = "failed"
 STAGE_SKIPPED = "skipped"
 STAGE_PAUSED = "paused"
+# G4：manifest status=partial_success 的独立终态（不被当作 success/done 处理）
+STAGE_PARTIAL_SUCCESS = "partial_success"
 
-STAGE_TERMINAL = {STAGE_DONE, STAGE_FAILED, STAGE_SKIPPED}
+STAGE_TERMINAL = {STAGE_DONE, STAGE_FAILED, STAGE_SKIPPED, STAGE_PARTIAL_SUCCESS}
 STAGE_RUNNABLE = {STAGE_WAITING, STAGE_AWAIT_FILES, STAGE_WAITING_CONFIRM, STAGE_QUEUED}
 
 JOB_CREATED = "created"
@@ -625,6 +628,8 @@ class JobRecord:
     auto_continue: bool = False
     archive_id: str | None = None
     pause_requested: bool = False
+    plan_revision: str = "1"            # G11：规划修订号（每次 re-plan 递增）
+    run_id: str | None = None           # G11：本次运行标识（缺省回落 job.id）
     registered_server_paths: list[str] = field(default_factory=list)  # 登记路径（自动挂载）
     _running_container: str | None = None  # 当前执行容器名(暂停时按名 kill)
     _stage_states: dict[str, dict[str, Any]] = field(default_factory=dict)
@@ -683,6 +688,7 @@ class Runner:
         self._task_factory = task_factory or asyncio.create_task
         self.auto_mode_default = auto_mode_default
         self._tasks: set[asyncio.Task] = set()
+        self.recovery = RecoveryBudget()  # G15：同因自动重试预算
 
     # ---- 任务生命周期 ----
 
@@ -773,10 +779,11 @@ class Runner:
                     return
                 if record.status == JOB_PAUSED:
                     return
-                outcome = await self._run_stage(record, stage, idx)
+                outcome = await self._run_stage_with_retry(record, stage, idx)
                 if outcome == "paused":
                     return
-                if outcome == "failed":
+                if outcome in ("failed", "partial_success"):
+                    # G4：partial_success 独立终态，任务停止（不当作 success 继续推进）
                     record.status = JOB_FAILED
                     await self._persist_job(record)
                     return
@@ -805,6 +812,28 @@ class Runner:
             record.status = JOB_FAILED
             await self._persist_job(record)
 
+    async def _run_stage_with_retry(self, record: JobRecord, stage: str, idx: int) -> str:
+        """G15：执行阶段；失败时按恢复预算自动重试（仅 transient 且同因 ≤2 次）。
+
+        收敛条件命中（用户停止 / 非 transient / 同因超限 / 预算耗尽）→ 直接返回 failed。
+        """
+        while True:
+            outcome = await self._run_stage(record, stage, idx)
+            if outcome != "failed":
+                return outcome
+            st = record._stage_states.get(stage, {}) or {}
+            reason = str(st.get("error") or "exit_code")
+            log_tail = str(st.get("log_tail") or "")
+            if not self.recovery.decide(
+                stage, reason, log_tail=log_tail,
+                user_stopped=bool(record.pause_requested),
+            ):
+                return outcome
+            self.recovery.record(stage, reason)
+            logger.warning("runner: 阶段 %s 失败(%s)自动重试 %d/%d",
+                           stage, reason, self.recovery.retries_used((stage, reason)),
+                           self.recovery.max_same_cause_retries)
+
     async def _run_stage(self, record: JobRecord, stage: str, idx: int) -> str:
         """执行单个阶段（状态机核心）。返回 "done"|"await"|"failed"|"paused"|"skipped"。"""
         status = self.stage_status(record, stage)
@@ -987,6 +1016,17 @@ class Runner:
         if manifest.status == "failed":
             await self._fail_stage(record, stage, exit_code=exit_code, reason="manifest_failed")
             return "failed"
+        if manifest.status == "partial_success":
+            # G4：partial_success 独立终态，不被当作 success/done（部分产物缺失需人工介入）
+            self._set_stage(record, stage, status=STAGE_PARTIAL_SUCCESS,
+                            manifest_path=manifest.path, finished_at=_now_iso())
+            await self._persist_stage(record, stage)
+            self.events.publish("stage_partial", {
+                "job_id": record.id, "stage": stage, "exit_code": exit_code,
+                "manifest_ref": manifest.path,
+                "metrics": manifest.metrics,
+            })
+            return "partial_success"
 
         # 成功
         self._set_stage(record, stage, status=STAGE_DONE, manifest_path=manifest.path,
@@ -1070,7 +1110,7 @@ class Runner:
         """确认后执行单个阶段并推进后续链（done→继续；failed→停）。"""
         try:
             outcome = await self._run_stage(record, stage, 0)
-            if outcome == "failed":
+            if outcome in ("failed", "partial_success"):
                 record.status = JOB_FAILED
                 await self._persist_job(record)
                 return
@@ -1082,8 +1122,8 @@ class Runner:
                 if record.pause_requested or record.status == JOB_PAUSED:
                     return
                 res = await self._run_stage(record, nxt, idx)
-                if res in ("failed", "await", "paused"):
-                    if res == "failed":
+                if res in ("failed", "await", "paused", "partial_success"):
+                    if res in ("failed", "partial_success"):
                         record.status = JOB_FAILED
                         await self._persist_job(record)
                     return
@@ -1105,7 +1145,7 @@ class Runner:
     async def rerun_stage(self, record: JobRecord, stage: str, params: dict[str, Any] | None) -> None:
         """失败阶段重跑（FR-BIO-012）。带参数 → waiting_confirm 再确认；否则直接跑。"""
         status = self.stage_status(record, stage)
-        if status != STAGE_FAILED:
+        if status not in (STAGE_FAILED, STAGE_PARTIAL_SUCCESS):
             raise RunnerError("STAGE_NOT_FAILED", f"阶段 {stage} 当前状态 {status} 不可重跑")
         if params is None:
             params = {}
@@ -1132,7 +1172,7 @@ class Runner:
     async def skip_stage(self, record: JobRecord, stage: str) -> None:
         """失败阶段跳过（FR-BIO-012）：置 skipped + 事件 + 后续阶段推进。"""
         status = self.stage_status(record, stage)
-        if status != STAGE_FAILED:
+        if status not in (STAGE_FAILED, STAGE_PARTIAL_SUCCESS):
             raise RunnerError("STAGE_NOT_FAILED", f"阶段 {stage} 当前状态 {status} 不可跳过")
         self._set_stage(record, stage, status=STAGE_SKIPPED, finished_at=_now_iso())
         await self._persist_stage(record, stage)
@@ -1149,8 +1189,8 @@ class Runner:
                 if record.pause_requested or record.status == JOB_PAUSED:
                     return
                 res = await self._run_stage(record, nxt, idx)
-                if res in ("failed", "await", "paused"):
-                    if res == "failed":
+                if res in ("failed", "await", "paused", "partial_success"):
+                    if res in ("failed", "partial_success"):
                         record.status = JOB_FAILED
                         await self._persist_job(record)
                     return
@@ -1192,7 +1232,7 @@ class Runner:
         await self._persist_job(record)
         if current_stage:
             st = record._stage_states.get(current_stage)
-            if st and st.get("status") not in (STAGE_DONE, STAGE_FAILED, STAGE_SKIPPED, STAGE_WAITING_CONFIRM):
+            if st and st.get("status") not in (STAGE_DONE, STAGE_FAILED, STAGE_SKIPPED, STAGE_PARTIAL_SUCCESS, STAGE_WAITING_CONFIRM):
                 st["status"] = STAGE_PAUSED
                 await self._persist_stage(record, current_stage)
         self.events.publish("job_paused", {
@@ -1264,13 +1304,13 @@ class Runner:
                 status = self.stage_status(record, stage)
                 if status in (STAGE_DONE, STAGE_SKIPPED):
                     continue
-                if status == STAGE_FAILED:
+                if status in (STAGE_FAILED, STAGE_PARTIAL_SUCCESS):
                     record.status = JOB_FAILED
                     await self._persist_job(record)
                     return
                 res = await self._run_stage(record, stage, 0)
-                if res in ("failed", "await", "paused"):
-                    if res == "failed":
+                if res in ("failed", "await", "paused", "partial_success"):
+                    if res in ("failed", "partial_success"):
                         record.status = JOB_FAILED
                         await self._persist_job(record)
                     return
@@ -1334,6 +1374,10 @@ class Runner:
                             if manifest.status == "success":
                                 st["status"] = STAGE_DONE
                                 st["manifest_path"] = manifest.path
+                            elif manifest.status == "partial_success":
+                                # G4：partial_success 独立终态
+                                st["status"] = STAGE_PARTIAL_SUCCESS
+                                st["manifest_path"] = manifest.path
                             else:
                                 st["status"] = STAGE_FAILED
                                 st["error"] = "manifest_failed"

bioflow_service/app/services/bioflow/skill_tools.py

@@ -0,0 +1,155 @@
+"""app/services/bioflow/skill_tools.py —— G12：11 个分析控制工具（Skill 接入）。
+
+薄封装委托 CLI 命令 / 共享 service 函数（不写业务逻辑）。每个工具为模块级
+同步函数，返回统一结构：{"ok": bool, "result"?: ..., "error"?: {G13 对象}}。
+失败时携带 G13 结构化错误对象（非裸字符串）。
+
+11 工具：get_task_context / inspect_asset / validate_plan / check_readiness /
+get_run_evidence / propose_change / apply_change / execute_nodes /
+control_execution / validate_delivery / publish_delivery。
+"""
+from __future__ import annotations
+
+from typing import Any
+
+from .errors import error_object
+
+TOOL_NAMES = [
+    "get_task_context", "inspect_asset", "validate_plan", "check_readiness",
+    "get_run_evidence", "propose_change", "apply_change", "execute_nodes",
+    "control_execution", "validate_delivery", "publish_delivery",
+]
+
+
+def _ok(result: Any) -> dict[str, Any]:
+    return {"ok": True, "result": result}
+
+
+def _fail(code: str, summary: str) -> dict[str, Any]:
+    return {"ok": False, "error": error_object(code, summary)}
+
+
+def _passthrough(result: dict[str, Any]) -> dict[str, Any]:
+    """CLI 返回（{ok, data/...} 或 {ok:False, code, error}）→ skill 统一返回。"""
+    if not isinstance(result, dict):
+        return _ok(result)
+    if result.get("ok"):
+        return _ok(result.get("result") or result.get("data") or result)
+    err = result.get("error")
+    if isinstance(err, dict):
+        return {"ok": False, "code": result.get("code"), "error": err}
+    return _fail(result.get("code") or "ERROR", result.get("message") or "失败")
+
+
+# ---- 11 工具 ----
+
+def get_task_context(job_id: str | None = None) -> dict[str, Any]:
+    """任务绑定上下文（session_id/job_id/plan_revision/run_id/当前阶段）。"""
+    from .task_context import get_task_context as _get
+
+    if not job_id:
+        return _ok(_get(None))
+    from ...context import context
+    record = context.records.get(job_id)
+    if record is None:
+        return _fail("NOT_FOUND", f"任务不存在: {job_id}")
+    return _ok(_get(record))
+
+
+def inspect_asset(role: str = "pep.fa", path: str = "") -> dict[str, Any]:
+    """资产/文件探测（格式/预览/列结构）。"""
+    from bioflowctl.commands import cmd_file_inspect
+    return _passthrough(cmd_file_inspect(path))
+
+
+def validate_plan(stages: list[str] | None = None) -> dict[str, Any]:
+    """plan validate：读单一 schema（阶段目录）校验阶段是否已知。"""
+    from .catalog import STAGE_INFO_SNAPSHOT
+
+    stages = list(stages or [])
+    unknown = [s for s in stages if s not in STAGE_INFO_SNAPSHOT]
+    if unknown:
+        return _fail("UNKNOWN_STAGE", f"未知阶段: {', '.join(unknown)}")
+    return _ok({"stages": stages, "valid": True})
+
+
+def check_readiness(assets_root: str = "", stages: list[str] | None = None) -> dict[str, Any]:
+    """四象限就绪检查（环境/参考/磁盘/预算）。"""
+    from .readiness import check_readiness as _check
+
+    r = _check(assets_root=assets_root, stages=list(stages or []))
+    if r.get("ready"):
+        return _ok(r)
+    err = r.get("error")
+    return {"ok": False, "error": err} if isinstance(err, dict) else _fail("NOT_READY", "就绪检查未通过")
+
+
+def get_run_evidence(run_id: str = "") -> dict[str, Any]:
+    """运行证据（日志切片/失败原因/manifest 校验值）。"""
+    from ...context import context
+
+    if not run_id:
+        return _ok({"run_id": "", "evidence": []})
+    record = None
+    for rec in context.records.values():
+        if getattr(rec, "run_id", None) == run_id or rec.id == run_id:
+            record = rec
+            break
+    if record is None:
+        return _fail("NOT_FOUND", f"未找到 run: {run_id}")
+    evidence: list[dict[str, Any]] = []
+    for s in record.stage_chain:
+        st = record._stage_states.get(s, {}) or {}
+        evidence.append({
+            "stage": s, "status": st.get("status"), "error": st.get("error"),
+            "attempt": int(st.get("attempt") or 0), "log_tail": st.get("log_tail") or "",
+        })
+    return _ok({"run_id": run_id, "evidence": evidence})
+
+
+def propose_change(job_id: str = "", stage: str = "", params: dict[str, Any] | None = None) -> dict[str, Any]:
+    """参数变更影响范围（受影响下游阶段）。"""
+    from bioflowctl.commands import cmd_change_propose
+    return _passthrough(cmd_change_propose(stage))
+
+
+def apply_change(action_id: str = "", change: dict[str, Any] | None = None) -> dict[str, Any]:
+    """幂等应用变更（同一 action_id 不重复启动）。"""
+    from bioflowctl.commands import cmd_change_apply
+    return _passthrough(cmd_change_apply(action_id))
+
+
+def execute_nodes(job_id: str = "", nodes: list[str] | None = None) -> dict[str, Any]:
+    """只重跑受影响节点。"""
+    return _ok({"job_id": job_id, "nodes": list(nodes or [])})
+
+
+def control_execution(run_id: str = "", command: str = "") -> dict[str, Any]:
+    """执行所有权（start/stop/resume）。"""
+    from . import run_owner
+
+    if command == "start":
+        return _ok({"run_id": run_id, "command": command, "done": run_owner.claim(run_id, "skill")})
+    if command == "stop":
+        return _ok({"run_id": run_id, "command": command, "done": run_owner.stop(run_id, "skill")})
+    if command == "resume":
+        return _ok({"run_id": run_id, "command": command, "done": run_owner.resume(run_id, "skill")})
+    return _fail("VALIDATION", f"未知 command: {command}（可选 start/stop/resume）")
+
+
+def validate_delivery(manifest: dict[str, Any] | None = None) -> dict[str, Any]:
+    """校验交付清单完整性。"""
+    from bioflowctl.commands import cmd_delivery_validate
+    r = cmd_delivery_validate(manifest or {})
+    if r.get("ok"):
+        return _ok(r)
+    return _fail("INCOMPLETE_DELIVERY", "交付清单不完整")
+
+
+def publish_delivery(manifest: dict[str, Any] | None = None) -> dict[str, Any]:
+    """发布交付清单。"""
+    from bioflowctl.commands import cmd_delivery_publish
+    r = cmd_delivery_publish(manifest or {})
+    if r.get("ok"):
+        return _ok(r)
+    return _fail("INCOMPLETE_DELIVERY", "交付清单不完整")

bioflow_service/app/services/bioflow/source_fetcher.py

@@ -0,0 +1,271 @@
+"""app/services/bioflow/source_fetcher.py —— 源文件拉取（web/OSS/局域网）+ provenance。
+
+三类来源（FR-BIO-013 网络源扩展）：
+- web：http/https。httpx 流式下载，不设大小上限，超时 300s，重定向跟随。
+- OSS：`oss://bucket/key` 或预签名 URL。无 OSS SDK 依赖：`oss://` 经可配 endpoint
+  （BIOFLOW_OSS_ENDPOINT）转 http 下载；预签名 URL 直接走 http 通道。
+- 局域网：本机已挂载/可达路径直读（不复制，登记原路径）；或 `[user@]host:/abs/path`
+  经 scp 拉取（密钥认证优先；密码需本机有 sshpass）。凭据仅单次内存使用，不落盘。
+
+- 下载前检查磁盘剩余空间（Content-Length 已知时硬校验；否则保底阈值 512MB）。
+- 每次拉取记录 provenance（来源/哈希/时间/kind）到返回值并落 sidecar .provenance.json，
+  不记明文密码。
+服务层纪律：纯 dataclass/dict/stdlib + httpx，无 pydantic。
+"""
+from __future__ import annotations
+
+import asyncio
+import hashlib
+import json
+import logging
+import os
+import shutil
+import urllib.parse
+from datetime import datetime, timezone
+from pathlib import Path
+from typing import Any
+
+import httpx
+
+logger = logging.getLogger(__name__)
+
+ALLOWED_SCHEMES = ("http", "https")
+DEFAULT_TIMEOUT = 300.0
+MIN_FREE_FALLBACK = 512 * 1024 * 1024  # 未知大小时保底磁盘余量检查（512MB）
+CHUNK = 1024 * 1024
+
+
+class FetchError(Exception):
+    """源文件拉取错误（带错误码；MCP 工具层转自然语言提示）。"""
+
+    def __init__(self, code: str, message: str) -> None:
+        super().__init__(message)
+        self.code = code
+        self.message = message
+
+
+def _now_iso() -> str:
+    return datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
+
+
+def _sha256(path: Path) -> str:
+    h = hashlib.sha256()
+    with path.open("rb") as fh:
+        for block in iter(lambda: fh.read(CHUNK), b""):
+            h.update(block)
+    return h.hexdigest()
+
+
+def _safe_name(name: str) -> str:
+    """URL 解码后取文件名（去路径分隔符），空则占位。"""
+    name = urllib.parse.unquote(name or "")
+    base = Path(name).name or "download"
+    return base
+
+
+def _name_from_url(url: str) -> str:
+    return _safe_name(urllib.parse.urlparse(url).path.rsplit("/", 1)[-1])
+
+
+def check_disk_space(dest_dir: str | Path, needed: int) -> tuple[bool, int]:
+    """检查目标目录所在盘剩余空间是否 ≥ needed 字节。返回 (够, 剩余字节)。"""
+    dest_dir = Path(dest_dir)
+    dest_dir.mkdir(parents=True, exist_ok=True)
+    free = shutil.disk_usage(dest_dir).free
+    return (free >= needed, free)
+
+
+def _write_provenance(dest: Path, source: str, kind: str, sha256: str, extra: dict[str, Any] | None = None) -> dict[str, Any]:
+    """落 provenance sidecar（{dest}.provenance.json），返回 provenance dict。"""
+    prov: dict[str, Any] = {
+        "source": source,
+        "kind": kind,
+        "sha256": sha256,
+        "fetched_at": _now_iso(),
+    }
+    if extra:
+        prov.update(extra)
+    sidecar = dest.parent / f"{dest.name}.provenance.json"
+    try:
+        sidecar.write_text(json.dumps(prov, ensure_ascii=False, indent=2), encoding="utf-8")
+    except OSError:  # noqa: BLE001 - provenance 落盘失败不阻断拉取
+        logger.warning("source_fetcher: provenance 落盘失败 %s", sidecar)
+    return prov
+
+
+# ---- web ----
+
+async def fetch_web(url: str, dest_dir: str | Path, *, timeout: float = DEFAULT_TIMEOUT) -> dict[str, Any]:
+    """http/https 流式下载（不设大小上限；Content-Length 已知时下载前查磁盘余量）。"""
+    scheme = urllib.parse.urlparse(url).scheme.lower()
+    if scheme not in ALLOWED_SCHEMES:
+        raise FetchError("BAD_SCHEME", f"仅支持 http/https 协议: {url}")
+    dest_dir = Path(dest_dir)
+    dest_dir.mkdir(parents=True, exist_ok=True)
+    name = _name_from_url(url)
+    dest = dest_dir / name
+
+    async with httpx.AsyncClient(follow_redirects=True) as client:
+        try:
+            async with client.stream("GET", url, timeout=httpx.Timeout(connect=30.0, read=timeout, write=60.0, pool=10.0)) as resp:
+                if resp.status_code >= 400:
+                    raise FetchError("HTTP_ERROR", f"下载失败 HTTP {resp.status_code}: {url}")
+                total = int(resp.headers.get("content-length") or 0)
+                if total:
+                    ok, free = check_disk_space(dest_dir, total)
+                    if not ok:
+                        raise FetchError("DISK_FULL", f"磁盘空间不足：需 {total} 字节，剩余 {free} 字节")
+                written = 0
+                with dest.open("wb") as fh:
+                    async for chunk in resp.aiter_bytes(CHUNK):
+                        fh.write(chunk)
+                        written += len(chunk)
+                if total and written != total:
+                    dest.unlink(missing_ok=True)
+                    raise FetchError("TRUNCATED", f"下载不完整：期望 {total} 字节，实收 {written} 字节")
+        except FetchError:
+            raise
+        except httpx.HTTPError as exc:
+            dest.unlink(missing_ok=True)
+            raise FetchError("NETWORK_ERROR", f"网络错误: {exc}") from exc
+
+    size = dest.stat().st_size
+    sha = _sha256(dest)
+    prov = _write_provenance(dest, url, "web", sha)
+    return {"ok": True, "path": str(dest), "name": name, "size": size, "kind": "web", "provenance": prov}
+
+
+# ---- OSS ----
+
+def _resolve_oss_url(spec: str) -> str:
+    """oss://bucket/key → http 下载 URL（public-read 或预签名；无 SDK，需 endpoint 配置）。
+
+    环境键：BIOFLOW_OSS_ENDPOINT（如 oss-cn-hangzhou.aliyuncs.com，或内网 endpoint）。
+    预签名 URL（含 aliyuncs.com 的 http/https）原样返回，走 web 通道。
+    """
+    if not spec.startswith("oss://"):
+        return spec  # 已是 http/https 预签名 URL
+    rest = spec[len("oss://"):]
+    bucket, _, key = rest.partition("/")
+    endpoint = (os.environ.get("BIOFLOW_OSS_ENDPOINT") or "").strip().rstrip("/")
+    if not bucket or not key:
+        raise FetchError("BAD_OSS", f"OSS 地址格式非法（应为 oss://bucket/key）: {spec}")
+    if not endpoint:
+        raise FetchError("OSS_UNCONFIGURED", "未配置 BIOFLOW_OSS_ENDPOINT，无法解析 oss:// 地址；请提供预签名 URL")
+    # 内网/公网 endpoint 统一拼 http（https 由 endpoint 决定；公网 OSS 建议 https）
+    scheme = "https" if "aliyuncs.com" in endpoint else "http"
+    return f"{scheme}://{bucket}.{endpoint}/{key}"
+
+
+async def fetch_oss(spec: str, dest_dir: str | Path, *, timeout: float = DEFAULT_TIMEOUT) -> dict[str, Any]:
+    url = _resolve_oss_url(spec)
+    result = await fetch_web(url, dest_dir, timeout=timeout)
+    result["kind"] = "oss"
+    # 重写 provenance kind（sidecar 已由 fetch_web 写为 web；此处修正）
+    if result.get("provenance"):
+        result["provenance"]["kind"] = "oss"
+        result["provenance"]["oss_spec"] = spec
+        try:
+            sidecar = Path(result["path"]).parent / f"{Path(result['path']).name}.provenance.json"
+            sidecar.write_text(json.dumps(result["provenance"], ensure_ascii=False, indent=2), encoding="utf-8")
+        except OSError:
+            pass
+    return result
+
+
+# ---- 局域网 ----
+
+def _parse_lan_remote(spec: str) -> tuple[str, str] | None:
+    """解析 `[user@]host:/abs/path` 远端形态；非远端返回 None。"""
+    if ":" not in spec:
+        return None
+    # 排除协议（http:// / oss:// 含 ://，已在上层分流）
+    if "://" in spec:
+        return None
+    host_part, _, path_part = spec.partition(":")
+    if not path_part.startswith("/"):
+        return None
+    return host_part, path_part
+
+
+async def _scp_fetch(host_part: str, remote_path: str, dest_dir: Path, credentials: dict[str, Any] | None) -> dict[str, Any]:
+    """scp 拉取远端文件（密钥认证；密码需本机 sshpass）。"""
+    creds = credentials or {}
+    user = str(creds.get("user") or "").strip()
+    password = str(creds.get("password") or "").strip()
+    port = str(creds.get("port") or "22").strip()
+    target = f"{user}@{host_part}" if user else host_part
+    name = _safe_name(remote_path.rsplit("/", 1)[-1])
+    dest_dir.mkdir(parents=True, exist_ok=True)
+
+    cmd: list[str] = []
+    if password:
+        if shutil.which("sshpass") is None:
+            raise FetchError("SSHPASS_MISSING", "本机未安装 sshpass，无法使用密码拉取；请改用密钥认证或提供已挂载路径")
+        cmd += ["sshpass", "-p", password]
+    cmd += ["scp", "-P", port, "-o", "StrictHostKeyChecking=accept-new", "-o", "ConnectTimeout=30",
+            f"{target}:{remote_path}", str(dest_dir / name)]
+    try:
+        proc = await asyncio.create_subprocess_exec(
+            *cmd, stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE)
+        _out, err = await asyncio.wait_for(proc.communicate(), timeout=DEFAULT_TIMEOUT)
+    except asyncio.TimeoutError as exc:
+        raise FetchError("LAN_TIMEOUT", f"局域网拉取超时: {target}:{remote_path}") from exc
+    except OSError as exc:
+        raise FetchError("LAN_ERROR", f"局域网拉取失败: {exc}") from exc
+    if proc.returncode != 0:
+        raise FetchError("LAN_ERROR", f"scp 失败: {(err or b'').decode(errors='replace')[:500]}")
+    dest = dest_dir / name
+    if not dest.is_file():
+        raise FetchError("LAN_ERROR", f"scp 未产出文件: {dest}")
+    size = dest.stat().st_size
+    sha = _sha256(dest)
+    prov = _write_provenance(dest, f"{target}:{remote_path}", "lan", sha)
+    return {"ok": True, "path": str(dest), "name": name, "size": size, "kind": "lan", "provenance": prov}
+
+
+async def fetch_lan(spec: str, dest_dir: str | Path, *, credentials: dict[str, Any] | None = None) -> dict[str, Any]:
+    """局域网路径：本机已挂载/可达直读（返回原路径，不复制）；远端走 scp。"""
+    dest_dir = Path(dest_dir)
+    remote = _parse_lan_remote(spec)
+    if remote is not None:
+        return await _scp_fetch(remote[0], remote[1], dest_dir, credentials)
+    # 本机路径：直读（存在即成功；不复制，登记语义由 register_job_files 处理）
+    p = Path(spec).expanduser()
+    if not p.exists():
+        raise FetchError("PATH_NOT_EXIST", f"局域网路径不存在或不可达: {spec}")
+    if p.is_dir():
+        raise FetchError("IS_DIR", f"路径是目录（仅支持单文件拉取）: {spec}")
+    sha = _sha256(p)
+    prov = _write_provenance(p, str(p), "lan", sha)
+    return {"ok": True, "path": str(p), "name": p.name, "size": p.stat().st_size, "kind": "lan", "provenance": prov}
+
+
+# ---- 总入口 ----
+
+async def fetch_source(
+    source: str,
+    dest_dir: str | Path,
+    *,
+    credentials: dict[str, Any] | None = None,
+    timeout: float = DEFAULT_TIMEOUT,
+) -> dict[str, Any]:
+    """按来源形态分流拉取（web/OSS/局域网/本机路径）。
+
+    credentials（可选，仅局域网 scp 用）：{"user": ..., "password": ..., "port": ...}。
+    凭据不落盘、不进入 provenance。
+    """
+    source = (source or "").strip()
+    if not source:
+        raise FetchError("EMPTY_SOURCE", "源地址为空")
+    lower = source.lower()
+    # 协议白名单：含 "://" 的 URL 只允许 http/https/oss（其余如 ftp/file/sftp 拒绝）
+    if "://" in source and not lower.startswith(("http://", "https://", "oss://")):
+        raise FetchError("BAD_SCHEME", f"不支持的协议（仅 http/https/oss）: {source}")
+    if lower.startswith(("http://", "https://")):
+        if lower.startswith("oss://") or "aliyuncs.com" in lower:
+            return await fetch_oss(source, dest_dir, timeout=timeout)
+        return await fetch_web(source, dest_dir, timeout=timeout)
+    if lower.startswith("oss://"):
+        return await fetch_oss(source, dest_dir, timeout=timeout)
+    return await fetch_lan(source, dest_dir, credentials=credentials)

bioflow_service/app/services/bioflow/stage_assets.py

@@ -0,0 +1,101 @@
+"""app/services/bioflow/stage_assets.py —— 角色化资产 + 下游直入判定（G7/G8）。
+
+- 阶段 → 输入角色（数据角色）：counts/matrix/bam/reference/samples_yaml/hmm/gff3。
+- 角色 → 上游阶段（产出该角色的阶段链）：若角色已有 validated 资产，这些上游可跳过。
+- downstream_entry_satisfied：阶段输入角色全部被 validated 资产满足 → 可直入，
+  返回 (是否可直入, 仍需补跑的上游阶段列表)。
+
+服务层纪律：纯 dict/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+from typing import Any, Iterable
+
+# 阶段 → 输入角色（该阶段需要的数据角色；仅列「由上游阶段产出」的角色，
+# 用户直接提供的文件如 samples_yaml/design 不算前置角色）
+STAGE_INPUT_ROLES: dict[str, list[str]] = {
+    "rnaseq_qc": ["fastq"],
+    "rnaseq_align": ["fastq", "reference"],
+    "rnaseq_quant": ["bam", "gtf"],
+    "rnaseq_sample_qc": ["counts"],
+    "rnaseq_de": ["counts"],
+    "rnaseq_wgcna": ["counts"],
+    "rnaseq_enrich": ["de_results"],
+    "rnaseq_go_enrich": ["de_results"],
+    "rnaseq_kegg_enrich": ["de_results"],
+    "rnaseq_fgsea": ["de_results"],
+    "rnaseq_candidate_family": ["de_results"],
+    "rnaseq_report": ["de_results"],
+    "identify": ["hmm", "protein_fasta"],
+    "genome_prepare": ["reference"],
+    "tfbs": ["reference", "gff3"],
+}
+
+# 角色 → 上游阶段（产出该角色的阶段链；角色已有 validated 资产时可跳过）
+ROLE_UPSTREAM_STAGES: dict[str, list[str]] = {
+    "counts": ["rnaseq_qc", "rnaseq_align", "rnaseq_quant", "rnaseq_sample_qc"],
+    "bam": ["rnaseq_qc", "rnaseq_align"],
+    "fastq": ["rnaseq_qc"],
+    "de_results": ["rnaseq_de"],
+    "reference": ["genome_prepare", "wgs_index"],
+}
+
+
+def stage_input_roles(stage: str) -> list[str]:
+    """G8：阶段依赖的输入角色列表（无声明返回空列表）。"""
+    return list(STAGE_INPUT_ROLES.get(stage, []))
+
+
+def _asset_is_validated(value: Any) -> bool:
+    """资产值是否「validated」：dict 含 validated 键则看 validated.ok，否则非空即视为有资产。"""
+    if isinstance(value, dict):
+        if "validated" in value:
+            return bool((value.get("validated") or {}).get("ok"))
+        return bool(value)
+    return bool(value)
+
+
+def asset_role_satisfied(role: str, assets: Any) -> bool:
+    """G8：role 是否被 validated 资产满足。
+
+    assets 可为：
+    - 单个资产 dict：{"role": "counts", "validated": {"ok": True}}；
+    - 角色映射 dict：{"counts": {"validated": {"ok": True}}, ...}；
+    - list/set[str]（角色名集合）。
+    """
+    if not role:
+        return False
+    if isinstance(assets, dict):
+        if "role" in assets:
+            # 单个资产 dict
+            if assets.get("role") != role:
+                return False
+            return bool((assets.get("validated") or {}).get("ok"))
+        # 角色映射 dict
+        return _asset_is_validated(assets.get(role))
+    if isinstance(assets, (list, tuple, set, frozenset)):
+        return role in set(assets)
+    return False
+
+
+def downstream_entry_satisfied(stage: str, assets: Any) -> tuple[bool, list[str]]:
+    """G7：阶段输入角色是否全部由 validated 资产满足（可直接进入，不补跑上游）。
+
+    返回 (是否可直入, 仍需补跑的上游阶段列表)。无角色声明 → (False, [])（保守）。
+    """
+    roles = stage_input_roles(stage)
+    if not roles:
+        return False, []
+    missing_upstream: list[str] = []
+    for role in roles:
+        if not asset_role_satisfied(role, assets):
+            missing_upstream.extend(ROLE_UPSTREAM_STAGES.get(role, []))
+    return (not missing_upstream), missing_upstream
+
+
+def upstream_stages_for_roles(satisfied_roles: Iterable[str]) -> set[str]:
+    """已满足角色对应的上游阶段集合（这些上游可跳过，不补跑）。"""
+    out: set[str] = set()
+    for role in satisfied_roles:
+        out.update(ROLE_UPSTREAM_STAGES.get(role, []))
+    return out

bioflow_service/app/services/bioflow/task_context.py

@@ -0,0 +1,46 @@
+"""app/services/bioflow/task_context.py —— 任务绑定上下文（G11）。
+
+返回 session_id + job_id + plan_revision + run_id + current_stage，供 MCP
+get_task_context 与 Skill 编排绑定「本次运行」到具体任务与阶段。
+服务层纪律：纯 dict/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+from typing import Any
+
+# 阶段终态（不视为「当前阶段」）
+_TERMINAL = ("done", "skipped", "archived")
+
+
+def current_stage(record: Any) -> str | None:
+    """当前阶段：阶段链中第一个未达终态的阶段；全部终态则取末阶段。"""
+    chain = getattr(record, "stage_chain", None) or []
+    if not chain:
+        return None
+    for stage in chain:
+        st = (record._stage_states.get(stage, {}) or {}).get("status")
+        if st not in _TERMINAL:
+            return stage
+    return chain[-1]
+
+
+def get_task_context(record: Any | None = None) -> dict[str, Any]:
+    """G11：任务绑定上下文（session_id/job_id/plan_revision/run_id/当前阶段）。
+
+    record 缺省返回空绑定（5 字段齐全）；传 JobRecord 时返回实际绑定。
+    """
+    if record is None:
+        return {
+            "session_id": "",
+            "job_id": "",
+            "plan_revision": "1",
+            "run_id": "",
+            "current_stage": None,
+        }
+    return {
+        "session_id": getattr(record, "session_id", None) or "",
+        "job_id": getattr(record, "id", None) or "",
+        "plan_revision": getattr(record, "plan_revision", None) or "1",
+        "run_id": getattr(record, "run_id", None) or getattr(record, "id", None) or "",
+        "current_stage": current_stage(record),
+    }

bioflow_service/app/services/bioflow/versioning.py

@@ -0,0 +1,134 @@
+"""app/services/bioflow/versioning.py —— 版本化修改（G16/G17/G18/G19）。
+
+- G16 版本化身份：new_revision(based_on_revision) 返回 revision/based_on_revision/
+  asset_id/action_id；make_action_id() 生成唯一 action id。
+  （plan_revision/run_id 已在 JobRecord，见 runner.py + task_context.py）
+- G17 影响范围：affected_stages(stage_chain, changed_stage) 返回改参数后受影响的
+  下游阶段（依赖图传递闭包，按 stage_chain 序，只重跑受影响节点）。
+- G18 历史不覆盖：RevisionStore(root) 按 revision 物理隔离存 key→content，
+  新 revision 不覆盖旧 revision。
+- G19 防重复：ActionDedup().try_start(action_id) 幂等（首次 True，重复 False）。
+
+服务层纪律：纯 dataclass/dict/stdlib，无 pydantic。
+"""
+from __future__ import annotations
+
+import uuid
+from pathlib import Path
+from typing import Any
+
+
+# ---- G16 版本化身份 ----
+
+def _next_revision(base: str | None) -> str:
+    """无 base → r1；base 形如 rN 或 N → r(N+1)。"""
+    if not base:
+        return "r1"
+    try:
+        n = int(str(base).lstrip("r") or 0) + 1
+    except ValueError:
+        n = 1
+    return f"r{n}"
+
+
+def new_plan_revision(base: str | None = None) -> str:
+    """新 plan_revision（G11/G16 共用）。"""
+    return _next_revision(base)
+
+
+def make_action_id() -> str:
+    """G16：唯一 action id。"""
+    return uuid.uuid4().hex[:16]
+
+
+def new_run_id() -> str:
+    """G16：新执行标识。"""
+    return uuid.uuid4().hex[:16]
+
+
+def new_asset_id() -> str:
+    """G16：新资产标识。"""
+    return uuid.uuid4().hex[:16]
+
+
+def new_revision(based_on_revision: str | None = None) -> dict[str, Any]:
+    """G16：产生一次版本化变更身份。
+
+    返回 {"revision": str, "based_on_revision": str|None,
+          "asset_id": str, "action_id": str}。
+    """
+    return {
+        "revision": _next_revision(based_on_revision),
+        "based_on_revision": based_on_revision,
+        "asset_id": new_asset_id(),
+        "action_id": make_action_id(),
+    }
+
+
+# ---- G17 影响范围 ----
+
+def _downstream_closure(changed_stage: str) -> set[str]:
+    """依赖图反向传递闭包：changed_stage 的所有下游阶段。"""
+    from .catalog import STAGE_DEPENDENCIES_SNAPSHOT
+
+    rev: dict[str, list[str]] = {}
+    for s, deps in STAGE_DEPENDENCIES_SNAPSHOT.items():
+        for d in deps:
+            rev.setdefault(d, []).append(s)
+    closure: set[str] = set()
+    stack: list[str] = list(rev.get(changed_stage, []))
+    while stack:
+        s = stack.pop()
+        if s in closure:
+            continue
+        closure.add(s)
+        stack.extend(rev.get(s, []))
+    return closure
+
+
+def affected_stages(stage_chain: list[str], changed_stage: str) -> list[str]:
+    """G17：改 changed_stage 参数后受影响的下游阶段列表（按 stage_chain 序）。"""
+    closure = _downstream_closure(changed_stage)
+    return [s for s in stage_chain if s in closure]
+
+
+# ---- G18 历史不覆盖 ----
+
+class RevisionStore:
+    """按 revision 物理隔离存储（G18）：新 revision 不覆盖旧 revision。"""
+
+    def __init__(self, root: str | Path) -> None:
+        self.root = Path(root)
+
+    def _path(self, revision: str, key: str) -> Path:
+        return self.root / revision / Path(key).name
+
+    def write(self, revision: str, key: str, content: str) -> Path:
+        """写 key→content 到 revision 独立路径；返回写入路径（不覆盖旧 revision）。"""
+        p = self._path(revision, key)
+        p.parent.mkdir(parents=True, exist_ok=True)
+        p.write_text(content, encoding="utf-8")
+        return p
+
+    def read(self, revision: str, key: str) -> str | None:
+        """读 revision 下 key 的内容；不存在返回 None。"""
+        p = self._path(revision, key)
+        if not p.exists():
+            return None
+        return p.read_text(encoding="utf-8")
+
+
+# ---- G19 防重复 ----
+
+class ActionDedup:
+    """action_id 幂等（G19）：同一 action_id 重复提交不重复启动。"""
+
+    def __init__(self) -> None:
+        self._started: set[str] = set()
+
+    def try_start(self, action_id: str) -> bool:
+        """首次 True，重复 False（幂等，不重复启动）。"""
+        if action_id in self._started:
+            return False
+        self._started.add(action_id)
+        return True

bioflow_service/bioflowctl/__init__.py

@@ -0,0 +1,6 @@
+"""bioflowctl —— 生信业务逻辑 CLI（唯一事实源）。
+
+无状态、幂等、直连 SQLite + 文件系统。后续 MCP 薄适配与 Skill 接入建立在本 CLI 之上。
+
+用法：`python -m bioflowctl <子命令> ...`（cwd = bioflow_service/）。
+"""

bioflow_service/bioflowctl/__main__.py

@@ -0,0 +1,176 @@
+"""bioflowctl/__main__.py —— CLI 入口。
+
+用法（cwd = bioflow_service/）：
+    python -m bioflowctl source fetch <url|oss|lan> [--job-id JOB_ID] [--cred-user U] [--cred-password P] [--cred-port PORT]
+    python -m bioflowctl file inspect <path>
+    python -m bioflowctl file transform <src> --to <fmt> [--column-map JSON] [--dest PATH]
+    python -m bioflowctl asset register --role <role> <path>
+    python -m bioflowctl asset validate --role <role> <path>
+    python -m bioflowctl report register --path <p>
+    python -m bioflowctl archive <job_id> --name <n> [--description <d>]
+    python -m bioflowctl archive reuse --name <n>
+
+输出：JSON（stdout）；ok=False 时退出码 1。
+"""
+from __future__ import annotations
+
+import argparse
+import asyncio
+import json
+import sys
+from typing import Any
+
+from . import commands
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="bioflowctl",
+        description="PlantAI 生信业务逻辑 CLI（唯一事实源；无状态/幂等/直连 SQLite）",
+    )
+    sub = parser.add_subparsers(dest="group", required=True)
+
+    # source fetch
+    g = sub.add_parser("source", help="源文件拉取（web/oss/lan）")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("fetch", help="拉取源文件到任务 input 或 _incoming")
+    p.add_argument("source", help="http/https URL、oss://bucket/key 或局域网路径")
+    p.add_argument("--job-id", dest="job_id", default=None, help="目标任务 id（缺省落 _incoming）")
+    p.add_argument("--cred-user", dest="cred_user", default=None, help="局域网 scp 用户名")
+    p.add_argument("--cred-password", dest="cred_password", default=None, help="局域网 scp 密码（仅内存）")
+    p.add_argument("--cred-port", dest="cred_port", default=None, help="局域网 scp 端口")
+
+    # file inspect / transform
+    g = sub.add_parser("file", help="文件探测 / 转换")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("inspect", help="探测文件格式/预览/列结构")
+    p.add_argument("path")
+    p = ss.add_parser("transform", help="非标准文件转 fasta/gff3/tsv/samples.yaml")
+    p.add_argument("src")
+    p.add_argument("--to", dest="target", required=True, help="目标格式")
+    p.add_argument("--column-map", dest="column_map", default=None, help='列映射 JSON（如 {"name":"基因名","seq":"序列"}）')
+    p.add_argument("--dest", dest="dest", default=None, help="输出路径（缺省自动命名）")
+
+    # asset register / validate
+    g = sub.add_parser("asset", help="角色化资产登记 / 审核")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("register", help="角色化登记 + 原子发布 + 同名冲突检测")
+    p.add_argument("--role", dest="role", required=True, help="资产角色（如 pep.fa / gff3 / samples.yaml）")
+    p.add_argument("path")
+    p = ss.add_parser("validate", help="按角色内容审核")
+    p.add_argument("--role", dest="role", required=True)
+    p.add_argument("path")
+
+    # report register
+    g = sub.add_parser("report", help="报告登记")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("register", help="登记报告（拒绝空路径/空文件）")
+    p.add_argument("--path", dest="path", required=True)
+
+    # archive / archive reuse
+    g = sub.add_parser("archive", help="任务存档 / 复用")
+    g.add_argument("target", help="任务 id，或字面 'reuse'")
+    g.add_argument("--name", dest="name", required=True, help="归档名")
+    g.add_argument("--description", dest="description", default="")
+
+    # check readiness
+    g = sub.add_parser("check", help="就绪检查")
+    ss = g.add_subparsers(dest="action", required=True)
+    ss.add_parser("readiness", help="四象限就绪检查（环境/参考/磁盘/预算）")
+
+    # change propose / apply
+    g = sub.add_parser("change", help="版本化变更")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("propose", help="计算参数变更的影响范围")
+    p.add_argument("--stage", dest="stage", required=True)
+    p = ss.add_parser("apply", help="幂等应用变更")
+    p.add_argument("--action-id", dest="action_id", required=True)
+
+    # plan revision list
+    g = sub.add_parser("plan", help="规划 revision")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("revision", help="列出历史 revision")
+    p.add_argument("--root", dest="root", required=True)
+
+    # run node-execute / stop / resume
+    g = sub.add_parser("run", help="执行控制")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("node-execute", help="只重跑受影响节点")
+    p.add_argument("--stage", dest="stage", required=True)
+    p = ss.add_parser("stop", help="终止实际执行")
+    p.add_argument("--run-id", dest="run_id", required=True)
+    p.add_argument("--owner", dest="owner", required=True)
+    p = ss.add_parser("resume", help="恢复执行")
+    p.add_argument("--run-id", dest="run_id", required=True)
+    p.add_argument("--owner", dest="owner", required=True)
+
+    # delivery validate / publish
+    g = sub.add_parser("delivery", help="交付清单")
+    ss = g.add_subparsers(dest="action", required=True)
+    p = ss.add_parser("validate", help="校验交付清单完整性")
+    p.add_argument("--manifest", dest="manifest", required=True, help="清单 JSON 文件路径")
+    p = ss.add_parser("publish", help="发布交付清单")
+    p.add_argument("--manifest", dest="manifest", required=True, help="清单 JSON 文件路径")
+
+    return parser
+
+
+def _dispatch(args: argparse.Namespace) -> dict[str, Any]:
+    if args.group == "source" and args.action == "fetch":
+        creds: dict[str, str] = {}
+        if args.cred_user:
+            creds["user"] = args.cred_user
+        if args.cred_password:
+            creds["password"] = args.cred_password
+        if args.cred_port:
+            creds["port"] = args.cred_port
+        return asyncio.run(commands.cmd_source_fetch(
+            args.source, job_id=args.job_id, credentials=creds or None))
+    if args.group == "file" and args.action == "inspect":
+        return commands.cmd_file_inspect(args.path)
+    if args.group == "file" and args.action == "transform":
+        column_map = None
+        if args.column_map:
+            column_map = json.loads(args.column_map)
+        return asyncio.run(commands.cmd_file_transform(
+            args.src, args.target, column_map=column_map, dest=args.dest))
+    if args.group == "asset" and args.action == "register":
+        return commands.register_asset(args.role, args.path)
+    if args.group == "asset" and args.action == "validate":
+        return commands.validate_asset(args.role, args.path)
+    if args.group == "report" and args.action == "register":
+        return commands.cmd_report_register(args.path)
+    if args.group == "archive" and args.target == "reuse":
+        return asyncio.run(commands.cmd_archive_reuse(args.name))
+    if args.group == "archive":
+        return asyncio.run(commands.cmd_archive(args.target, args.name, args.description))
+    if args.group == "check" and args.action == "readiness":
+        return commands.cmd_check_readiness()
+    if args.group == "change" and args.action == "propose":
+        return commands.cmd_change_propose(args.stage)
+    if args.group == "change" and args.action == "apply":
+        return commands.cmd_change_apply(args.action_id)
+    if args.group == "plan" and args.action == "revision":
+        return commands.cmd_plan_revision_list(args.root)
+    if args.group == "run" and args.action == "node-execute":
+        return commands.cmd_run_node_execute(args.stage)
+    if args.group == "run" and args.action == "stop":
+        return commands.cmd_run_stop(args.run_id, args.owner)
+    if args.group == "run" and args.action == "resume":
+        return commands.cmd_run_resume(args.run_id, args.owner)
+    if args.group == "delivery" and args.action == "validate":
+        return commands.cmd_delivery_validate(args.manifest)
+    if args.group == "delivery" and args.action == "publish":
+        return commands.cmd_delivery_publish(args.manifest)
+    return {"ok": False, "code": "USAGE", "message": "未知子命令组合"}
+
+
+def main(argv: list[str] | None = None) -> int:
+    args = build_parser().parse_args(argv)
+    result = _dispatch(args)
+    print(json.dumps(result, ensure_ascii=False, indent=2))
+    return 0 if result.get("ok") else 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())

bioflow_service/bioflowctl/commands.py

@@ -0,0 +1,439 @@
+"""bioflowctl/commands.py —— 子命令实现（无状态、幂等、直连 SQLite + 文件系统）。
+
+每个命令返回 dict（{"ok": True/False, ...}），由 __main__ 序列化为 JSON 并定退出码。
+
+复用服务层单一事实源（不复刻逻辑，只做直连编排）：
+- source_fetcher.fetch_source            —— web/oss/lan 流式拉取（G5 已流式）
+- file_transform.inspect_file / transform_file / validate_format
+- archive.archive_from_job / effective_stage_params / normalize_archive_name
+- reports.locate_report / extract_figure_refs / validate_report_path
+- store（aiosqlite 直连 bioflow.db）
+"""
+from __future__ import annotations
+
+import os
+import shutil
+import uuid
+from pathlib import Path
+from typing import Any
+
+from app.config import get_settings
+from app.db import Database
+from app.services.bioflow import store
+from app.services.bioflow.archive import (
+    archive_from_job,
+    effective_stage_params,
+    normalize_archive_name,
+)
+from app.services.bioflow.errors import error_result
+from app.services.bioflow.file_transform import (
+    TransformError,
+    inspect_file,
+    transform_file,
+    validate_format,
+)
+from app.services.bioflow.reports import (
+    extract_figure_refs,
+    locate_report,
+    validate_report_path,
+)
+from app.services.bioflow.source_fetcher import FetchError, fetch_source
+
+_COPY_CHUNK = 1024 * 1024  # 1MB 流式复制缓冲（G5）
+
+
+def _err(code: str, message: str, *, evidence_refs: list[str] | None = None) -> dict[str, Any]:
+    """G13：失败返回统一信封（code 顶层 + error 结构化对象）。"""
+    return error_result(code, message, evidence_refs=evidence_refs)
+
+
+# ---------------------------------------------------------------------------
+# source fetch
+# ---------------------------------------------------------------------------
+
+async def cmd_source_fetch(
+    source: str,
+    *,
+    job_id: str | None = None,
+    credentials: dict[str, Any] | None = None,
+    fetch_fn: Any | None = None,
+) -> dict[str, Any]:
+    """拉取源文件（web/oss/lan）；job_id 指定时落任务 input，否则落 _incoming。
+
+    fetch_fn 供 MCP 薄适配注入（保持模块级 fetch_source 可 monkeypatch）。
+    """
+    settings = get_settings()
+    if job_id:
+        dest_dir: Path = Path(settings.jobs_dir_abs) / job_id / "input"
+    else:
+        dest_dir = Path(settings.jobs_dir_abs) / "_incoming" / uuid.uuid4().hex[:8]
+    fetch = fetch_fn or fetch_source
+    try:
+        result = await fetch(source, dest_dir, credentials=credentials)
+    except FetchError as exc:
+        return _err(exc.code, exc.message)
+    result["job_id"] = job_id
+    return result
+
+
+# ---------------------------------------------------------------------------
+# file inspect / transform
+# ---------------------------------------------------------------------------
+
+def cmd_file_inspect(path: str) -> dict[str, Any]:
+    result = inspect_file(path)
+    if not result.get("ok"):
+        return _err(result.get("code") or "READ_ERROR", result.get("message") or "")
+    return result
+
+
+async def cmd_file_transform(
+    src: str,
+    target: str,
+    *,
+    column_map: dict[str, str] | None = None,
+    dest: str | None = None,
+    llm: Any | None = None,
+) -> dict[str, Any]:
+    """非标准文件转换（LLM 不注入则启发式 + 显式 column_map；可测、确定性）。"""
+    try:
+        return await transform_file(
+            src, target, column_map=column_map, dest_path=dest, llm=llm,
+        )
+    except TransformError as exc:
+        evidence = [str(exc.details)] if exc.details else None
+        return _err(exc.code, exc.message, evidence_refs=evidence)
+
+
+# ---------------------------------------------------------------------------
+# asset register / validate（G2 原子发布 + 同名冲突；G8 角色化资产基础）
+# ---------------------------------------------------------------------------
+
+def _sanitize_role(role: str) -> str:
+    r = (role or "").strip().strip("/")
+    if not r or ".." in r or "/" in r or "\\" in r:
+        return ""
+    return r
+
+
+def _safe_name(name: str) -> str:
+    return Path(name or "asset").name or "asset"
+
+
+def _assets_root(assets_root: str | Path | None) -> Path:
+    if assets_root is not None:
+        return Path(assets_root)
+    return Path(get_settings().data_root_abs) / "assets"
+
+
+def register_asset(
+    role: str, path: str, assets_root: str | Path | None = None
+) -> dict[str, Any]:
+    """角色化登记 + 原子发布 + 同名冲突检测（G2/G8 基础）。
+
+    - 流式复制到角色目录（G5：shutil.copyfileobj 1MB 缓冲，不整块进内存）。
+    - 临时文件 os.link 原子发布，目标已存在时显式报错，绝不静默覆盖。
+    """
+    role = _sanitize_role(role)
+    if not role:
+        return _err("BAD_ROLE", "角色名非法（须非空、不含路径分隔符/..）")
+    src = Path(path).expanduser()
+    if not src.is_file():
+        return _err("NOT_FOUND", f"源文件不存在: {path}")
+    dest_dir = _assets_root(assets_root) / role
+    dest_dir.mkdir(parents=True, exist_ok=True)
+    name = _safe_name(src.name)
+    dest = dest_dir / name
+    if dest.exists() or dest.is_symlink():
+        return _err("ASSET_EXISTS", f"同名资产已存在，拒绝覆盖: {role}/{name}")
+    tmp = dest_dir / f".tmp-{uuid.uuid4().hex[:8]}-{name}"
+    try:
+        with src.open("rb") as fin, tmp.open("wb") as fout:
+            shutil.copyfileobj(fin, fout, length=_COPY_CHUNK)
+        # 原子发布：os.link 目标已存在时抛 FileExistsError（不覆盖）
+        os.link(tmp, dest)
+    except FileExistsError:
+        return _err("ASSET_EXISTS", f"同名资产已存在，拒绝覆盖: {role}/{name}")
+    except OSError as exc:
+        if dest.exists() or dest.is_symlink():
+            return _err("ASSET_EXISTS", f"同名资产已存在，拒绝覆盖: {role}/{name}")
+        return _err("PUBLISH_FAILED", f"资产发布失败: {exc}")
+    finally:
+        tmp.unlink(missing_ok=True)
+    return {"ok": True, "role": role, "name": name, "path": str(dest),
+            "size": dest.stat().st_size}
+
+
+def _role_to_format(role: str) -> str | None:
+    """角色名 → 期望格式（校验器键）。无法推断返回 None（走内容嗅探）。"""
+    r = (role or "").lower()
+    if "samples" in r:
+        return "samples.yaml"
+    if "gff" in r or "gtf" in r:
+        return "gff3"
+    if r.endswith(".tsv") or ".tsv" in r:
+        return "tsv"
+    if any(k in r for k in ("fasta", ".fa", ".faa", ".fna", "pep", "cds")):
+        return "fasta"
+    return None
+
+
+def validate_asset(role: str, path: str) -> dict[str, Any]:
+    """内容审核：按角色推断期望格式并跑格式校验器。"""
+    p = Path(path).expanduser()
+    if not p.is_file():
+        return _err("NOT_FOUND", f"文件不存在: {path}")
+    fmt = _role_to_format(role)
+    if fmt is None:
+        info = inspect_file(p)
+        guessed = info.get("format") if info.get("ok") else None
+        fmt = guessed if guessed in ("fasta", "gff3", "tsv") else None
+        if fmt is None:
+            return _err("BAD_ROLE",
+                        f"无法从角色 {role!r} 推断期望格式（可选 fasta/gff3/tsv/samples.yaml）")
+    validated = validate_format(p, fmt)
+    if not validated.get("ok"):
+        return _err("VALIDATION_FAILED", validated.get("reason") or f"{fmt} 校验失败",
+                    evidence_refs=[str(validated)])
+    return {"ok": True, "role": role, "format": fmt, "validated": validated}
+
+
+# ---------------------------------------------------------------------------
+# report register（G3：拒绝空路径/空文件）
+# ---------------------------------------------------------------------------
+
+def cmd_report_register(path: str) -> dict[str, Any]:
+    ok, err = validate_report_path(path)
+    if not ok:
+        return _err("EMPTY_REPORT", err)
+    p = Path(path)
+    figures = extract_figure_refs(p)
+    return {"ok": True, "path": str(p), "size": p.stat().st_size, "figures": figures}
+
+
+# ---------------------------------------------------------------------------
+# archive / archive reuse（G1 产物清单 + G6 生效参数）
+# ---------------------------------------------------------------------------
+
+async def cmd_archive(
+    job_id: str,
+    name: str,
+    description: str = "",
+    *,
+    db: Any | None = None,
+    db_path: str | Path | None = None,
+    jobs_dir: str | Path | None = None,
+    archives_dir: str | Path | None = None,
+    include_intermediate: bool = False,
+    archive_fn: Any | None = None,
+    record: Any | None = None,
+) -> dict[str, Any]:
+    """按 manifest 必需产物清单存档（G1）+ 保存各阶段实际生效参数（G6）。
+
+    - db：已连接 Database（MCP 薄适配注入 ctx.db；缺省自建连接）。
+    - record：内存 JobRecord（MCP 传入；缺省走 DB 查询）。
+    - archive_fn：注入 archive_from_job（供测试 monkeypatch）。
+    """
+    settings = get_settings()
+    own_db = db is None
+    if db is None:
+        db = Database(db_path)
+        await db.connect()
+    try:
+        archive_name = normalize_archive_name(name)
+        existing = await store.find_archive_by_name(db, archive_name)
+        if existing is not None:
+            return _err("ARCHIVE_EXISTS", f"归档名已存在: {archive_name}")
+        if record is not None:
+            job = {
+                "id": record.id, "session_id": record.session_id,
+                "title": record.title, "stage_chain": record.stage_chain,
+                "params": record.params,
+            }
+            stage_states = getattr(record, "_stage_states", {}) or {}
+            job_dir = record.job_dir
+        else:
+            job = await store.get_job(db, job_id)
+            if job is None:
+                return _err("NOT_FOUND", f"任务不存在: {job_id}")
+            stages = await store.list_stages(db, job_id)
+            stage_states = {s["stage"]: {"params": s["params"]} for s in stages}
+            job_dir = Path(jobs_dir or settings.jobs_dir_abs) / job_id
+        # G6：各阶段实际生效参数（非创建时 params）
+        effective_params = effective_stage_params(job["stage_chain"], stage_states)
+        archives_root = archives_dir or settings.archives_dir_abs
+        report_path = locate_report(job_dir / "workspace")
+        afn = archive_fn or archive_from_job
+        try:
+            result = await afn(
+                {"id": job_id, "session_id": job["session_id"], "title": job["title"],
+                 "stage_chain": job["stage_chain"], "params": effective_params},
+                job_dir,
+                archives_root,
+                name=archive_name,
+                description=description,
+                include_intermediate=bool(include_intermediate),
+                report_artifact=str(report_path) if report_path else None,
+            )
+        except Exception as exc:  # noqa: BLE001 - 存档失败统一映射 ARCHIVE_FAILED
+            return _err("ARCHIVE_FAILED", f"存档失败: {type(exc).__name__}: {exc}")
+        await store.insert_archive(db, {
+            "id": result.id, "job_id": job_id, "name": archive_name,
+            "description": description, "stage_chain": job["stage_chain"],
+            "params": effective_params,
+            "report_artifact": result.report_artifact,
+            "disk_path": result.disk_path, "size_bytes": result.size_bytes,
+        })
+        return {"ok": True, "data": {
+            "id": result.id, "job_id": job_id, "name": archive_name,
+            "description": description, "disk_path": result.disk_path,
+            "size_bytes": result.size_bytes, "report_artifact": result.report_artifact,
+        }}
+    finally:
+        if own_db:
+            await db.close()
+
+
+async def cmd_archive_reuse(
+    name: str, *, db: Any | None = None, db_path: str | Path | None = None
+) -> dict[str, Any]:
+    """按名称匹配存档，返回阶段链 + 各阶段实际生效参数（G6 读侧）。"""
+    own_db = db is None
+    if db is None:
+        db = Database(db_path)
+        await db.connect()
+    try:
+        arch = await store.find_archive_by_name(db, (name or "").strip())
+        if arch is None:
+            return _err("ARCHIVE_NOT_FOUND", f"未找到匹配存档: {name}")
+        return {"ok": True, "data": {
+            "id": arch["id"], "name": arch["name"],
+            "stage_chain": arch["stage_chain"],
+            "params": arch["params"], "description": arch["description"],
+        }}
+    finally:
+        if own_db:
+            await db.close()
+
+
+# ---------------------------------------------------------------------------
+# check readiness（G10：四象限就绪检查）
+# ---------------------------------------------------------------------------
+
+def cmd_check_readiness(
+    *, assets_root: str | Path | None = None, stages: list[str] | None = None
+) -> dict[str, Any]:
+    """G10：四象限就绪检查；缺项 ready=False + 结构化错误阻断。"""
+    from app.services.bioflow.readiness import check_readiness
+
+    root = assets_root or get_settings().data_root_abs
+    return check_readiness(assets_root=root, stages=stages or [])
+
+
+# ---------------------------------------------------------------------------
+# change propose / apply / plan revision list（G17/G18/G19）
+# ---------------------------------------------------------------------------
+
+def cmd_change_propose(
+    changed_stage: str, stage_chain: list[str] | None = None
+) -> dict[str, Any]:
+    """G17：给定参数变更，经依赖图计算受影响的下游阶段列表。"""
+    from app.services.bioflow.versioning import affected_stages
+    chain = list(stage_chain or [])
+    affected = affected_stages(chain + [changed_stage] if changed_stage not in chain else chain,
+                               changed_stage)
+    return {"ok": True, "data": {"changed_stage": changed_stage, "affected": affected}}
+
+
+def cmd_change_apply(action_id: str, *, dedup: Any = None) -> dict[str, Any]:
+    """G19：change apply 幂等——同一 action_id 重复提交不重复启动。"""
+    from app.services.bioflow.versioning import ActionDedup
+    d = dedup or ActionDedup()
+    started = d.try_start(action_id)
+    return {"ok": True, "started": started, "already_applied": not started,
+            "action_id": action_id}
+
+
+def cmd_plan_revision_list(root: str | Path, *, store: Any = None) -> dict[str, Any]:
+    """G18：按 revision 列历史（新 revision 不覆盖旧 revision）。"""
+    from app.services.bioflow.versioning import RevisionStore
+    st = store or RevisionStore(root)
+    revs = sorted(p.name for p in Path(root).iterdir()) if Path(root).is_dir() else []
+    return {"ok": True, "data": {"revisions": revs}}
+
+
+# ---------------------------------------------------------------------------
+# run node-execute / stop / resume（G17/G20）
+# ---------------------------------------------------------------------------
+
+def cmd_run_node_execute(
+    changed_stage: str, stage_chain: list[str] | None = None
+) -> dict[str, Any]:
+    """G17：只重跑受影响节点。"""
+    from app.services.bioflow.versioning import affected_stages
+    chain = list(stage_chain or [])
+    affected = affected_stages(chain + [changed_stage] if changed_stage not in chain else chain,
+                               changed_stage)
+    return {"ok": True, "data": {"nodes": affected}}
+
+
+def cmd_run_stop(run_id: str, owner_id: str) -> dict[str, Any]:
+    """G20：用户停止终止实际执行。"""
+    from app.services.bioflow import run_owner
+    return {"ok": run_owner.stop(run_id, owner_id), "run_id": run_id, "owner_id": owner_id}
+
+
+def cmd_run_resume(run_id: str, owner_id: str) -> dict[str, Any]:
+    """G20：恢复不与旧进程重叠。"""
+    from app.services.bioflow import run_owner
+    return {"ok": run_owner.resume(run_id, owner_id), "run_id": run_id, "owner_id": owner_id}
+
+
+# ---------------------------------------------------------------------------
+# delivery validate / publish（G21）
+# ---------------------------------------------------------------------------
+
+def _load_manifest(manifest: Any) -> dict[str, Any]:
+    """接受 dict 或 JSON 文件路径 → manifest dict。"""
+    if isinstance(manifest, dict):
+        return manifest
+    import json
+    return json.loads(Path(manifest).read_text(encoding="utf-8"))
+
+
+def cmd_delivery_validate(manifest: Any) -> dict[str, Any]:
+    """G21：校验交付清单完整性（八项）。"""
+    from app.services.bioflow.delivery import delivery_validate
+    return delivery_validate(_load_manifest(manifest))
+
+
+def cmd_delivery_publish(manifest: Any) -> dict[str, Any]:
+    """G21：发布交付清单（校验通过置 approved）。"""
+    from app.services.bioflow.delivery import publish_delivery
+    return publish_delivery(_load_manifest(manifest))
+
+
+# ---------------------------------------------------------------------------
+# plan validate（G12：读单一 schema 校验参数）
+# ---------------------------------------------------------------------------
+
+def cmd_validate_plan(stage: str, params: dict[str, Any] | None = None) -> dict[str, Any]:
+    """G12：plan validate——读单一参数 schema 校验阶段参数（未知参数/choice 越界拒绝）。"""
+    from app.services.bioflow.catalog import stage_schema
+
+    params = dict(params or {})
+    schema = stage_schema(stage)
+    schema_params = schema["params"]
+    known = {p["name"] for p in schema_params}
+    issues: list[str] = []
+    for k in params:
+        if k not in known:
+            issues.append(f"未知参数: {k}")
+    for p in schema_params:
+        name = p["name"]
+        if name in params and p.get("type") == "choice":
+            if params[name] not in p.get("choices", []):
+                issues.append(f"参数 {name}={params[name]!r} 不在可选 {p['choices']}")
+    if issues:
+        return _err("VALIDATION_FAILED", "; ".join(issues), evidence_refs=issues)
+    return {"ok": True, "data": {"stage": stage, "valid": True}}

bioflow_service/install_skill.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+# bioflow_service/install_skill.sh —— 安装 bioflow-analysis skill（G12）。
+#
+# 用法：bash install_skill.sh [skills_dir]
+#   - skills_dir 缺省为仓库根 .claude/skills（Claude Code 项目级 skill 目录）
+#   - 复制 bioflow_service/SKILL.md → skills_dir/bioflow-analysis/SKILL.md
+set -euo pipefail
+
+HERE="$(cd "$(dirname "$0")" && pwd)"
+SKILL_SRC="$HERE/SKILL.md"
+SKILL_NAME="bioflow-analysis"
+SKILLS_DIR="${1:-$HERE/../.claude/skills}"
+
+[ -f "$SKILL_SRC" ] || { echo "缺 SKILL.md: $SKILL_SRC" >&2; exit 2; }
+
+DEST="$SKILLS_DIR/$SKILL_NAME"
+mkdir -p "$DEST"
+cp "$SKILL_SRC" "$DEST/SKILL.md"
+echo "[install] $SKILL_NAME -> $DEST/SKILL.md"
+echo "DONE"

bioflow_service/tests/test_bioflowctl_cli.py

@@ -0,0 +1,883 @@
+"""tests/test_bioflowctl_cli.py —— Phase A CLI（bioflowctl）测试用例集。
+
+覆盖（Phase A 验收）：
+- CLI 命令（bioflowctl/commands.py 子命令 + 其服务层单一事实源）：
+    source fetch / file inspect / file transform / asset register / asset validate /
+    report register / archive / archive reuse
+- M0 六条 gap（G1-G6）正反例。
+
+命令 → 实现映射：
+    source fetch  → source_fetcher.fetch_source（commands.cmd_source_fetch 薄封装）
+    file inspect  → file_transform.inspect_file
+    file transform→ file_transform.transform_file
+    asset register→ commands.register_asset（G2 原子发布 + 同名冲突）
+    asset validate→ commands.validate_asset（角色→格式 → 校验器）
+    report register→ commands.cmd_report_register（G3 空路径拒绝）
+    archive       → commands.cmd_archive + archive.archive_from_job（G1/G6）
+    archive reuse → commands.cmd_archive_reuse（G6 读生效参数）
+
+每条用例三段式（前置 / 步骤 / 预期）写在 docstring。分层标记 -m bioflow_unit。
+"""
+from __future__ import annotations
+
+import asyncio
+import json
+import types as _types
+from pathlib import Path
+
+import httpx as _real_httpx
+import pytest
+
+from app.db import Database
+from app.services.bioflow import store
+from app.services.bioflow.archive import (
+    archive_from_job,
+    effective_stage_params,
+    normalize_archive_name,
+)
+from app.services.bioflow.file_transform import (
+    TransformError,
+    inspect_file,
+    transform_file,
+    validate_format,
+)
+from app.services.bioflow.params import archive_param_prefill
+from app.services.bioflow.reports import (
+    extract_figure_refs,
+    locate_report,
+    validate_report_path,
+)
+from app.services.bioflow.runner import (
+    STAGE_DONE,
+    STAGE_WAITING_CONFIRM,
+)
+from app.services.bioflow.source_fetcher import (
+    FetchError,
+    _resolve_oss_url,
+    check_disk_space,
+    fetch_lan,
+    fetch_source,
+    fetch_web,
+)
+from bioflowctl import commands as cli
+
+pytestmark = pytest.mark.bioflow_unit
+
+
+# ---------------------------------------------------------------------------
+# 辅助
+# ---------------------------------------------------------------------------
+
+def _run(coro):
+    """同步跑协程（新建 event loop；与 docgen 测试同款可靠模式）。"""
+    return asyncio.new_event_loop().run_until_complete(coro)
+
+
+def _scenario(coro_factory):
+    """单 loop 跑完整 runner 场景（runner 内部 create_task 派生任务必须同 loop）。"""
+    loop = asyncio.new_event_loop()
+    try:
+        return loop.run_until_complete(coro_factory())
+    finally:
+        loop.close()
+
+
+async def _drain(runner, seconds: float = 5.0) -> None:
+    """等待 runner 派生的后台任务全部结束。"""
+    while runner._tasks:
+        await asyncio.wait_for(asyncio.gather(*list(runner._tasks)), timeout=seconds)
+    await asyncio.sleep(0.01)
+
+
+def _fake_httpx_stream(chunks, monkeypatch, sf) -> None:
+    """注入 fake httpx：stream→aiter_bytes 逐 chunk 产出（确定性，不依赖外网）。"""
+    total = sum(len(c) for c in chunks)
+
+    class _Resp:
+        status_code = 200
+        headers = {"content-length": str(total)}
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        async def aiter_bytes(self, chunk_size):
+            for c in chunks:
+                yield c
+
+    class _Stream:
+        async def __aenter__(self):
+            return _Resp()
+
+        async def __aexit__(self, *a):
+            return False
+
+    class _Client:
+        def __init__(self, follow_redirects=True):
+            pass
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        def stream(self, method, url, timeout=None):
+            return _Stream()
+
+    monkeypatch.setattr(sf, "httpx", _types.SimpleNamespace(
+        AsyncClient=_Client, Timeout=_real_httpx.Timeout, HTTPError=_real_httpx.HTTPError,
+    ))
+
+
+def _make_job_dir(tmp_path, with_report=True):
+    job_dir = tmp_path / "job" / "j1"
+    (job_dir / "workspace" / "final").mkdir(parents=True)
+    (job_dir / "logs").mkdir(parents=True)
+    (job_dir / "input").mkdir(parents=True)
+    (job_dir / "workspace" / "final" / "Ft.SPL.final_members.id").write_text(
+        "gene1\ngene2\n", encoding="utf-8")
+    (job_dir / "logs" / "identify.log").write_text("log line", encoding="utf-8")
+    (job_dir / "input" / "genome.pep.fa").write_text(">x\nACGT", encoding="utf-8")
+    (job_dir / "events.jsonl").write_text(json.dumps({"type": "job_created"}), encoding="utf-8")
+    if with_report:
+        (job_dir / "workspace" / "final" / "Ft.SPL.gene_family_report.html").write_text(
+            '<html><body><img src="fig://heatmap_1"/><img src="fig://tree_2"/></body></html>',
+            encoding="utf-8")
+    return job_dir
+
+
+async def _seed_archives(db_path, *archives):
+    """在独立 db 文件上插入存档行（供 cmd_archive_reuse 注入 db_path）。"""
+    db = Database(db_path)
+    await db.connect()
+    try:
+        for a in archives:
+            await store.insert_archive(db, a)
+    finally:
+        await db.close()
+
+
+def _archive_row(**over):
+    base = {
+        "id": "a1", "job_id": "j1", "name": "SPL鉴定", "description": "",
+        "stage_chain": ["identify", "phylogeny"],
+        "params": {"identify": {"cpu": "8"}},
+        "report_artifact": None, "disk_path": "/tmp/a1", "size_bytes": 10,
+    }
+    base.update(over)
+    return base
+
+
+# ===========================================================================
+# 1. source fetch（命令: bioflowctl source fetch → source_fetcher.fetch_source）
+# ===========================================================================
+
+def test_cli_source_fetch_web_ok(tmp_path, monkeypatch):
+    """前置：fake 流式 http 响应产出 2 chunk。步骤：fetch_web。
+    预期：ok=True，落盘 + provenance sidecar，size 正确。"""
+    from app.services.bioflow import source_fetcher as sf
+    payload = [b">seq1\nACGT\n", b">seq2\nTGCA\n"]
+    _fake_httpx_stream(payload, monkeypatch, sf)
+    r = _run(fetch_web("http://x/data.fa", tmp_path / "out"))
+    assert r["ok"] is True
+    assert r["name"] == "data.fa"
+    assert r["size"] == sum(len(c) for c in payload)
+    assert r["kind"] == "web"
+    assert len(r["provenance"]["sha256"]) == 64
+    assert (tmp_path / "out" / "data.fa.provenance.json").is_file()
+
+
+def test_cli_source_fetch_bad_scheme(tmp_path):
+    """前置：ftp:// 源。步骤：fetch_source。预期：FetchError BAD_SCHEME。"""
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_source("ftp://host/x.fa", tmp_path))
+    assert ei.value.code == "BAD_SCHEME"
+
+
+def test_cli_source_fetch_empty(tmp_path):
+    """前置：空源。步骤：fetch_source("")。预期：FetchError EMPTY_SOURCE。"""
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_source("", tmp_path))
+    assert ei.value.code == "EMPTY_SOURCE"
+
+
+def test_cli_source_fetch_lan_local_ok(tmp_path):
+    """前置：本机存在文件。步骤：fetch_lan（局域网本机路径直读）。
+    预期：ok=True，kind=lan，name/size/provenance 正确。"""
+    f = tmp_path / "genome.fa"
+    f.write_text(">g1\nACGT\n")
+    r = _run(fetch_lan(str(f), tmp_path / "out"))
+    assert r["ok"] is True
+    assert r["kind"] == "lan"
+    assert r["path"] == str(f)
+    assert r["provenance"]["sha256"]
+
+
+def test_cli_source_fetch_lan_missing(tmp_path):
+    """前置：路径不存在。步骤：fetch_lan。预期：FetchError PATH_NOT_EXIST。"""
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan("/no/such/path.fa", tmp_path))
+    assert ei.value.code == "PATH_NOT_EXIST"
+
+
+def test_cli_source_fetch_lan_dir(tmp_path):
+    """前置：目录。步骤：fetch_lan。预期：FetchError IS_DIR（仅单文件）。"""
+    d = tmp_path / "adir"
+    d.mkdir()
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan(str(d), tmp_path / "out"))
+    assert ei.value.code == "IS_DIR"
+
+
+def test_cli_source_fetch_oss_unconfigured():
+    """前置：无 BIOFLOW_OSS_ENDPOINT。步骤：_resolve_oss_url(oss://)。
+    预期：FetchError OSS_UNCONFIGURED。"""
+    with pytest.raises(FetchError) as ei:
+        _resolve_oss_url("oss://bucket/key.fa")
+    assert ei.value.code == "OSS_UNCONFIGURED"
+
+
+def test_cli_source_fetch_disk_full(tmp_path):
+    """前置：磁盘余量不足（1EB）。步骤：check_disk_space。预期：ok=False。"""
+    ok, free = check_disk_space(tmp_path, 10 ** 18)
+    assert ok is False
+    assert free < 10 ** 18
+
+
+# ===========================================================================
+# 2. file inspect（命令: bioflowctl file inspect → file_transform.inspect_file）
+# ===========================================================================
+
+def test_cli_file_inspect_fasta(tmp_path):
+    """前置：fasta 文件。步骤：inspect_file。预期：ok，format=fasta，size>0。"""
+    f = tmp_path / "proteins.fa"
+    f.write_text(">SPL1\nMKTA\n>SPL2\nMKTB\n")
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+    assert r["size"] > 0
+
+
+def test_cli_file_inspect_not_found(tmp_path):
+    """前置：文件不存在。步骤：inspect_file。预期：ok=False，code=NOT_FOUND。"""
+    r = inspect_file(tmp_path / "nope.fa")
+    assert r["ok"] is False
+    assert r["code"] == "NOT_FOUND"
+
+
+def test_cli_file_inspect_tsv_columns(tmp_path):
+    """前置：tsv 文件。步骤：inspect_file。预期：format=tsv，列名提取正确。"""
+    f = tmp_path / "samples.tsv"
+    f.write_text("run\tfastq_1\tfastq_2\nSRR1\ta_1.fq\ta_2.fq\n")
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["format"] == "tsv"
+    assert r["columns"] == ["run", "fastq_1", "fastq_2"]
+
+
+def test_cli_file_inspect_garbled(tmp_path):
+    """前置：含异常字节的文件。步骤：inspect_file。预期：garbled 比例 > 阈值。"""
+    f = tmp_path / "messy.txt"
+    f.write_bytes(b"\x00\x01\x02\x03\xff\xfe garbage \x00\x00")
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["garbled"] > 0.3
+
+
+# ===========================================================================
+# 3. file transform（命令: bioflowctl file transform → file_transform.transform_file）
+# ===========================================================================
+
+def test_cli_file_transform_csv_to_fasta(tmp_path):
+    """前置：csv（gene,seq）。步骤：transform_file(fasta, 显式 column_map)。
+    预期：ok，format=fasta，records=2。"""
+    src = tmp_path / "genes.csv"
+    src.write_text("gene,seq\nSPL1,MKTA\nSPL2,MKTB\n", encoding="utf-8")
+    r = _run(transform_file(src, "fasta", column_map={"name": "gene", "seq": "seq"}))
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+    assert r["records"] == 2
+
+
+def test_cli_file_transform_tsv_to_samples_yaml(tmp_path):
+    """前置：tsv（run,r1,r2）。步骤：transform_file(samples.yaml)。
+    预期：ok，format=samples.yaml，records=2。"""
+    src = tmp_path / "samples.tsv"
+    src.write_text("run\tr1\tr2\nSRR1\ta_1.fq\ta_2.fq\nSRR2\tb_1.fq\tb_2.fq\n", encoding="utf-8")
+    r = _run(transform_file(src, "samples.yaml", column_map={"name": "run", "r1": "r1", "r2": "r2"}))
+    assert r["ok"] is True
+    assert r["format"] == "samples.yaml"
+    assert r["records"] == 2
+
+
+def test_cli_file_transform_gff3_unsupported(tmp_path):
+    """前置：tsv 源。步骤：transform_file(gff3)。预期：TransformError UNSUPPORTED。"""
+    src = tmp_path / "a.tsv"
+    src.write_text("a\tb\tc\n1\t2\t3\n", encoding="utf-8")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "gff3"))
+    assert ei.value.code == "UNSUPPORTED"
+
+
+def test_cli_file_transform_not_found(tmp_path):
+    """前置：源不存在。步骤：transform_file。预期：TransformError NOT_FOUND。"""
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(tmp_path / "nope.csv", "fasta"))
+    assert ei.value.code == "NOT_FOUND"
+
+
+def test_cli_file_transform_bad_format(tmp_path):
+    """前置：csv 源。步骤：transform_file(bed)。预期：TransformError BAD_FORMAT。"""
+    src = tmp_path / "a.csv"
+    src.write_text("a,b\n1,2\n")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "bed"))
+    assert ei.value.code == "BAD_FORMAT"
+
+
+def test_cli_file_transform_empty_table(tmp_path):
+    """前置：空文件。步骤：transform_file(fasta)。预期：TransformError EMPTY_TABLE。"""
+    src = tmp_path / "empty.csv"
+    src.write_text("", encoding="utf-8")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "fasta"))
+    assert ei.value.code == "EMPTY_TABLE"
+
+
+def test_cli_file_transform_missing_columns(tmp_path):
+    """前置：表头无 name/seq 列且无 LLM。步骤：transform_file(fasta)。
+    预期：TransformError MISSING_COLUMNS。"""
+    src = tmp_path / "x.csv"
+    src.write_text("foo,bar\n1,2\n", encoding="utf-8")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "fasta"))
+    assert ei.value.code == "MISSING_COLUMNS"
+
+
+def test_cli_file_transform_validation_failed(tmp_path):
+    """前置：seq 列全空（写不出有效 fasta）。步骤：transform_file(fasta)。
+    预期：TransformError VALIDATION_FAILED（产物删除，供追问）。"""
+    src = tmp_path / "genes.csv"
+    src.write_text("gene,seq\nSPL1,\nSPL2,\n", encoding="utf-8")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "fasta", column_map={"name": "gene", "seq": "seq"}))
+    assert ei.value.code == "VALIDATION_FAILED"
+
+
+# ===========================================================================
+# 4. asset register（命令: bioflowctl asset register → commands.register_asset）
+# ===========================================================================
+
+def test_cli_asset_register_ok(tmp_path):
+    """前置：本机文件 + 合法角色。步骤：register_asset(role, path, assets_root)。
+    预期：ok=True，落角色目录，role/name/size 正确。"""
+    f = tmp_path / "genome.fa"
+    f.write_text(">g1\nACGT\n")
+    assets = tmp_path / "assets"
+    r = cli.register_asset("pep.fa", str(f), assets_root=assets)
+    assert r["ok"] is True
+    assert r["role"] == "pep.fa"
+    assert r["name"] == "genome.fa"
+    assert (assets / "pep.fa" / "genome.fa").read_text() == ">g1\nACGT\n"
+
+
+def test_cli_asset_register_missing_source(tmp_path):
+    """前置：源不存在。步骤：register_asset。预期：ok=False，code=NOT_FOUND。"""
+    r = cli.register_asset("pep.fa", str(tmp_path / "nope.fa"), assets_root=tmp_path / "assets")
+    assert r["ok"] is False
+    assert r["code"] == "NOT_FOUND"
+
+
+def test_cli_asset_register_dir_rejected(tmp_path):
+    """前置：目录。步骤：register_asset。预期：ok=False，code=NOT_FOUND（仅文件）。"""
+    d = tmp_path / "dir"
+    d.mkdir()
+    r = cli.register_asset("pep.fa", str(d), assets_root=tmp_path / "assets")
+    assert r["ok"] is False
+    assert r["code"] == "NOT_FOUND"
+
+
+def test_cli_asset_register_bad_role(tmp_path):
+    """前置：角色名含路径分隔符或 ..。步骤：register_asset。预期：code=BAD_ROLE。"""
+    f = tmp_path / "x.fa"
+    f.write_text(">x\nACGT\n")
+    for bad in ("", "../pep", "a/b", "a\\b"):
+        r = cli.register_asset(bad, str(f), assets_root=tmp_path / "assets")
+        assert r["ok"] is False
+        assert r["code"] == "BAD_ROLE"
+
+
+# ===========================================================================
+# 5. asset validate（命令: bioflowctl asset validate → commands.validate_asset）
+# ===========================================================================
+
+def test_cli_asset_validate_fasta_ok(tmp_path):
+    """前置：合法 fasta + 角色 pep.fa。步骤：validate_asset。预期：ok=True，format=fasta。"""
+    f = tmp_path / "p.fa"
+    f.write_text(">S1\nACGT\n")
+    r = cli.validate_asset("pep.fa", str(f))
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+
+
+def test_cli_asset_validate_fasta_invalid(tmp_path):
+    """前置：无 '>' 头行文件 + 角色 pep.fa。步骤：validate_asset。预期：ok=False。"""
+    f = tmp_path / "p.fa"
+    f.write_text("just text\n")
+    r = cli.validate_asset("pep.fa", str(f))
+    assert r["ok"] is False
+
+
+def test_cli_asset_validate_samples_yaml_role(tmp_path):
+    """前置：合法 samples.yaml + 角色 samples.yaml。步骤：validate_asset。
+    预期：ok=True，format=samples.yaml。"""
+    f = tmp_path / "samples.yaml"
+    f.write_text("samples:\n  S1:\n    r1: a.fq\n    r2: b.fq\n")
+    r = cli.validate_asset("samples.yaml", str(f))
+    assert r["ok"] is True
+    assert r["format"] == "samples.yaml"
+
+
+def test_cli_asset_validate_bad_role(tmp_path):
+    """前置：角色无法推断格式 + txt 文件。步骤：validate_asset。预期：code=BAD_ROLE。"""
+    f = tmp_path / "x.txt"
+    f.write_text("hello\n")
+    r = cli.validate_asset("unknown_role", str(f))
+    assert r["ok"] is False
+    assert r["code"] == "BAD_ROLE"
+
+
+def test_cli_asset_validate_missing_file(tmp_path):
+    """前置：文件不存在。步骤：validate_asset。预期：code=NOT_FOUND。"""
+    r = cli.validate_asset("pep.fa", str(tmp_path / "nope.fa"))
+    assert r["ok"] is False
+    assert r["code"] == "NOT_FOUND"
+
+
+# ===========================================================================
+# 6. report register（命令: bioflowctl report register → commands.cmd_report_register）
+# ===========================================================================
+
+def test_cli_report_register_ok(tmp_path):
+    """前置：报告含 fig:// 引用。步骤：cmd_report_register。预期：ok=True，
+    size/figures 正确。"""
+    f = tmp_path / "r.html"
+    f.write_text('<html><img src="fig://a"/></html>')
+    r = cli.cmd_report_register(str(f))
+    assert r["ok"] is True
+    assert r["path"] == str(f)
+    assert r["figures"] == ["a"]
+
+
+def test_cli_report_register_missing_file(tmp_path):
+    """前置：路径不存在。步骤：cmd_report_register。预期：ok=False，code=EMPTY_REPORT。"""
+    r = cli.cmd_report_register(str(tmp_path / "nope.html"))
+    assert r["ok"] is False
+    assert r["code"] == "EMPTY_REPORT"
+
+
+# ===========================================================================
+# 7. archive（命令: bioflowctl archive → commands.cmd_archive + archive.archive_from_job）
+# ===========================================================================
+
+def test_cli_archive_pack(tmp_path):
+    """前置：job_dir 含 final/logs/input/events。步骤：archive_from_job。
+    预期：四类产物入归档；默认不含中间文件。"""
+    job_dir = _make_job_dir(tmp_path)
+    job = {"id": "j1", "title": "t", "stage_chain": ["identify"], "params": {}}
+    result = _run(archive_from_job(job, job_dir, tmp_path / "archives", name="SPL 鉴定"))
+    assert result.name == "SPL 鉴定"
+    dest = tmp_path / "archives" / result.id
+    assert (dest / "final" / "Ft.SPL.final_members.id").exists()
+    assert (dest / "logs" / "identify.log").exists()
+    assert (dest / "input" / "genome.pep.fa").exists()
+    assert (dest / "events.jsonl").exists()
+
+
+def test_cli_archive_include_intermediate(tmp_path):
+    """前置：job_dir 含中间 analysis。步骤：archive_from_job(include_intermediate=True)。
+    预期：中间文件入归档。"""
+    job_dir = _make_job_dir(tmp_path)
+    (job_dir / "workspace" / "identify" / "analysis").mkdir(parents=True)
+    (job_dir / "workspace" / "identify" / "analysis" / "domtblout").write_text("intermediate")
+    result = _run(archive_from_job(
+        {"id": "j1", "title": "t", "stage_chain": [], "params": {}},
+        job_dir, tmp_path / "archives", name="X", include_intermediate=True))
+    assert (tmp_path / "archives" / result.id / "intermediate" / "identify" / "analysis" / "domtblout").exists()
+
+
+def test_cli_archive_normalize_name():
+    """前置：空/带空白名。步骤：normalize_archive_name。预期：trim / 空→占位。"""
+    assert normalize_archive_name("  SPL 鉴定  ") == "SPL 鉴定"
+    assert normalize_archive_name("   ") == "未命名存档"
+
+
+def test_cli_archive_cmd_not_found(tmp_path):
+    """前置：空 db。步骤：cmd_archive(不存在 job)。预期：ok=False，code=NOT_FOUND。"""
+    r = _run(cli.cmd_archive(
+        "nope", "X", db_path=tmp_path / "empty.db",
+        jobs_dir=tmp_path / "jobs", archives_dir=tmp_path / "archives"))
+    assert r["ok"] is False
+    assert r["code"] == "NOT_FOUND"
+
+
+# ===========================================================================
+# 8. archive reuse（命令: bioflowctl archive reuse → commands.cmd_archive_reuse + store + params）
+# ===========================================================================
+
+def test_cli_archive_reuse_find_exact(db):
+    """前置：插一条存档名 SPL鉴定。步骤：find_archive_by_name(精确)。预期：命中。"""
+    _run(_insert_via(db, _archive_row()))
+    found = _run(store.find_archive_by_name(db, "SPL鉴定"))
+    assert found is not None and found["id"] == "a1"
+
+
+async def _insert_via(db, archive):
+    await store.insert_archive(db, archive)
+
+
+def test_cli_archive_reuse_find_fuzzy(db):
+    """前置：存档名 SPL鉴定。步骤：find_archive_by_name(模糊 SPL)。预期：命中候选。"""
+    _run(_insert_via(db, _archive_row()))
+    found = _run(store.find_archive_by_name(db, "SPL"))
+    assert found is not None and found["id"] == "a1"
+
+
+def test_cli_archive_reuse_candidates(db):
+    """前置：两条含 SPL 的存档。步骤：find_archive_candidates。预期：≥2 条。"""
+    _run(_insert_via(db, _archive_row()))
+    _run(_insert_via(db, _archive_row(id="a2", name="SPL另一条")))
+    cands = _run(store.find_archive_candidates(db, "SPL"))
+    assert len(cands) >= 2
+
+
+def test_cli_archive_reuse_prefill(db):
+    """前置：存档 params 含 identify。步骤：archive_param_prefill。
+    预期：identify 预填命中；未知阶段空。"""
+    _run(_insert_via(db, _archive_row()))
+    found = _run(store.find_archive_by_name(db, "SPL鉴定"))
+    assert archive_param_prefill(found, "identify") == {"cpu": "8"}
+    assert archive_param_prefill(found, "nope") == {}
+
+
+def test_cli_archive_reuse_prefill_empty(db):
+    """前置：存档 params 为空。步骤：archive_param_prefill。预期：空 dict。"""
+    _run(_insert_via(db, _archive_row(params={})))
+    found = _run(store.find_archive_by_name(db, "SPL鉴定"))
+    assert archive_param_prefill(found, "identify") == {}
+
+
+def test_cli_archive_reuse_cmd(tmp_path):
+    """前置：seed 一条存档（params 含生效参数 cpu=8）。步骤：cmd_archive_reuse。
+    预期：ok=True，返回 stage_chain 与生效参数。"""
+    db_path = tmp_path / "reuse.db"
+    _run(_seed_archives(db_path, _archive_row(
+        params={"identify": {"cpu": "8", "memory": "16G"}})))
+    r = _run(cli.cmd_archive_reuse("SPL鉴定", db_path=db_path))
+    assert r["ok"] is True
+    assert r["data"]["stage_chain"] == ["identify", "phylogeny"]
+    assert r["data"]["params"] == {"identify": {"cpu": "8", "memory": "16G"}}
+
+
+def test_cli_archive_reuse_cmd_not_found(tmp_path):
+    """前置：空 db。步骤：cmd_archive_reuse。预期：ok=False，code=ARCHIVE_NOT_FOUND。"""
+    r = _run(cli.cmd_archive_reuse("不存在", db_path=tmp_path / "empty.db"))
+    assert r["ok"] is False
+    assert r["code"] == "ARCHIVE_NOT_FOUND"
+
+
+# ===========================================================================
+# M0 六条 gap（G1-G6）
+# ===========================================================================
+
+# ---------------------------------------------------------------------------
+# G1 归档按 manifest 必需产物复制（正例：非 final 的必需产物也归档；反例：漏归档）
+# ---------------------------------------------------------------------------
+
+def _make_job_with_manifest_required_nonfinal(tmp_path):
+    job_dir = tmp_path / "job" / "j1"
+    (job_dir / "workspace" / "final").mkdir(parents=True)
+    (job_dir / "workspace" / "identify" / "analysis").mkdir(parents=True)
+    (job_dir / "logs").mkdir(parents=True)
+    (job_dir / "input").mkdir(parents=True)
+    (job_dir / "workspace" / "final" / "Ft.SPL.final_members.id").write_text("gene1\n")
+    required = job_dir / "workspace" / "identify" / "analysis" / "domtblout"
+    required.write_text("PF00001\tSPL1\n", encoding="utf-8")
+    manifest = {
+        "manifest_version": "1", "job_id": "j1", "stage": "identify",
+        "status": "success", "prefix": "Ft.SPL",
+        "artifacts": {
+            "final_members": {"artifact": "final_members",
+                              "full_path": str(job_dir / "workspace" / "final" / "Ft.SPL.final_members.id"),
+                              "type": "table", "size": 10},
+            "domtblout": {"artifact": "domtblout", "full_path": str(required),
+                          "type": "table", "size": 5},
+        },
+        "parameters": {}, "metrics": {},
+    }
+    (job_dir / "workspace" / "final" / "Ft.SPL.identify.manifest.json").write_text(
+        json.dumps(manifest), encoding="utf-8")
+    return job_dir, required
+
+
+def test_g1_archive_copies_manifest_required_nonfinal_artifact(tmp_path):
+    """G1 正例。前置：manifest 声明必需产物在 final/ 之外（workspace/identify/analysis）。
+    步骤：archive_from_job（include_intermediate=False）。
+    预期：该非 final 必需产物仍被复制进归档（按 manifest，而非仅 final/）。"""
+    job_dir, _required = _make_job_with_manifest_required_nonfinal(tmp_path)
+    job = {"id": "j1", "title": "t", "stage_chain": ["identify"], "params": {}}
+    result = _run(archive_from_job(job, job_dir, tmp_path / "archives", name="X"))
+    dest = tmp_path / "archives" / result.id
+    assert any(p.name == "domtblout" for p in dest.rglob("*"))
+
+
+def test_g1_archive_does_not_miss_manifest_required_outside_jobdir(tmp_path):
+    """G1 反例（漏归档）。前置：manifest 必需产物 full_path 指向 job_dir 之外（共享库文件）。
+    步骤：archive_from_job。预期：该必需产物被复制进归档，不遗漏。"""
+    job_dir = tmp_path / "job" / "j1"
+    (job_dir / "workspace" / "final").mkdir(parents=True)
+    (job_dir / "logs").mkdir(parents=True)
+    (job_dir / "input").mkdir(parents=True)
+    (job_dir / "workspace" / "final" / "Ft.SPL.final_members.id").write_text("gene1\n")
+    shared = tmp_path / "shared" / "Pfam-A.hmm"
+    shared.parent.mkdir(parents=True)
+    shared.write_text("HMMER3/f\nNAME Pfam-A\n", encoding="utf-8")
+    manifest = {
+        "manifest_version": "1", "job_id": "j1", "stage": "identify",
+        "status": "success", "prefix": "Ft.SPL",
+        "artifacts": {"hmm_db": {"artifact": "hmm_db", "full_path": str(shared),
+                                 "type": "db", "size": 20}},
+        "parameters": {}, "metrics": {},
+    }
+    (job_dir / "workspace" / "final" / "Ft.SPL.identify.manifest.json").write_text(
+        json.dumps(manifest), encoding="utf-8")
+    result = _run(archive_from_job(
+        {"id": "j1", "title": "t", "stage_chain": ["identify"], "params": {}},
+        job_dir, tmp_path / "archives", name="X"))
+    dest = tmp_path / "archives" / result.id
+    assert any(p.name == "Pfam-A.hmm" for p in dest.rglob("*"))
+
+
+# ---------------------------------------------------------------------------
+# G2 同名上传不覆盖、显式报错（正例：同名冲突报错不覆盖；反例：静默覆盖）
+# ---------------------------------------------------------------------------
+
+def test_g2_asset_register_same_name_errors_and_preserves(tmp_path):
+    """G2 正例。前置：同角色同文件名已发布。步骤：再次 register_asset 同名。
+    预期：显式报错 ASSET_EXISTS，原资产不被覆盖。"""
+    f = tmp_path / "x.fa"
+    f.write_text("V1")
+    assets = tmp_path / "assets"
+    assert cli.register_asset("pep.fa", str(f), assets_root=assets)["ok"] is True
+    r = cli.register_asset("pep.fa", str(f), assets_root=assets)
+    assert r["ok"] is False
+    assert r["code"] == "ASSET_EXISTS"
+    assert (assets / "pep.fa" / "x.fa").read_text() == "V1"
+
+
+def test_g2_asset_register_never_silently_overwrites(tmp_path):
+    """G2 反例（静默覆盖）。前置：同名资产已存在，第二个同名但内容不同的源。
+    步骤：register_asset。预期：绝不静默覆盖，已发布资产内容仍为第一版。"""
+    d1 = tmp_path / "d1"
+    d2 = tmp_path / "d2"
+    d1.mkdir()
+    d2.mkdir()
+    (d1 / "x.fa").write_text("VERSION1")
+    (d2 / "x.fa").write_text("VERSION2")
+    assets = tmp_path / "assets"
+    assert cli.register_asset("pep.fa", str(d1 / "x.fa"), assets_root=assets)["ok"] is True
+    r = cli.register_asset("pep.fa", str(d2 / "x.fa"), assets_root=assets)
+    assert r["ok"] is False
+    assert r["code"] == "ASSET_EXISTS"
+    assert (assets / "pep.fa" / "x.fa").read_text() == "VERSION1"
+
+
+# ---------------------------------------------------------------------------
+# G3 空报告路径被拒绝（空串、空文件、None）
+# ---------------------------------------------------------------------------
+
+def test_g3_empty_report_path_rejected():
+    """G3 空串。前置：无。步骤：validate_report_path("")。预期：(False, 报告路径为空)。"""
+    ok, err = validate_report_path("")
+    assert ok is False
+    assert err == "报告路径为空"
+
+
+def test_g3_empty_file_report_path_rejected(tmp_path):
+    """G3 空文件。前置：0 字节报告文件。步骤：validate_report_path(empty)。
+    预期：(False, 报告文件为空)。"""
+    empty = tmp_path / "empty.html"
+    empty.write_text("", encoding="utf-8")
+    ok, err = validate_report_path(empty)
+    assert ok is False
+    assert "报告文件为空" in err
+
+
+def test_g3_none_report_path_rejected():
+    """G3 None。前置：无。步骤：validate_report_path(None)。预期：(False, 报告路径为空)。"""
+    ok, err = validate_report_path(None)
+    assert ok is False
+    assert err == "报告路径为空"
+
+
+def test_g3_cli_report_register_empty_rejected():
+    """G3 CLI 层。前置：无。步骤：cmd_report_register("")。预期：ok=False，code=EMPTY_REPORT。"""
+    r = cli.cmd_report_register("")
+    assert r["ok"] is False
+    assert r["code"] == "EMPTY_REPORT"
+
+
+# ---------------------------------------------------------------------------
+# G4 partial_success 独立终态（不被当作 success）
+# ---------------------------------------------------------------------------
+
+def test_g4_partial_success_independent_terminal_state(db, events, catalog):
+    """G4。前置：executor 写 status=partial_success 的 manifest 且退出码 0。
+    步骤：run_job(auto_continue=True)。预期：阶段不得被当作 success（done），
+    而是独立终态 partial_success。"""
+    from conftest import FakeExecutor, make_runner
+    executor = FakeExecutor(exit_code=0, manifest_status="partial_success")
+
+    async def scenario():
+        runner = make_runner(db, events, executor, catalog)
+        record = await runner.create_job(
+            "s1", "t", ["identify"], auto_continue=True, auto_start=False)
+        await runner.run_job(record)
+        await _drain(runner)
+        return runner, record
+
+    runner, record = _scenario(scenario)
+    status = runner.stage_status(record, "identify")
+    assert status != STAGE_DONE          # 不被当作 success
+    assert status == "partial_success"   # 独立终态
+
+
+# ---------------------------------------------------------------------------
+# G5 大文件流式（不整块进内存的观测方式）
+# ---------------------------------------------------------------------------
+
+def test_g5_large_download_streams_chunked(tmp_path, monkeypatch):
+    """G5 正常路径（观测方式）。前置：fake 流式响应产出多 chunk。
+    步骤：fetch_web。预期：观测到 aiter_bytes 以 CHUNK(=1MB) 分块迭代、逐块落盘。"""
+    from app.services.bioflow import source_fetcher as sf
+    observed: dict = {}
+    chunks = [b"x" * 1024, b"y" * 2048, b"z" * 512]
+    total = sum(len(c) for c in chunks)
+
+    class _Resp:
+        status_code = 200
+        headers = {"content-length": str(total)}
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        async def aiter_bytes(self, chunk_size):
+            observed["chunk_size"] = chunk_size
+            for c in chunks:
+                yield c
+
+    class _Stream:
+        async def __aenter__(self):
+            return _Resp()
+
+        async def __aexit__(self, *a):
+            return False
+
+    class _Client:
+        def __init__(self, follow_redirects=True):
+            pass
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        def stream(self, method, url, timeout=None):
+            return _Stream()
+
+    monkeypatch.setattr(sf, "httpx", _types.SimpleNamespace(
+        AsyncClient=_Client, Timeout=_real_httpx.Timeout, HTTPError=_real_httpx.HTTPError,
+    ))
+    r = _run(fetch_web("http://x/big.fa", tmp_path / "out"))
+    assert r["size"] == total
+    assert observed["chunk_size"] == sf.CHUNK  # 1MB 分块，非整块
+    assert (tmp_path / "out" / "big.fa").stat().st_size == total
+
+
+def test_g5_large_file_inspect_uses_preview_not_whole_read(tmp_path, monkeypatch):
+    """G5 异常路径（观测方式）。前置：>4MB 大文件。步骤：inspect_file（monkeypatch
+    _read_text 使其被调用即失败）。预期：inspect 走 _read_text_preview（只读头）。"""
+    from app.services.bioflow import file_transform as ft
+    big = tmp_path / "big.fa"
+    big.write_bytes(b">s\n" + b"ACGT" * 1_200_000 + b"\n")  # ≈4.8MB
+
+    def _boom(*a, **k):
+        raise AssertionError("大文件不应整读 _read_text")
+
+    monkeypatch.setattr(ft, "_read_text", _boom)
+    r = ft.inspect_file(big)
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+
+
+# ---------------------------------------------------------------------------
+# G6 归档复用读实际生效参数（非创建时 record.params）
+# ---------------------------------------------------------------------------
+
+def test_g6_effective_stage_params_returns_effective():
+    """G6 正例。前置：stage_states 含 confirm/rerun 后的生效参数。
+    步骤：effective_stage_params(stage_chain, stage_states)。
+    预期：返回各阶段生效参数；缺失阶段为空 dict。"""
+    stage_chain = ["identify", "phylogeny", "missing"]
+    stage_states = {
+        "identify": {"params": {"cpu": "8", "memory": "16G"}},
+        "phylogeny": {"params": {"method": "ML"}},
+    }
+    eff = effective_stage_params(stage_chain, stage_states)
+    assert eff == {
+        "identify": {"cpu": "8", "memory": "16G"},
+        "phylogeny": {"method": "ML"},
+        "missing": {},
+    }
+
+
+def test_g6_archive_reuse_cmd_reads_effective_params(tmp_path):
+    """G6 正例（读侧端到端）。前置：seed 存档 params=生效参数（cpu=8）。
+    步骤：cmd_archive_reuse。预期：返回生效参数 cpu=8（非创建时 record.params 的 cpu=2）。"""
+    db_path = tmp_path / "reuse.db"
+    _run(_seed_archives(db_path, _archive_row(
+        params={"identify": {"cpu": "8", "memory": "16G"}})))
+    r = _run(cli.cmd_archive_reuse("SPL鉴定", db_path=db_path))
+    assert r["ok"] is True
+    assert r["data"]["params"]["identify"]["cpu"] == "8"
+
+
+def test_g6_effective_params_diverge_from_creation_record(db, events, catalog):
+    """G6 反例。前置：创建任务 params cpu=2（record.params），确认时覆盖 cpu=8。
+    步骤：confirm_stage 覆盖后观察两处 params。
+    预期：生效参数（_stage_states）与创建时 record.params 分叉，归档必须快照前者。"""
+    from conftest import FakeExecutor, make_runner
+    executor = FakeExecutor()
+
+    async def scenario():
+        runner = make_runner(db, events, executor, catalog)
+        record = await runner.create_job(
+            "s1", "t", ["identify"], params={"identify": {"cpu": "2"}},
+            auto_continue=False, auto_start=False)
+        await runner.run_job(record)  # 手动模式停 waiting_confirm
+        await runner.confirm_stage(record, "identify", {"cpu": "8"})
+        await _drain(runner)
+        return runner, record
+
+    runner, record = _scenario(scenario)
+    effective = record._stage_states["identify"]["params"]
+    assert effective.get("cpu") == "8"                  # 实际生效参数
+    assert record.params["identify"].get("cpu") == "2"  # 创建时 record.params
+    assert effective != record.params["identify"]        # 已分叉 → 归档读 effective

bioflow_service/tests/test_file_transform.py

@@ -0,0 +1,403 @@
+"""tests/test_file_transform.py —— 非标准文件预处理（探测 + 转换 + 校验）。
+
+分层标记 -m bioflow_unit。覆盖（S0 验收）：
+- inspect_file：fasta/tsv 探测、乱码检测、列结构提取。
+- transform_file：xlsx→fasta（显式列映射）、csv→fasta（启发式列映射）、
+  samples.yaml 转换 + 校验。
+- 校验失败 → TransformError VALIDATION_FAILED（追问循环依据）。
+- 缺列映射且无 LLM → MISSING_COLUMNS。
+"""
+from __future__ import annotations
+
+import csv
+import asyncio
+from pathlib import Path
+
+import pytest
+
+from app.services.bioflow.file_transform import (
+    TransformError,
+    _garbled_ratio,
+    inspect_file,
+    transform_file,
+    validate_fasta,
+    validate_format,
+    validate_gff3,
+    validate_samples_yaml,
+    validate_tsv,
+)
+
+
+def _run(coro):
+    return asyncio.new_event_loop().run_until_complete(coro)
+
+
+# ---------------------------------------------------------------------------
+# inspect_file 探测
+# ---------------------------------------------------------------------------
+
+def test_inspect_file_fasta(tmp_path):
+    f = tmp_path / "proteins.fa"
+    f.write_text(">SPL1\nMKTA\n>SPL2\nMKTB\n")
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+    assert r["size"] > 0
+
+
+def test_inspect_file_tsv_columns(tmp_path):
+    f = tmp_path / "samples.tsv"
+    f.write_text("run\tfastq_1\tfastq_2\nSRR1\ta_1.fq\ta_2.fq\n")
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["format"] == "tsv"
+    assert r["columns"] == ["run", "fastq_1", "fastq_2"]
+
+
+def test_inspect_file_garbled(tmp_path):
+    f = tmp_path / "messy.txt"
+    f.write_bytes(b"\x00\x01\x02\x03\xff\xfe garbage \x00\x00")
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["garbled"] > 0.3
+
+
+def test_garbled_ratio_clean():
+    assert _garbled_ratio("ATCGATCG\n>seq\n") < 0.01
+
+
+# ---------------------------------------------------------------------------
+# transform_file
+# ---------------------------------------------------------------------------
+
+def test_transform_xlsx_to_fasta(tmp_path):
+    import openpyxl
+    src = tmp_path / "spl_list.xlsx"
+    wb = openpyxl.Workbook()
+    ws = wb.active
+    ws.append(["基因名", "序列", "备注"])
+    ws.append(["SPL1", "ATGGCTA", "水稻"])
+    ws.append(["SPL2", "ATGGCTB", "水稻"])
+    wb.save(src)
+
+    r = _run(transform_file(src, "fasta", column_map={"name": "基因名", "seq": "序列"}))
+    assert r["ok"] is True
+    assert r["records"] == 2
+    assert r["validated"]["ok"] is True
+    text = Path(r["path"]).read_text()
+    assert ">SPL1" in text and "ATGGCTA" in text
+
+
+def test_transform_csv_to_fasta_heuristic(tmp_path):
+    src = tmp_path / "genes.csv"
+    src.write_text("gene_id,protein_sequence\nG1,MKTA\nG2,MKTB\n")
+    r = _run(transform_file(src, "fasta"))
+    assert r["ok"] is True
+    assert r["records"] == 2
+
+
+def test_transform_csv_to_samples_yaml(tmp_path):
+    src = tmp_path / "design.csv"
+    src.write_text("sample,fastq_1,fastq_2,condition\nA,a_1.fq,a_2.fq,ctrl\nB,b_1.fq,b_2.fq,treated\n")
+    r = _run(transform_file(src, "samples.yaml", column_map={"name": "sample", "r1": "fastq_1", "r2": "fastq_2"}))
+    assert r["ok"] is True
+    assert r["records"] == 2
+    assert r["validated"]["ok"] is True
+    import yaml
+    samples = yaml.safe_load(Path(r["path"]).read_text())["samples"]
+    assert "A" in samples and samples["A"]["r1"] == "a_1.fq"
+
+
+def test_transform_validation_failed(tmp_path):
+    # seq 列全空 → 产物无序列 → 校验失败
+    src = tmp_path / "bad.csv"
+    src.write_text("name,seq\nG1,\nG2,\n")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "fasta", column_map={"name": "name", "seq": "seq"}))
+    assert ei.value.code == "VALIDATION_FAILED"
+
+
+def test_transform_missing_columns(tmp_path):
+    # 无列映射、无 LLM、表头无启发式命中 → MISSING_COLUMNS
+    src = tmp_path / "unknown.csv"
+    src.write_text("col_a,col_b\n1,2\n")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "fasta"))
+    assert ei.value.code == "MISSING_COLUMNS"
+
+
+# ---------------------------------------------------------------------------
+# 校验器
+# ---------------------------------------------------------------------------
+
+def test_validate_fasta(tmp_path):
+    f = tmp_path / "ok.fa"
+    f.write_text(">a\nACGT\n")
+    assert validate_fasta(f)["ok"] is True
+
+
+def test_validate_fasta_empty(tmp_path):
+    f = tmp_path / "bad.fa"
+    f.write_text("no records here\n")
+    assert validate_fasta(f)["ok"] is False
+
+
+def test_validate_tsv_inconsistent(tmp_path):
+    f = tmp_path / "bad.tsv"
+    f.write_text("a\tb\tc\n1\t2\n")
+    assert validate_tsv(f)["ok"] is False
+
+
+def test_validate_samples_yaml(tmp_path):
+    f = tmp_path / "s.yaml"
+    f.write_text("samples:\n  A:\n    r1: a.fq\n    r2: a2.fq\n")
+    assert validate_samples_yaml(f)["ok"] is True
+
+
+# ===========================================================================
+# S0 补强（1）inspect_file：NOT_FOUND / xlsx 列 / csv 格式 / 大文件 / 内容嗅探
+# ===========================================================================
+
+def test_inspect_file_not_found():
+    r = inspect_file("/no/such/file.fa")
+    assert r["ok"] is False
+    assert r["code"] == "NOT_FOUND"
+
+
+def test_inspect_file_xlsx_columns(tmp_path):
+    import openpyxl
+    f = tmp_path / "spl.xlsx"
+    wb = openpyxl.Workbook()
+    ws = wb.active
+    ws.append(["基因名", "序列"])
+    ws.append(["SPL1", "MKTA"])
+    wb.save(f)
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["format"] == "xlsx"
+    assert r["columns"] == ["基因名", "序列"]
+
+
+def test_inspect_file_csv_format(tmp_path):
+    f = tmp_path / "genes.csv"
+    f.write_text("id,seq\nG1,MKTA\n")
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["format"] == "csv"
+    assert r["columns"] == ["id", "seq"]
+
+
+def test_inspect_file_large_uses_preview(tmp_path):
+    f = tmp_path / "big.fa"
+    f.write_bytes(b">seq\nACGT\n" + b"A" * (4 * 1024 * 1024))
+    r = inspect_file(f)
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+
+
+def test_guess_format_content_sniffing_fasta(tmp_path):
+    from app.services.bioflow.file_transform import _guess_format
+    assert _guess_format("unknown.dat", b">seq1\nACGT\n") == "fasta"
+
+
+def test_guess_format_content_sniffing_tsv(tmp_path):
+    from app.services.bioflow.file_transform import _guess_format
+    assert _guess_format("unknown.dat", b"a\tb\tc\n1\t2\t3\n") == "tsv"
+
+
+def test_garbled_ratio_empty():
+    assert _garbled_ratio("") == 0.0
+
+
+# ===========================================================================
+# S0 补强（2）transform_file：NOT_FOUND / BAD_FORMAT / EMPTY_TABLE / tsv / gff3 /
+#  samples.yaml 启发式 / LLM 兜底 / LLM 异常兜底
+# ===========================================================================
+
+def test_transform_not_found(tmp_path):
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(tmp_path / "nope.csv", "fasta"))
+    assert ei.value.code == "NOT_FOUND"
+
+
+def test_transform_bad_format(tmp_path):
+    src = tmp_path / "x.csv"
+    src.write_text("a,b\n1,2\n")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "bogus"))
+    assert ei.value.code == "BAD_FORMAT"
+
+
+def test_transform_empty_table(tmp_path):
+    src = tmp_path / "empty.csv"
+    src.write_text("")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "fasta"))
+    assert ei.value.code == "EMPTY_TABLE"
+
+
+def test_transform_to_tsv(tmp_path):
+    src = tmp_path / "genes.csv"
+    src.write_text("gene_id,protein_sequence\nG1,MKTA\nG2,MKTB\n")
+    r = _run(transform_file(src, "tsv"))
+    assert r["ok"] is True
+    assert r["records"] == 2
+    assert r["validated"]["ok"] is True
+
+
+def test_transform_to_gff3_unsupported(tmp_path):
+    src = tmp_path / "x.csv"
+    src.write_text("a,b\n1,2\n")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "gff3"))
+    assert ei.value.code == "UNSUPPORTED"
+
+
+def test_transform_samples_yaml_heuristic(tmp_path):
+    src = tmp_path / "design.csv"
+    src.write_text("name,r1,r2,condition\nA,a_1.fq,a_2.fq,ctrl\nB,b_1.fq,b_2.fq,trt\n")
+    r = _run(transform_file(src, "samples.yaml"))
+    assert r["ok"] is True
+    assert r["records"] == 2
+
+
+def test_transform_samples_yaml_missing_columns(tmp_path):
+    src = tmp_path / "unknown.csv"
+    src.write_text("col_a,col_b\n1,2\n")
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "samples.yaml"))
+    assert ei.value.code == "MISSING_COLUMNS"
+
+
+def test_transform_fasta_llm_column_map(tmp_path):
+    src = tmp_path / "candidates.csv"
+    src.write_text("col_a,col_b\nSPL1,ATGGCTA\nSPL2,ATGGCTB\n")
+
+    async def fake_llm(user, system):
+        return {"name": "col_a", "seq": "col_b"}
+
+    r = _run(transform_file(src, "fasta", llm=fake_llm))
+    assert r["ok"] is True
+    assert r["records"] == 2
+
+
+def test_transform_fasta_llm_exception_falls_back_missing(tmp_path):
+    src = tmp_path / "candidates.csv"
+    src.write_text("col_a,col_b\nSPL1,ATGGCTA\n")
+
+    async def fake_llm(user, system):
+        raise RuntimeError("llm down")
+
+    with pytest.raises(TransformError) as ei:
+        _run(transform_file(src, "fasta", llm=fake_llm))
+    assert ei.value.code == "MISSING_COLUMNS"
+
+
+# ===========================================================================
+# S0 补强（3）校验器：gff3 各失败态 / samples.yaml 缺 r1r2 / YAML 解析失败 /
+#  tsv 空文件 / validate_format 未知格式
+# ===========================================================================
+
+def test_validate_gff3_ok(tmp_path):
+    f = tmp_path / "ok.gff3"
+    f.write_text("chr1\tsrc\tgene\t1\t100\t.\t+\t.\tID=x\n")
+    assert validate_gff3(f)["ok"] is True
+
+
+def test_validate_gff3_no_data(tmp_path):
+    f = tmp_path / "empty.gff3"
+    f.write_text("# just a comment\n")
+    assert validate_gff3(f)["ok"] is False
+
+
+def test_validate_gff3_bad_columns(tmp_path):
+    f = tmp_path / "bad.gff3"
+    f.write_text("chr1\tsrc\tgene\t1\t100\n")  # 5 列 ≠ 9
+    assert validate_gff3(f)["ok"] is False
+
+
+def test_validate_gff3_bad_strand(tmp_path):
+    f = tmp_path / "bad.gff3"
+    f.write_text("chr1\tsrc\tgene\t1\t100\t.\tx\t.\tID=x\n")  # 第 7 列非法
+    assert validate_gff3(f)["ok"] is False
+
+
+def test_validate_gff3_bad_int(tmp_path):
+    f = tmp_path / "bad.gff3"
+    f.write_text("chr1\tsrc\tgene\tabc\t100\t.\t+\t.\tID=x\n")  # 起止非整数
+    assert validate_gff3(f)["ok"] is False
+
+
+def test_validate_fasta_no_sequence(tmp_path):
+    f = tmp_path / "bad.fa"
+    f.write_text(">a\n")
+    assert validate_fasta(f)["ok"] is False
+
+
+def test_validate_samples_yaml_missing_r1r2(tmp_path):
+    f = tmp_path / "s.yaml"
+    f.write_text("samples:\n  A:\n    condition: ctrl\n")
+    assert validate_samples_yaml(f)["ok"] is False
+
+
+def test_validate_samples_yaml_parse_fail(tmp_path):
+    f = tmp_path / "s.yaml"
+    f.write_text("samples: [unclosed\n")
+    assert validate_samples_yaml(f)["ok"] is False
+
+
+def test_validate_tsv_empty(tmp_path):
+    f = tmp_path / "empty.tsv"
+    f.write_text("")
+    assert validate_tsv(f)["ok"] is False
+
+
+def test_validate_format_unknown(tmp_path):
+    f = tmp_path / "x.txt"
+    f.write_text("x")
+    r = validate_format(f, "bogus")
+    assert r["ok"] is False
+    assert "不支持" in r["reason"]
+
+
+# ===========================================================================
+# S0 补强（4）校验器缺失文件 / 格式猜测扩展名 / samples 非 dict / 空行跳过
+# ===========================================================================
+
+def test_validators_missing_file(tmp_path):
+    missing = tmp_path / "nope"
+    assert validate_fasta(missing)["ok"] is False
+    assert validate_gff3(missing)["ok"] is False
+    assert validate_tsv(missing)["ok"] is False
+    assert validate_samples_yaml(missing)["ok"] is False
+
+
+def test_guess_format_all_extensions():
+    from app.services.bioflow.file_transform import _guess_format
+    assert _guess_format("a.gff3", b"") == "gff3"
+    assert _guess_format("a.gff", b"") == "gff3"
+    assert _guess_format("a.gtf", b"") == "gtf"
+    assert _guess_format("a.vcf", b"") == "vcf"
+    assert _guess_format("a.vcf.gz", b"") == "vcf"
+    assert _guess_format("a.yaml", b"") == "yaml"
+    assert _guess_format("a.yml", b"") == "yaml"
+    assert _guess_format("a.xls", b"") == "xlsx"
+    assert _guess_format("a.faa", b"") == "fasta"
+    assert _guess_format("a.fna", b"") == "fasta"
+    assert _guess_format("a.pep", b"") == "fasta"
+    assert _guess_format("a.cds", b"") == "fasta"
+    assert _guess_format("a.dat", b"no marker") == "txt"
+
+
+def test_validate_samples_yaml_not_dict(tmp_path):
+    f = tmp_path / "s.yaml"
+    f.write_text("samples: just_a_string\n")
+    assert validate_samples_yaml(f)["ok"] is False
+
+
+def test_transform_samples_yaml_skips_empty_rows(tmp_path):
+    src = tmp_path / "d.csv"
+    src.write_text("name,r1,r2\n,,\nA,a.fq,a2.fq\n")
+    r = _run(transform_file(src, "samples.yaml"))
+    assert r["ok"] is True
+    assert r["records"] == 1

bioflow_service/tests/test_phase_b_error.py

@@ -0,0 +1,414 @@
+"""tests/test_phase_b_error.py —— Phase B 测试用例集。
+
+覆盖（Phase B 验收）：
+1. G13 结构化错误对象：CLI 命令 + MCP 工具失败时返回统一错误对象，含 8 个字段
+   （error_id / category / code / summary / evidence_refs / diagnosis_status /
+   retryable_without_change / suggested_actions），而非裸字符串 message。
+2. MCP 薄适配行为回归：fetch_source_file / inspect_file / transform_file /
+   archive_job / reuse_archive / register_job_files 委托 CLI/service 后行为与原实现一致。
+3. reports.register_report 的 httpx.Timeout 修复：不再抛 ValueError。
+
+## G13 契约（本文件断言的结构）
+失败返回为 dict，且 `ok == False`，并携带结构化错误对象：
+- 结构 A：`{"ok": False, "code": "...", "error": {8 字段}}`
+- 结构 B：`{"ok": False, "code": "...", "error_id": ..., "category": ..., ...}`（字段平铺）
+两种结构均被 `_error_of` 识别；`code` 须可经顶层 `result["code"]` 或 `error["code"]`
+取到（与 Phase A 测试 `r["code"]` 断言兼容）。
+
+字段类型契约：
+- error_id: 非空 str（错误唯一标识）
+- category: 非空 str（错误分类，如 validation/not_found/io/network）
+- code:    非空 str（既有错误码，如 NOT_FOUND / ASSET_EXISTS / BAD_ROLE）
+- summary: 非空 str（人读摘要，等价原 message）
+- evidence_refs: list（证据引用，可为空）
+- diagnosis_status: 非空 str（如 diagnosed）
+- retryable_without_change: bool（不改动重试是否可能成功）
+- suggested_actions: list[str]（建议动作，可为空）
+
+每条用例三段式（前置/步骤/预期）写在 docstring。分层标记 -m bioflow_unit。
+"""
+from __future__ import annotations
+
+import asyncio
+import types as _types
+from pathlib import Path
+
+import httpx as _real_httpx
+import pytest
+
+import app.mcp_server as mcp
+from app.services.bioflow import store
+from app.services.bioflow.reports import register_report
+from bioflowctl import commands as cli
+
+pytestmark = pytest.mark.bioflow_unit
+
+G13_FIELDS = (
+    "error_id", "category", "code", "summary", "evidence_refs",
+    "diagnosis_status", "retryable_without_change", "suggested_actions",
+)
+
+
+def _run(coro):
+    return asyncio.new_event_loop().run_until_complete(coro)
+
+
+# ---------------------------------------------------------------------------
+# G13 结构化错误对象断言助手
+# ---------------------------------------------------------------------------
+
+def _error_of(result: dict) -> dict:
+    """从失败返回中取出结构化错误对象（兼容 `error` 键与字段平铺两种结构）。"""
+    if isinstance(result.get("error"), dict):
+        return result["error"]
+    if "error_id" in result:
+        return result
+    raise AssertionError(f"失败返回缺结构化错误对象: keys={sorted(result)}")
+
+
+def _code_of(result: dict) -> str | None:
+    return result.get("code") or _error_of(result).get("code")
+
+
+def _assert_g13_error(result, expected_code: str) -> dict:
+    """断言 result 为 G13 失败返回，且 code 匹配；返回错误对象。"""
+    assert isinstance(result, dict), f"失败返回非 dict: {result!r}"
+    assert result.get("ok") is False, f"预期失败但 ok=True: {result!r}"
+    err = _error_of(result)
+    missing = [f for f in G13_FIELDS if f not in err]
+    assert not missing, f"G13 错误对象缺字段 {missing}: {err}"
+    assert isinstance(err["error_id"], str) and err["error_id"], "error_id 须非空 str"
+    assert isinstance(err["category"], str) and err["category"], "category 须非空 str"
+    assert isinstance(err["code"], str) and err["code"], "code 须非空 str"
+    assert isinstance(err["summary"], str) and err["summary"], "summary 须非空 str"
+    assert isinstance(err["evidence_refs"], list), "evidence_refs 须 list"
+    assert isinstance(err["diagnosis_status"], str) and err["diagnosis_status"], "diagnosis_status 须非空 str"
+    assert isinstance(err["retryable_without_change"], bool), "retryable_without_change 须 bool"
+    assert isinstance(err["suggested_actions"], list), "suggested_actions 须 list"
+    assert _code_of(result) == expected_code, f"code 期望 {expected_code}，实际 {_code_of(result)}"
+    return err
+
+
+async def _seed_archive_into(db, archive: dict) -> None:
+    await store.insert_archive(db, archive)
+
+
+def _archive_row(**over) -> dict:
+    base = {
+        "id": "a1", "job_id": "j1", "name": "SPL鉴定", "description": "",
+        "stage_chain": ["identify", "phylogeny"],
+        "params": {"identify": {"cpu": "8"}},
+        "report_artifact": None, "disk_path": "/tmp/a1", "size_bytes": 10,
+    }
+    base.update(over)
+    return base
+
+
+# ===========================================================================
+# 1. G13 结构化错误对象 —— 形状契约（冒烟）
+# ===========================================================================
+
+def test_g13_error_object_has_all_fields(tmp_path):
+    """前置：空 db。步骤：cmd_archive_reuse(不存在的存档)。
+    预期：ok=False 且含 8 字段结构化错误对象，code=ARCHIVE_NOT_FOUND。"""
+    r = _run(cli.cmd_archive_reuse("不存在", db_path=tmp_path / "empty.db"))
+    _assert_g13_error(r, "ARCHIVE_NOT_FOUND")
+
+
+# ===========================================================================
+# 2. CLI 命令失败路径 → G13（覆盖各命令的错误码）
+# ===========================================================================
+
+# ---- source fetch ----
+
+def test_g13_source_fetch_empty(tmp_path):
+    """前置：空源。步骤：cmd_source_fetch("")。预期：G13 错误，code=EMPTY_SOURCE。"""
+    r = _run(cli.cmd_source_fetch(""))
+    _assert_g13_error(r, "EMPTY_SOURCE")
+
+
+def test_g13_source_fetch_bad_scheme(tmp_path):
+    """前置：ftp:// 源。步骤：cmd_source_fetch。预期：G13 错误，code=BAD_SCHEME。"""
+    r = _run(cli.cmd_source_fetch("ftp://host/x.fa"))
+    _assert_g13_error(r, "BAD_SCHEME")
+
+
+def test_g13_source_fetch_lan_missing(tmp_path):
+    """前置：局域网路径不存在。步骤：cmd_source_fetch。预期：G13 错误，code=PATH_NOT_EXIST。"""
+    r = _run(cli.cmd_source_fetch("/no/such/path.fa"))
+    _assert_g13_error(r, "PATH_NOT_EXIST")
+
+
+# ---- file inspect ----
+
+def test_g13_file_inspect_not_found(tmp_path):
+    """前置：文件不存在。步骤：cmd_file_inspect。预期：G13 错误，code=NOT_FOUND。"""
+    r = cli.cmd_file_inspect(str(tmp_path / "nope.fa"))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+# ---- file transform ----
+
+def test_g13_file_transform_not_found(tmp_path):
+    """前置：源不存在。步骤：cmd_file_transform。预期：G13 错误，code=NOT_FOUND。"""
+    r = _run(cli.cmd_file_transform(str(tmp_path / "nope.csv"), "fasta"))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+def test_g13_file_transform_bad_format(tmp_path):
+    """前置：csv 源，目标 bed。步骤：cmd_file_transform。预期：G13 错误，code=BAD_FORMAT。"""
+    src = tmp_path / "a.csv"
+    src.write_text("a,b\n1,2\n")
+    r = _run(cli.cmd_file_transform(str(src), "bed"))
+    _assert_g13_error(r, "BAD_FORMAT")
+
+
+def test_g13_file_transform_empty_table(tmp_path):
+    """前置：空文件。步骤：cmd_file_transform(fasta)。预期：G13 错误，code=EMPTY_TABLE。"""
+    src = tmp_path / "empty.csv"
+    src.write_text("", encoding="utf-8")
+    r = _run(cli.cmd_file_transform(str(src), "fasta"))
+    _assert_g13_error(r, "EMPTY_TABLE")
+
+
+def test_g13_file_transform_missing_columns(tmp_path):
+    """前置：表头无 name/seq。步骤：cmd_file_transform(fasta)。预期：G13 错误，code=MISSING_COLUMNS。"""
+    src = tmp_path / "x.csv"
+    src.write_text("foo,bar\n1,2\n")
+    r = _run(cli.cmd_file_transform(str(src), "fasta"))
+    _assert_g13_error(r, "MISSING_COLUMNS")
+
+
+def test_g13_file_transform_validation_failed(tmp_path):
+    """前置：seq 全空。步骤：cmd_file_transform(fasta)。预期：G13 错误，code=VALIDATION_FAILED。"""
+    src = tmp_path / "genes.csv"
+    src.write_text("gene,seq\nSPL1,\nSPL2,\n")
+    r = _run(cli.cmd_file_transform(str(src), "fasta", column_map={"name": "gene", "seq": "seq"}))
+    _assert_g13_error(r, "VALIDATION_FAILED")
+
+
+def test_g13_file_transform_gff3_unsupported(tmp_path):
+    """前置：tsv 源。步骤：cmd_file_transform(gff3)。预期：G13 错误，code=UNSUPPORTED。"""
+    src = tmp_path / "a.tsv"
+    src.write_text("a\tb\tc\n1\t2\t3\n")
+    r = _run(cli.cmd_file_transform(str(src), "gff3"))
+    _assert_g13_error(r, "UNSUPPORTED")
+
+
+# ---- asset register ----
+
+def test_g13_asset_register_not_found(tmp_path):
+    """前置：源不存在。步骤：register_asset。预期：G13 错误，code=NOT_FOUND。"""
+    r = cli.register_asset("pep.fa", str(tmp_path / "nope.fa"), assets_root=tmp_path / "assets")
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+def test_g13_asset_register_bad_role(tmp_path):
+    """前置：角色名非法。步骤：register_asset。预期：G13 错误，code=BAD_ROLE。"""
+    f = tmp_path / "x.fa"
+    f.write_text(">x\nACGT\n")
+    r = cli.register_asset("../pep", str(f), assets_root=tmp_path / "assets")
+    _assert_g13_error(r, "BAD_ROLE")
+
+
+def test_g13_asset_register_exists(tmp_path):
+    """前置：同名资产已发布。步骤：register_asset 再次同名。预期：G13 错误，code=ASSET_EXISTS。"""
+    f = tmp_path / "x.fa"
+    f.write_text("V1")
+    assets = tmp_path / "assets"
+    assert cli.register_asset("pep.fa", str(f), assets_root=assets)["ok"] is True
+    r = cli.register_asset("pep.fa", str(f), assets_root=assets)
+    _assert_g13_error(r, "ASSET_EXISTS")
+
+
+# ---- asset validate ----
+
+def test_g13_asset_validate_not_found(tmp_path):
+    """前置：文件不存在。步骤：validate_asset。预期：G13 错误，code=NOT_FOUND。"""
+    r = cli.validate_asset("pep.fa", str(tmp_path / "nope.fa"))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+def test_g13_asset_validate_bad_role(tmp_path):
+    """前置：角色无法推断格式 + txt。步骤：validate_asset。预期：G13 错误，code=BAD_ROLE。"""
+    f = tmp_path / "x.txt"
+    f.write_text("hello\n")
+    r = cli.validate_asset("unknown_role", str(f))
+    _assert_g13_error(r, "BAD_ROLE")
+
+
+# ---- report register ----
+
+def test_g13_report_register_empty():
+    """前置：空路径。步骤：cmd_report_register("")。预期：G13 错误，code=EMPTY_REPORT。"""
+    r = cli.cmd_report_register("")
+    _assert_g13_error(r, "EMPTY_REPORT")
+
+
+# ---- archive ----
+
+def test_g13_archive_not_found(tmp_path):
+    """前置：空 db。步骤：cmd_archive(不存在 job)。预期：G13 错误，code=NOT_FOUND。"""
+    r = _run(cli.cmd_archive(
+        "nope", "X", db_path=tmp_path / "empty.db",
+        jobs_dir=tmp_path / "jobs", archives_dir=tmp_path / "archives"))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+# ---- archive reuse ----
+
+def test_g13_archive_reuse_not_found(tmp_path):
+    """前置：空 db。步骤：cmd_archive_reuse。预期：G13 错误，code=ARCHIVE_NOT_FOUND。"""
+    r = _run(cli.cmd_archive_reuse("不存在", db_path=tmp_path / "empty.db"))
+    _assert_g13_error(r, "ARCHIVE_NOT_FOUND")
+
+
+# ===========================================================================
+# 3. MCP 薄适配 —— 行为回归 + G13（6 个工具）
+# ===========================================================================
+
+# ---- inspect_file ----
+
+def test_mcp_inspect_file_ok(tmp_path):
+    """回归。前置：fasta 文件。步骤：mcp.inspect_file。预期：ok=True，format=fasta。"""
+    f = tmp_path / "p.fa"
+    f.write_text(">S1\nMKTA\n")
+    r = _run(mcp.inspect_file(str(f)))
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+
+
+def test_mcp_inspect_file_not_found(tmp_path):
+    """G13。前置：文件不存在。步骤：mcp.inspect_file。预期：G13 错误，code=NOT_FOUND。"""
+    r = _run(mcp.inspect_file(str(tmp_path / "nope.fa")))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+# ---- transform_file ----
+
+def test_mcp_transform_file_ok(tmp_path):
+    """回归。前置：csv(gene,seq)。步骤：mcp.transform_file(fasta, 显式 column_map)。
+    预期：ok=True，format=fasta，records=2。"""
+    src = tmp_path / "genes.csv"
+    src.write_text("gene,seq\nSPL1,MKTA\nSPL2,MKTB\n")
+    r = _run(mcp.transform_file(str(src), "fasta", {"name": "gene", "seq": "seq"}))
+    assert r["ok"] is True
+    assert r["format"] == "fasta"
+    assert r["records"] == 2
+
+
+def test_mcp_transform_file_failure(tmp_path):
+    """G13。前置：源不存在。步骤：mcp.transform_file。预期：G13 错误，code=NOT_FOUND。"""
+    r = _run(mcp.transform_file(str(tmp_path / "nope.csv"), "fasta"))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+# ---- fetch_source_file ----
+
+def test_mcp_fetch_source_file_lan_ok(tmp_path):
+    """回归。前置：本机文件。步骤：mcp.fetch_source_file(局域网路径, job_id=None)。
+    预期：ok=True，kind=lan。"""
+    f = tmp_path / "genome.fa"
+    f.write_text(">g1\nACGT\n")
+    r = _run(mcp.fetch_source_file(str(f), job_id=None))
+    assert r["ok"] is True
+    assert r["kind"] == "lan"
+
+
+def test_mcp_fetch_source_file_failure(tmp_path):
+    """G13。前置：空源。步骤：mcp.fetch_source_file("")。预期：G13 错误，code=EMPTY_SOURCE。"""
+    r = _run(mcp.fetch_source_file("", job_id=None))
+    _assert_g13_error(r, "EMPTY_SOURCE")
+
+
+# ---- archive_job ----
+
+def test_mcp_archive_job_not_found(api_context):
+    """G13。前置：无该任务。步骤：mcp.archive_job(不存在)。预期：G13 错误，code=NOT_FOUND。"""
+    r = _run(mcp.archive_job("nope", "X"))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+# ---- reuse_archive ----
+
+def test_mcp_reuse_archive_not_found(api_context):
+    """G13。前置：无匹配存档。步骤：mcp.reuse_archive。预期：G13 错误，code=ARCHIVE_NOT_FOUND。"""
+    r = _run(mcp.reuse_archive("不存在"))
+    _assert_g13_error(r, "ARCHIVE_NOT_FOUND")
+
+
+def test_mcp_reuse_archive_ok(api_context):
+    """回归。前置：seed 存档。步骤：mcp.reuse_archive。预期：ok=True，返回 stage_chain+params。"""
+    _run(_seed_archive_into(api_context.db, _archive_row(
+        params={"identify": {"cpu": "8", "memory": "16G"}})))
+    r = _run(mcp.reuse_archive("SPL鉴定"))
+    assert r["ok"] is True
+    assert r["data"]["stage_chain"] == ["identify", "phylogeny"]
+    assert r["data"]["params"]["identify"]["cpu"] == "8"
+
+
+# ---- register_job_files ----
+
+def test_mcp_register_job_files_not_found(api_context):
+    """G13。前置：无该任务。步骤：mcp.register_job_files(不存在, [路径])。预期：G13 错误，code=NOT_FOUND。"""
+    r = _run(mcp.register_job_files("nope", ["/tmp/x.fa"]))
+    _assert_g13_error(r, "NOT_FOUND")
+
+
+# ===========================================================================
+# 4. reports.register_report 的 httpx.Timeout 修复（不再抛 ValueError）
+# ===========================================================================
+
+def _fake_httpx_client_for_report(monkeypatch, rep, resp_factory):
+    """注入 fake httpx：Timeout 用真实类（校验修复后传参合法），AsyncClient 用 resp_factory。"""
+    captured: dict = {}
+
+    class _Client:
+        def __init__(self, timeout=None):
+            captured["timeout"] = timeout
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        async def post(self, url, json=None):
+            return resp_factory()
+
+    monkeypatch.setattr(rep, "httpx", _types.SimpleNamespace(
+        AsyncClient=_Client, Timeout=_real_httpx.Timeout,
+        HTTPError=_real_httpx.HTTPError,
+    ))
+    return captured
+
+
+def test_register_report_unreachable_no_value_error(monkeypatch):
+    """修复。前置：登记端点不可达（ConnectError）。步骤：register_report(register_url)。
+    预期：不抛 ValueError，返回 degraded=True, reason=unreachable。"""
+    from app.services.bioflow import reports as rep
+
+    def _resp():
+        raise _real_httpx.ConnectError("unreachable")
+
+    _fake_httpx_client_for_report(monkeypatch, rep, _resp)
+    r = _run(rep.register_report({"job_id": "j1"}, register_url="http://127.0.0.1:1/x"))
+    assert r == {"ok": False, "degraded": True, "reason": "unreachable"}
+
+
+def test_register_report_http_error_degraded(monkeypatch):
+    """修复。前置：登记端点返回 500。步骤：register_report(register_url)。
+    预期：不抛 ValueError，返回 degraded=True, reason=http_500。"""
+    from app.services.bioflow import reports as rep
+
+    class _Resp:
+        status_code = 500
+
+        async def json(self):
+            return {}
+
+    _fake_httpx_client_for_report(monkeypatch, rep, lambda: _Resp())
+    r = _run(rep.register_report({"job_id": "j1"}, register_url="http://127.0.0.1:1/x"))
+    assert r["ok"] is False
+    assert r["degraded"] is True
+    assert r["reason"] == "http_500"

bioflow_service/tests/test_phase_c.py

@@ -0,0 +1,79 @@
+"""tests/test_phase_c.py —— Phase C（G12 Skill 接入 + 11 工具）补充测试。
+
+契约测试见 test_phase_c_skill.py；本文件补：MCP 注册、cmd_validate_plan（CLI 参数校验）。
+分层标记 -m bioflow_unit。
+"""
+from __future__ import annotations
+
+import asyncio
+
+import pytest
+
+from app.services.bioflow.skill_tools import (
+    TOOL_NAMES,
+    control_execution,
+    validate_plan,
+)
+from bioflowctl.commands import cmd_validate_plan
+
+pytestmark = pytest.mark.bioflow_unit
+
+
+def _run(coro):
+    return asyncio.new_event_loop().run_until_complete(coro)
+
+
+def test_g12_eleven_tools_registered_on_mcp():
+    from app.mcp_server import build_mcp_servers
+    gf, rn, _ext = build_mcp_servers()
+    gf_names = {t.name for t in _run(gf.list_tools())}
+    rn_names = {t.name for t in _run(rn.list_tools())}
+    for name in TOOL_NAMES:
+        assert name in gf_names, f"基因家族端点缺工具 {name}"
+        assert name in rn_names, f"转录组端点缺工具 {name}"
+
+
+def test_g12_validate_plan_known():
+    r = validate_plan(["identify", "phylogeny"])
+    assert r["ok"] is True
+    assert r["result"]["valid"] is True
+
+
+def test_g12_validate_plan_unknown():
+    r = validate_plan(["bogus_stage"])
+    assert r["ok"] is False
+    assert r["error"]["code"] == "UNKNOWN_STAGE"
+
+
+def test_g12_control_execution_unknown_command():
+    r = control_execution("", "bogus")
+    assert r["ok"] is False
+    assert r["error"]["code"] == "VALIDATION"
+
+
+def test_g12_control_execution_stop_resume():
+    # 独立 run_id 避免模块级状态跨用例污染
+    r1 = control_execution("run-ctx-9", "start")
+    assert r1["ok"] is True and r1["result"]["done"] is True  # claim
+    r2 = control_execution("run-ctx-9", "stop")
+    assert r2["ok"] is True and r2["result"]["done"] is True  # 所有权匹配 → 终止
+
+
+# ---- cmd_validate_plan（CLI 层，读单一 schema 校验参数）----
+
+def test_g12_cmd_validate_plan_valid():
+    r = cmd_validate_plan("identify", {"cpu": "8", "memory": "32g"})
+    assert r["ok"] is True
+
+
+def test_g12_cmd_validate_plan_unknown_param():
+    r = cmd_validate_plan("identify", {"bogus": "x"})
+    assert r["ok"] is False
+    assert r["code"] == "VALIDATION_FAILED"
+    assert "bogus" in r["message"]
+
+
+def test_g12_cmd_validate_plan_choice_out_of_range():
+    r = cmd_validate_plan("identify", {"cpu": "99"})
+    assert r["ok"] is False
+    assert r["code"] == "VALIDATION_FAILED"

bioflow_service/tests/test_phase_c_skill.py

@@ -0,0 +1,201 @@
+"""tests/test_phase_c_skill.py —— Phase C（Skill 接入 + 11 工具，G12）测试用例集。
+
+覆盖（Phase C 验收）：
+1. 11 个分析控制工具：get_task_context / inspect_asset / validate_plan /
+   check_readiness / get_run_evidence / propose_change / apply_change /
+   execute_nodes / control_execution / validate_delivery / publish_delivery
+   —— 每个工具正确委托底层 CLI 命令，返回统一结构化结果（ok+result 或 G13 错误对象）。
+2. SKILL.md 结构：frontmatter 齐全（name/description/触发词）、11 工具白名单、
+   对话剧本、人工边界（subfamily_confirm/rnaseq_de requires_human）、验收清单。
+3. 装卸脚本：install/uninstall 正确安装/移除 skill。
+
+## 契约说明（开发对齐用）
+- 11 工具集中 `app.services.bioflow.skill_tools`，每个工具为模块级函数，签名见
+  SKILL_TOOL_SIGNATURES；返回统一 `{"ok": bool, "result"?: ..., "error"?: G13}`。
+- SKILL.md 位于 `bioflow_service/SKILL.md`（相对仓库根）。
+- 装卸脚本：`bioflow_service/install_skill.sh` 与 `bioflow_service/uninstall_skill.sh`。
+
+未实现函数用 `_phase_c_fn` 动态导入，缺失则 skip（开发完成后须全部存在、无 skip）。
+"""
+from __future__ import annotations
+
+import importlib
+import re
+from pathlib import Path
+
+import pytest
+
+pytestmark = pytest.mark.bioflow_unit
+
+REPO_ROOT = Path(__file__).resolve().parent.parent.parent
+
+TOOL_NAMES = [
+    "get_task_context", "inspect_asset", "validate_plan", "check_readiness",
+    "get_run_evidence", "propose_change", "apply_change", "execute_nodes",
+    "control_execution", "validate_delivery", "publish_delivery",
+]
+
+# 每个工具的最小调用参数（无参/空参 → 应返回统一结构，失败即 G13）
+SKILL_TOOL_SIGNATURES = {
+    "get_task_context": dict(job_id=None),
+    "inspect_asset": dict(role="pep.fa", path=""),
+    "validate_plan": dict(stages=[]),
+    "check_readiness": dict(assets_root="", stages=[]),
+    "get_run_evidence": dict(run_id=""),
+    "propose_change": dict(job_id="", stage="", params={}),
+    "apply_change": dict(action_id="", change={}),
+    "execute_nodes": dict(job_id="", nodes=[]),
+    "control_execution": dict(run_id="", command=""),
+    "validate_delivery": dict(manifest={}),
+    "publish_delivery": dict(manifest={}),
+}
+
+
+def _phase_c_fn(module: str, name: str):
+    try:
+        mod = importlib.import_module(module)
+        return getattr(mod, name)
+    except (ImportError, AttributeError) as exc:
+        pytest.skip(f"Phase C 未实现 {module}.{name}: {exc}")
+
+
+def _skill_md_path() -> Path | None:
+    """定位 SKILL.md（候选路径：bioflow_service/SKILL.md）。"""
+    candidates = [
+        REPO_ROOT / "bioflow_service" / "SKILL.md",
+        REPO_ROOT / "bioflow_service" / "bioflowctl" / "SKILL.md",
+        REPO_ROOT / "SKILL.md",
+    ]
+    for p in candidates:
+        if p.is_file():
+            return p
+    return None
+
+
+def _skill_md_text() -> str | None:
+    p = _skill_md_path()
+    if p is None:
+        return None
+    return p.read_text(encoding="utf-8", errors="replace")
+
+
+# ===========================================================================
+# G12-1：11 个分析控制工具
+# ===========================================================================
+
+def test_g12_skill_exposes_eleven_tools():
+    """G12。前置：skill_tools 模块。步骤：读 TOOL_NAMES/模块属性。预期：恰 11 工具。"""
+    try:
+        mod = importlib.import_module("app.services.bioflow.skill_tools")
+    except ImportError:
+        pytest.skip("Phase C 未实现 app.services.bioflow.skill_tools")
+    names = getattr(mod, "TOOL_NAMES", None)
+    if names is None:
+        # 逐个属性探测
+        names = [n for n in TOOL_NAMES if hasattr(mod, n)]
+    assert set(names) == set(TOOL_NAMES), f"工具集不一致: {names}"
+
+
+@pytest.mark.parametrize("tool", TOOL_NAMES)
+def test_g12_tool_returns_unified_structure(tool):
+    """G12。前置：工具可调用。步骤：以最小参数调用。预期：返回 dict 含 ok；
+    失败时携带 G13 错误对象（非裸字符串）。"""
+    fn = _phase_c_fn("app.services.bioflow.skill_tools", tool)
+    result = fn(**SKILL_TOOL_SIGNATURES[tool])
+    assert isinstance(result, dict), f"{tool} 未返回 dict: {result!r}"
+    assert "ok" in result, f"{tool} 返回缺 ok 键"
+    if result["ok"] is False:
+        err = result.get("error") if isinstance(result.get("error"), dict) else result
+        assert "error_id" in err or "code" in err, f"{tool} 失败返回缺 G13 错误对象"
+
+
+def test_g12_get_task_context_delegates():
+    """G12。前置：get_task_context 工具。步骤：调用。预期：返回 5 字段任务上下文。"""
+    fn = _phase_c_fn("app.services.bioflow.skill_tools", "get_task_context")
+    r = fn(job_id=None)
+    if r.get("ok") is True:
+        ctx = r.get("result") or r.get("data") or {}
+        for k in ("session_id", "job_id", "plan_revision", "run_id", "current_stage"):
+            assert k in ctx, f"缺字段 {k}"
+
+
+def test_g12_validate_delivery_delegates():
+    """G12。前置：validate_delivery 工具。步骤：不完整 manifest。预期：ok=False + G13。"""
+    fn = _phase_c_fn("app.services.bioflow.skill_tools", "validate_delivery")
+    r = fn(manifest={})
+    assert isinstance(r, dict) and "ok" in r
+
+
+# ===========================================================================
+# G12-2：SKILL.md 结构
+# ===========================================================================
+
+def test_skill_md_exists():
+    """SKILL.md。前置：文件存在。步骤：定位。预期：找到 SKILL.md。"""
+    assert _skill_md_path() is not None, "未找到 SKILL.md"
+
+
+def test_skill_md_frontmatter():
+    """SKILL.md。前置：frontmatter。步骤：解析 name/description/触发词。
+    预期：name/description 非空，含触发词。"""
+    text = _skill_md_text()
+    assert text is not None
+    m = re.match(r"^---\s*\n(.*?)\n---", text, flags=re.S)
+    assert m is not None, "缺 frontmatter"
+    fm = m.group(1)
+    assert "name:" in fm, "frontmatter 缺 name"
+    assert "description:" in fm, "frontmatter 缺 description"
+    # 触发词（name 或 description 或 triggers 字段）
+    assert any(k in fm for k in ("triggers", "触发", "生物", "基因家族", "生信")), "缺触发词"
+
+
+def test_skill_md_eleven_tools_whitelist():
+    """SKILL.md。前置：正文。步骤：检查 11 工具白名单。预期：11 工具名全部列出。"""
+    text = _skill_md_text()
+    assert text is not None
+    for tool in TOOL_NAMES:
+        assert tool in text, f"SKILL.md 缺工具 {tool}"
+
+
+def test_skill_md_human_boundaries():
+    """SKILL.md。前置：正文。步骤：检查人工边界。预期：subfamily_confirm/rnaseq_de 标 requires_human。"""
+    text = _skill_md_text()
+    assert text is not None
+    assert "subfamily_confirm" in text, "缺 subfamily_confirm 人工边界"
+    assert "rnaseq_de" in text, "缺 rnaseq_de 人工边界"
+    assert "requires_human" in text, "缺 requires_human 标注"
+
+
+def test_skill_md_acceptance_checklist():
+    """SKILL.md。前置：正文。步骤：检查验收清单。预期：含验收/检查清单。"""
+    text = _skill_md_text()
+    assert text is not None
+    assert any(k in text for k in ("验收", "acceptance", "检查清单", "checklist")), "缺验收清单"
+
+
+# ===========================================================================
+# G12-3：装卸脚本
+# ===========================================================================
+
+def test_skill_install_script_exists():
+    """装卸。前置：install 脚本。步骤：定位。预期：存在 install_skill.sh。"""
+    p = REPO_ROOT / "bioflow_service" / "install_skill.sh"
+    assert p.is_file(), f"未找到 install 脚本: {p}"
+
+
+def test_skill_uninstall_script_exists():
+    """装卸。前置：uninstall 脚本。步骤：定位。预期：存在 uninstall_skill.sh。"""
+    p = REPO_ROOT / "bioflow_service" / "uninstall_skill.sh"
+    assert p.is_file(), f"未找到 uninstall 脚本: {p}"
+
+
+def test_skill_install_uninstall_scripts_content():
+    """装卸。前置：两脚本。步骤：读内容。预期：install 含安装、uninstall 含移除逻辑。"""
+    install = REPO_ROOT / "bioflow_service" / "install_skill.sh"
+    uninstall = REPO_ROOT / "bioflow_service" / "uninstall_skill.sh"
+    assert install.is_file(), f"未找到 install 脚本: {install}"
+    assert uninstall.is_file(), f"未找到 uninstall 脚本: {uninstall}"
+    itxt = install.read_text(encoding="utf-8", errors="replace")
+    utxt = uninstall.read_text(encoding="utf-8", errors="replace")
+    assert "SKILL" in itxt or "skill" in itxt
+    assert "rm" in utxt or "remove" in utxt.lower() or "uninstall" in utxt.lower()

bioflow_service/tests/test_phase_d.py

@@ -0,0 +1,228 @@
+"""tests/test_phase_d.py —— Phase D（G7-G11 + G14 + G15）补充测试（契约测试见 test_phase_d_contract.py）。
+
+覆盖契约未直接断言的实现细节：
+- classify_reason（runner 失败原因 + 退出码/日志证据定类）。
+- auto_fill_prerequisites 的 satisfied_roles 跳过上游（G7 端到端）。
+- stage_schema 单一 schema 访问点（G9）。
+- RecoveryBudget.decide 的 runner 集成语义 + runner 自动重试（G15）。
+- task_context.current_stage。
+分层标记 -m bioflow_unit。
+"""
+from __future__ import annotations
+
+import asyncio
+
+import pytest
+
+from app.services.bioflow.catalog import build_catalog, stage_schema
+from app.services.bioflow.errors import classify_reason
+from app.services.bioflow.kernel import ImageMap
+from app.services.bioflow.readiness import check_readiness
+from app.services.bioflow.recovery import RecoveryBudget
+from app.services.bioflow.runner import JOB_FAILED, STAGE_FAILED, JobRecord
+from app.services.bioflow.stage_assets import (
+    downstream_entry_satisfied,
+    stage_input_roles,
+    upstream_stages_for_roles,
+)
+from app.services.bioflow.task_context import current_stage, get_task_context
+from conftest import FakeTimedOutExecutor, make_runner
+
+pytestmark = pytest.mark.bioflow_unit
+
+
+def _scenario(coro_factory):
+    loop = asyncio.new_event_loop()
+    try:
+        return loop.run_until_complete(coro_factory())
+    finally:
+        loop.close()
+
+
+def _rnaseq_catalog():
+    im = ImageMap(stages={
+        "rnaseq_qc": {"image": "bioflow-rnaseq", "module": "cli.run_rnaseq_qc", "executable": True},
+        "rnaseq_align": {"image": "bioflow-rnaseq", "module": "cli.run_rnaseq_align", "executable": True},
+        "rnaseq_quant": {"image": "bioflow-rnaseq", "module": "cli.run_rnaseq_quant", "executable": True},
+        "rnaseq_sample_qc": {"image": "bioflow-rnaseq", "module": "cli.run_rnaseq_sample_qc", "executable": True},
+        "rnaseq_de": {"image": "bioflow-rnaseq", "module": "cli.run_rnaseq_de", "executable": True},
+    })
+    return build_catalog(im)
+
+
+# ===========================================================================
+# G14 classify_reason（runner 失败原因 + 证据）
+# ===========================================================================
+
+def test_g14_reason_timeout_transient():
+    cat, diag, retry, _ = classify_reason("timeout")
+    assert cat == "transient" and retry is True
+
+
+def test_g14_reason_exit_code_undiagnosed():
+    cat, diag, retry, _ = classify_reason("exit_code")
+    assert cat == "adapter" and diag == "undiagnosed" and retry is False
+
+
+def test_g14_reason_no_manifest_artifact():
+    cat, *_ = classify_reason("no_manifest")
+    assert cat == "artifact"
+
+
+def test_g14_exit_code_137_resource():
+    cat, *_ = classify_reason("exit_code", exit_code=137)
+    assert cat == "resource"
+
+
+def test_g14_log_oom_resource():
+    cat, *_ = classify_reason("exit_code", log_tail="Error: out of memory in container")
+    assert cat == "resource"
+
+
+def test_g14_log_image_environment():
+    cat, *_ = classify_reason("exit_code", log_tail="docker: no such image")
+    assert cat == "environment"
+
+
+def test_g14_log_scientific_precondition():
+    cat, *_ = classify_reason("exit_code", log_tail="no significant DEGs found")
+    assert cat == "scientific_precondition"
+
+
+def test_g14_log_reference():
+    cat, *_ = classify_reason("exit_code", log_tail="reference genome index not found")
+    assert cat == "reference"
+
+
+# ===========================================================================
+# G7/G8 角色化资产 + 下游直入
+# ===========================================================================
+
+def test_g8_stage_input_roles_counts_only():
+    assert stage_input_roles("rnaseq_de") == ["counts"]
+    assert stage_input_roles("unknown") == []
+
+
+def test_g7_downstream_entry_satisfied_tuple():
+    ok, missing = downstream_entry_satisfied("rnaseq_de", {"counts": {"validated": {"ok": True}}})
+    assert ok is True and missing == []
+
+
+def test_g7_auto_fill_skips_counts_upstream():
+    catalog = _rnaseq_catalog()
+    ordered, _ = catalog.auto_fill_prerequisites(["rnaseq_de"])
+    assert set(["rnaseq_qc", "rnaseq_align", "rnaseq_quant", "rnaseq_sample_qc"]) <= set(ordered)
+    ordered2, added2 = catalog.auto_fill_prerequisites(["rnaseq_de"], satisfied_roles=["counts"])
+    assert "rnaseq_qc" not in ordered2 and "rnaseq_align" not in ordered2
+    assert "rnaseq_quant" not in ordered2 and "rnaseq_sample_qc" not in ordered2
+    assert ordered2 == ["rnaseq_de"] and added2 == []
+
+
+def test_g7_upstream_stages_for_roles():
+    up = upstream_stages_for_roles(["counts"])
+    assert set(["rnaseq_qc", "rnaseq_align", "rnaseq_quant", "rnaseq_sample_qc"]) <= up
+
+
+# ===========================================================================
+# G9 单一参数 schema
+# ===========================================================================
+
+def test_g9_stage_schema_single_source():
+    schema = stage_schema("identify")
+    assert schema["name"] == "基因家族鉴定"
+    assert isinstance(schema["params"], list) and schema["params"]
+    assert schema["dependencies"] == []
+    assert schema["input_roles"] == ["hmm", "protein_fasta"]
+
+
+def test_g9_stage_schema_unknown_fallback():
+    schema = stage_schema("no_such_stage")
+    assert schema["name"] == "no_such_stage"
+    assert schema["params"] and schema["params"][0]["name"] == "cpu"
+
+
+# ===========================================================================
+# G10 就绪检查（四象限）
+# ===========================================================================
+
+def test_g10_check_readiness_all_ready(tmp_path):
+    r = check_readiness(assets_root=tmp_path, stages=[])
+    assert r["ready"] is True
+    for q in ("environment", "reference", "space", "budget"):
+        assert q in r and r[q]["ok"] is True
+
+
+def test_g10_check_readiness_missing_reference(tmp_path):
+    r = check_readiness(assets_root=tmp_path, stages=["identify"])
+    assert r["ready"] is False
+    assert r["reference"]["ok"] is False
+    assert r["reference"]["error"]["category"] == "reference"
+
+
+# ===========================================================================
+# G11 任务绑定
+# ===========================================================================
+
+def test_g11_get_task_context_empty_binding():
+    ctx = get_task_context()
+    for k in ("session_id", "job_id", "plan_revision", "run_id", "current_stage"):
+        assert k in ctx
+
+
+def test_g11_get_task_context_with_record():
+    rec = JobRecord(id="j1", session_id="s1", stage_chain=["identify", "phylogeny"])
+    rec._stage_states = {"identify": {"status": "done"}, "phylogeny": {"status": "running"}}
+    ctx = get_task_context(rec)
+    assert ctx["session_id"] == "s1" and ctx["job_id"] == "j1"
+    assert ctx["current_stage"] == "phylogeny"
+
+
+def test_g11_current_stage():
+    rec = JobRecord(id="j1", stage_chain=["a", "b", "c"])
+    rec._stage_states = {"a": {"status": "done"}, "b": {"status": "done"}, "c": {"status": "running"}}
+    assert current_stage(rec) == "c"
+
+
+# ===========================================================================
+# G15 恢复预算 + runner 自动重试
+# ===========================================================================
+
+def test_g15_recovery_can_retry_semantics():
+    b = RecoveryBudget(max_same_cause_retries=2)
+    assert b.can_retry("x") is True
+    b.record_retry("x")
+    assert b.can_retry("x") is True
+    b.record_retry("x")
+    assert b.can_retry("x") is False
+
+
+def test_g15_recovery_decide_non_transient():
+    b = RecoveryBudget()
+    assert b.decide("s", "exit_code") is False
+    assert b.decide("s", "no_manifest") is False
+
+
+def test_g15_recovery_decide_user_stopped():
+    b = RecoveryBudget()
+    assert b.decide("s", "timeout", user_stopped=True) is False
+
+
+def test_g15_recovery_decide_resource_gate():
+    b = RecoveryBudget()
+    assert b.decide("s", "exit_code", log_tail="out of memory") is False
+
+
+def test_g15_runner_auto_retries_transient(db, events, catalog):
+    executor = FakeTimedOutExecutor()
+
+    async def scenario():
+        runner = make_runner(db, events, executor, catalog)
+        record = await runner.create_job(
+            "s1", "t", ["identify"], auto_continue=True, auto_start=False)
+        await runner.run_job(record)
+        return runner, record
+
+    runner, record = _scenario(scenario)
+    assert runner.stage_status(record, "identify") == STAGE_FAILED
+    assert record.status == JOB_FAILED
+    assert len(executor.calls) == 3  # 1 初试 + 2 自动重试

bioflow_service/tests/test_phase_d_contract.py

@@ -0,0 +1,264 @@
+"""tests/test_phase_d_contract.py —— Phase D（契约与就绪 + 诊断）测试用例集。
+
+覆盖（Phase D 验收）：G7 / G8 / G9 / G10 / G11 / G14 / G15。
+
+## 契约说明（开发对齐用）
+- G14 错误分类：`app.services.bioflow.errors.CATEGORIES`（8 类）+ `classify(code, summary)`。
+  8 类确定性分类：input / scientific_precondition / reference / environment /
+  transient / resource / adapter / artifact。OOM→resource、镜像缺→environment、
+  科学前提→scientific_precondition、参考缺失→reference。
+- G10 就绪检查：`check_readiness` 四象限（environment/reference/space/budget），
+  缺项返回结构化错误并阻断（阻断 = ready=False）。
+- G11 任务绑定：`get_task_context` 返回 session_id+job_id+plan_revision+run_id+当前阶段。
+- G7/G8：`stage_input_roles(stage)` 返回阶段依赖输入角色；`asset_role_satisfied` 判断
+  角色是否有 validated 资产；下游直入（counts→DE）不补跑上游 QC/align/quant。
+- G9 单一参数 schema：所有入口读 `catalog.get(stage).params`（无多份不一致）。
+- G15 恢复预算：同因重试 ≤2；收敛条件（scientific_precondition / 无新证据 /
+  用户停止 / 资源门禁）终止重试。
+
+未实现函数用 `_phase_d_fn` 动态导入，缺失则 skip（开发完成后须全部可导入、无 skip）。
+"""
+from __future__ import annotations
+
+import importlib
+from pathlib import Path
+
+import pytest
+
+from app.services.bioflow import errors
+from app.services.bioflow.catalog import build_catalog
+
+pytestmark = pytest.mark.bioflow_unit
+
+
+def _phase_d_fn(module: str, name: str):
+    """动态取 Phase D 函数；未实现则 skip（开发完成后须全部存在）。"""
+    try:
+        mod = importlib.import_module(module)
+        return getattr(mod, name)
+    except (ImportError, AttributeError) as exc:
+        pytest.skip(f"Phase D 未实现 {module}.{name}: {exc}")
+
+
+# ===========================================================================
+# G14 错误分类（8 类确定性分类）
+# ===========================================================================
+
+def test_g14_categories_exactly_eight():
+    """前置：errors 模块。步骤：读 CATEGORIES。预期：恰 8 类。"""
+    assert set(errors.CATEGORIES) == {
+        "input", "scientific_precondition", "reference", "environment",
+        "transient", "resource", "adapter", "artifact",
+    }
+
+
+def test_g14_classify_resource():
+    """前置：DISK_FULL。步骤：classify。预期：category=resource，不可重试。"""
+    cat, diag, retry, actions = errors.classify("DISK_FULL", "")
+    assert cat == "resource"
+    assert diag == "diagnosed"
+    assert retry is False
+    assert isinstance(actions, list)
+
+
+def test_g14_classify_environment():
+    """前置：OSS_UNCONFIGURED。步骤：classify。预期：category=environment。"""
+    cat, *_ = errors.classify("OSS_UNCONFIGURED", "")
+    assert cat == "environment"
+
+
+def test_g14_classify_transient_retryable():
+    """前置：NETWORK_ERROR。步骤：classify。预期：category=transient，可重试。"""
+    cat, diag, retry, _ = errors.classify("NETWORK_ERROR", "")
+    assert cat == "transient"
+    assert retry is True
+
+
+def test_g14_classify_input():
+    """前置：NOT_FOUND。步骤：classify。预期：category=input。"""
+    cat, *_ = errors.classify("NOT_FOUND", "")
+    assert cat == "input"
+
+
+def test_g14_classify_adapter():
+    """前置：UNSUPPORTED。步骤：classify。预期：category=adapter。"""
+    cat, *_ = errors.classify("UNSUPPORTED", "")
+    assert cat == "adapter"
+
+
+def test_g14_classify_artifact():
+    """前置：ARCHIVE_EXISTS。步骤：classify。预期：category=artifact。"""
+    cat, *_ = errors.classify("ARCHIVE_EXISTS", "")
+    assert cat == "artifact"
+
+
+def test_g14_classify_oom_keyword_to_resource():
+    """G14 确定性：OOM→resource。前置：无枚举码、摘要含 out of memory。
+    步骤：classify(None, "container out of memory")。预期：category=resource。"""
+    cat, *_ = errors.classify(None, "container out of memory")
+    assert cat == "resource"
+
+
+def test_g14_classify_image_keyword_to_environment():
+    """G14 确定性：镜像缺→environment。前置：摘要含 image。步骤：classify。
+    预期：category=environment。"""
+    cat, *_ = errors.classify(None, "docker image not found")
+    assert cat == "environment"
+
+
+def test_g14_classify_scientific_precondition():
+    """G14 确定性：科学前提→scientific_precondition。前置：摘要含科学前提语义。
+    步骤：classify。预期：category=scientific_precondition（开发须补齐该映射）。"""
+    cat, *_ = errors.classify(None, "上游科学前提未满足，无法继续")
+    assert cat == "scientific_precondition"
+
+
+def test_g14_classify_reference():
+    """G14 确定性：参考缺失→reference。前置：摘要含参考基因组缺失。
+    步骤：classify。预期：category=reference（开发须补齐该映射）。"""
+    cat, *_ = errors.classify(None, "参考基因组缺失")
+    assert cat == "reference"
+
+
+def test_g14_classify_category_invariant():
+    """G14 不变量：任意输入分类结果 category 必在 8 类内。"""
+    samples = [
+        ("DISK_FULL", ""), ("NOT_FOUND", ""), (None, "timeout"), (None, "unknown_xyz"),
+        ("BAD_SCHEME", ""), ("ASSET_EXISTS", ""),
+    ]
+    for code, summary in samples:
+        cat, *_ = errors.classify(code, summary)
+        assert cat in errors.CATEGORIES, f"分类结果 {cat!r} 不在 8 类内"
+
+
+def test_g14_error_object_carries_category():
+    """G14 集成：error_object 携带 classify 的 category。"""
+    obj = errors.error_object("DISK_FULL", "磁盘不足")
+    assert obj["category"] == "resource"
+    assert obj["retryable_without_change"] is False
+
+
+# ===========================================================================
+# G9 单一参数 schema（所有入口读 catalog.get(stage).params）
+# ===========================================================================
+
+def test_g9_catalog_is_single_param_source(image_map):
+    """G9。前置：image_map。步骤：两次 build_catalog。预期：参数定义一致（单一来源）。"""
+    c1 = build_catalog(image_map)
+    c2 = build_catalog(image_map)
+    assert c1.get("identify").params == c2.get("identify").params
+
+
+def test_g9_catalog_params_consistent_shape(image_map):
+    """G9。前置：image_map。步骤：读 identify 参数。预期：参数为 list[dict]，含 name。"""
+    entry = build_catalog(image_map).get("identify")
+    assert isinstance(entry.params, list)
+    if entry.params:
+        assert all("name" in p for p in entry.params)
+
+
+# ===========================================================================
+# G10 就绪检查（check_readiness 四象限：环境/参考/空间/预算）
+# ===========================================================================
+
+def test_g10_check_readiness_all_ready(tmp_path):
+    """G10。前置：四象限齐备。步骤：check_readiness。预期：ready=True，四象限均 ok。"""
+    check_readiness = _phase_d_fn("app.services.bioflow.readiness", "check_readiness")
+    r = check_readiness(assets_root=tmp_path, stages=[])
+    assert r["ready"] is True
+    for q in ("environment", "reference", "space", "budget"):
+        assert q in r, f"缺象限 {q}"
+        assert r[q].get("ok") is True
+
+
+def test_g10_check_readiness_missing_reference(tmp_path):
+    """G10。前置：参考缺失。步骤：check_readiness。预期：ready=False，结构化错误+阻断。"""
+    check_readiness = _phase_d_fn("app.services.bioflow.readiness", "check_readiness")
+    r = check_readiness(assets_root=tmp_path, stages=["identify"])
+    assert r["ready"] is False
+    # 缺项返回结构化错误（G13 对象）
+    err = r.get("error") or (r.get("reference") or {}).get("error")
+    assert err is not None, "缺项应返回结构化错误对象"
+    for f in ("error_id", "category", "code", "summary", "diagnosis_status"):
+        assert f in err, f"缺字段 {f}"
+
+
+def test_g10_check_readiness_four_quadrants_keys(tmp_path):
+    """G10。前置：任意。步骤：check_readiness。预期：返回值含四象限键。"""
+    check_readiness = _phase_d_fn("app.services.bioflow.readiness", "check_readiness")
+    r = check_readiness(assets_root=tmp_path, stages=[])
+    for q in ("environment", "reference", "space", "budget"):
+        assert q in r, f"缺象限键 {q}"
+
+
+# ===========================================================================
+# G11 任务绑定（get_task_context）
+# ===========================================================================
+
+def test_g11_get_task_context_fields():
+    """G11。前置：绑定态任务。步骤：get_task_context。预期：返回 5 字段。"""
+    get_task_context = _phase_d_fn("app.services.bioflow.task_context", "get_task_context")
+    ctx = get_task_context()
+    for k in ("session_id", "job_id", "plan_revision", "run_id", "current_stage"):
+        assert k in ctx, f"缺字段 {k}"
+
+
+# ===========================================================================
+# G7/G8 角色化资产 + 下游直入
+# ===========================================================================
+
+def test_g8_stage_input_roles():
+    """G8。前置：阶段 rnaseq_de。步骤：stage_input_roles。预期：返回 counts 等输入角色。"""
+    stage_input_roles = _phase_d_fn("app.services.bioflow.stage_assets", "stage_input_roles")
+    roles = stage_input_roles("rnaseq_de")
+    assert isinstance(roles, list)
+    assert roles, "rnaseq_de 应声明输入角色（如 counts）"
+
+
+def test_g8_role_satisfied_by_validated_asset():
+    """G8。前置：validated 资产。步骤：asset_role_satisfied。预期：有 validated 资产即满足。"""
+    asset_role_satisfied = _phase_d_fn("app.services.bioflow.stage_assets", "asset_role_satisfied")
+    assert asset_role_satisfied("counts", {"role": "counts", "validated": {"ok": True}}) is True
+    assert asset_role_satisfied("counts", {"role": "counts", "validated": {"ok": False}}) is False
+
+
+def test_g7_downstream_direct_entry_counts():
+    """G7。前置：提供 counts 资产做 DE。步骤：下游直入判断。
+    预期：不补跑上游 QC/align/quant（上游角色由 counts 资产满足）。"""
+    downstream_entry_satisfied = _phase_d_fn(
+        "app.services.bioflow.stage_assets", "downstream_entry_satisfied")
+    ok, missing_upstream = downstream_entry_satisfied(
+        "rnaseq_de", {"counts": {"validated": {"ok": True}}})
+    assert ok is True
+    assert missing_upstream == []
+
+
+# ===========================================================================
+# G15 恢复预算（同因重试≤2 + 收敛条件）
+# ===========================================================================
+
+def test_g15_same_cause_retry_le_2():
+    """G15。前置：恢复预算。步骤：同因连续重试。预期：≤2 次后拒绝。"""
+    RecoveryBudget = _phase_d_fn("app.services.bioflow.recovery", "RecoveryBudget")
+    b = RecoveryBudget(max_same_cause_retries=2)
+    assert b.can_retry("cause_x") is True   # 第 1 次
+    b.record_retry("cause_x")
+    assert b.can_retry("cause_x") is True   # 第 2 次
+    b.record_retry("cause_x")
+    assert b.can_retry("cause_x") is False  # 第 3 次拒绝（≤2）
+
+
+def test_g15_convergence_scientific_precondition():
+    """G15。前置：scientific_precondition 分类。步骤：判断是否可重试。
+    预期：科学前提类不重试（收敛）。"""
+    cat, diag, retry, _ = errors.classify(None, "科学前提未满足")
+    assert cat == "scientific_precondition"
+    assert retry is False
+
+
+def test_g15_convergence_resource_gate():
+    """G15。前置：resource 门禁（如 DISK_FULL）。步骤：classify。
+    预期：资源类不可重试（资源门禁收敛）。"""
+    cat, diag, retry, _ = errors.classify("DISK_FULL", "")
+    assert cat == "resource"
+    assert retry is False

bioflow_service/tests/test_phase_e_versioning.py

@@ -0,0 +1,184 @@
+"""tests/test_phase_e_versioning.py —— Phase E（版本化修改）测试用例集。
+
+覆盖（Phase E 验收）：G16 / G17 / G18 / G19 / G20。
+
+## 契约说明（开发对齐用，预期模块 + 函数签名）
+- G16 版本化身份字段：plan_revision / run_id（已存在于 JobRecord + task_context.get_task_context）；
+  新增 asset_id / based_on_revision / action_id，落在
+  `app.services.bioflow.versioning`：
+    new_revision(based_on_revision: str = None) -> dict
+        # 返回 {"revision": str, "based_on_revision": str|None,
+        #        "asset_id": str, "action_id": str}
+    make_action_id() -> str                       # 唯一 action id
+- G17 影响范围：`versioning.affected_stages(stage_chain: list[str], changed_stage: str) -> list[str]`
+    返回改参数后受影响的下游阶段（只重跑受影响节点；含 changed_stage 之后的所有下游）。
+- G18 历史不覆盖：`versioning.RevisionStore(root: str|Path)`
+    write(revision: str, key: str, content: str) -> Path   # 写到 revision 独立路径，不覆盖旧 revision
+    read(revision: str, key: str) -> str | None
+- G19 防重复：`versioning.ActionDedup()`
+    try_start(action_id: str) -> bool             # 首次 True，重复 False（幂等，不重复启动）
+- G20 执行所有权：`app.services.bioflow.run_owner`：
+    claim(run_id: str, owner_id: str) -> bool     # 首次 True（取得所有权），重复/他人 False
+    release(run_id: str, owner_id: str) -> bool
+    stop(run_id: str, owner_id: str) -> bool      # 终止实际执行（非仅置状态）
+    resume(run_id: str, owner_id: str) -> bool    # 已运行则 False（不重叠）
+
+未实现函数用 `_phase_e_fn` 动态导入，缺失则 skip（开发完成后须全部存在、无 skip）。
+"""
+from __future__ import annotations
+
+import importlib
+
+import pytest
+
+from app.services.bioflow.runner import JobRecord
+from app.services.bioflow.task_context import get_task_context
+
+pytestmark = pytest.mark.bioflow_unit
+
+
+def _phase_e_fn(module: str, name: str):
+    """动态取 Phase E 函数/类；未实现则 skip（开发完成后须全部存在）。"""
+    try:
+        mod = importlib.import_module(module)
+        return getattr(mod, name)
+    except (ImportError, AttributeError) as exc:
+        pytest.skip(f"Phase E 未实现 {module}.{name}: {exc}")
+
+
+# ===========================================================================
+# G16 版本化身份（plan_revision / run_id / asset_id / based_on_revision / action_id）
+# ===========================================================================
+
+def test_g16_job_record_revision_fields():
+    """G16。前置：JobRecord。步骤：构造。预期：含 plan_revision + run_id 字段。"""
+    rec = JobRecord(id="j1")
+    assert rec.plan_revision == "1"
+    assert rec.run_id is None
+
+
+def test_g16_task_context_revision_fields():
+    """G16。前置：无 record。步骤：get_task_context()。预期：返回 plan_revision + run_id。"""
+    ctx = get_task_context()
+    assert "plan_revision" in ctx
+    assert "run_id" in ctx
+
+
+def test_g16_new_revision_identity_fields():
+    """G16。前置：versioning.new_revision。步骤：调用。预期：返回 4 个身份字段。"""
+    new_revision = _phase_e_fn("app.services.bioflow.versioning", "new_revision")
+    rev = new_revision(based_on_revision="1")
+    for k in ("revision", "based_on_revision", "asset_id", "action_id"):
+        assert k in rev, f"缺字段 {k}"
+    assert rev["based_on_revision"] == "1"
+
+
+def test_g16_action_id_unique():
+    """G16。前置：versioning.make_action_id。步骤：两次调用。预期：action_id 唯一。"""
+    make_action_id = _phase_e_fn("app.services.bioflow.versioning", "make_action_id")
+    a = make_action_id()
+    b = make_action_id()
+    assert a and b
+    assert a != b
+
+
+# ===========================================================================
+# G17 影响范围（改参数 → 依赖图 → 受影响下游阶段，只重跑受影响节点）
+# ===========================================================================
+
+def test_g17_affected_stages_downstream():
+    """G17。前置：链 identify→phylogeny→motif。步骤：affected_stages(changed=identify)。
+    预期：返回下游 phylogeny/motif（不含已完成的 identify 之外无关节点）。"""
+    affected_stages = _phase_e_fn("app.services.bioflow.versioning", "affected_stages")
+    out = affected_stages(["identify", "phylogeny", "motif"], "identify")
+    assert out == ["phylogeny", "motif"]
+
+
+def test_g17_affected_stages_no_downstream():
+    """G17。前置：改末阶段 motif。步骤：affected_stages。预期：无下游，空列表。"""
+    affected_stages = _phase_e_fn("app.services.bioflow.versioning", "affected_stages")
+    out = affected_stages(["identify", "phylogeny", "motif"], "motif")
+    assert out == []
+
+
+# ===========================================================================
+# G18 历史不覆盖（新 revision 不覆盖旧 revision 的 manifest/产物/参数）
+# ===========================================================================
+
+def test_g18_revision_store_preserves_old(tmp_path):
+    """G18。前置：RevisionStore。步骤：rev1 写 key，rev2 写同名 key。
+    预期：rev1 内容不被 rev2 覆盖。"""
+    RevisionStore = _phase_e_fn("app.services.bioflow.versioning", "RevisionStore")
+    store = RevisionStore(tmp_path)
+    store.write("rev1", "params.json", '{"cpu": "2"}')
+    store.write("rev2", "params.json", '{"cpu": "8"}')
+    assert store.read("rev1", "params.json") == '{"cpu": "2"}'
+    assert store.read("rev2", "params.json") == '{"cpu": "8"}'
+
+
+def test_g18_revision_paths_isolated(tmp_path):
+    """G18。前置：RevisionStore。步骤：rev1/rev2 各写产物。
+    预期：落不同路径（物理隔离，不互覆）。"""
+    RevisionStore = _phase_e_fn("app.services.bioflow.versioning", "RevisionStore")
+    store = RevisionStore(tmp_path)
+    p1 = store.write("rev1", "final.txt", "v1")
+    p2 = store.write("rev2", "final.txt", "v2")
+    assert str(p1) != str(p2)
+    assert p1.read_text() == "v1"
+    assert p2.read_text() == "v2"
+
+
+# ===========================================================================
+# G19 防重复（action_id 幂等，重复提交不重复启动）
+# ===========================================================================
+
+def test_g19_action_dedup_idempotent():
+    """G19。前置：ActionDedup。步骤：同 action_id 两次 try_start。
+    预期：首次 True，第二次 False（幂等）。"""
+    ActionDedup = _phase_e_fn("app.services.bioflow.versioning", "ActionDedup")
+    dedup = ActionDedup()
+    assert dedup.try_start("act-1") is True
+    assert dedup.try_start("act-1") is False
+
+
+def test_g19_duplicate_action_not_restarted():
+    """G19。前置：ActionDedup。步骤：两个不同 action_id 各自启动，重复一个。
+    预期：不同 id 各自 True；重复 id 不重复启动。"""
+    ActionDedup = _phase_e_fn("app.services.bioflow.versioning", "ActionDedup")
+    dedup = ActionDedup()
+    assert dedup.try_start("act-1") is True
+    assert dedup.try_start("act-2") is True
+    assert dedup.try_start("act-1") is False  # 不重复启动
+
+
+# ===========================================================================
+# G20 执行所有权（stop 终止实际执行 / resume 不重叠 / 重启不重复接管）
+# ===========================================================================
+
+def test_g20_claim_single_owner():
+    """G20。前置：run_owner.claim。步骤：owner A 取得 run，owner B 再 claim。
+    预期：A True，B False（单一所有权，不重复接管）。"""
+    claim = _phase_e_fn("app.services.bioflow.run_owner", "claim")
+    assert claim("run-1", "owner-A") is True
+    assert claim("run-1", "owner-B") is False
+
+
+def test_g20_resume_no_overlap():
+    """G20。前置：run_owner.resume。步骤：已运行 run 再 resume。
+    预期：False（不重叠执行）。"""
+    claim = _phase_e_fn("app.services.bioflow.run_owner", "claim")
+    resume = _phase_e_fn("app.services.bioflow.run_owner", "resume")
+    assert claim("run-2", "owner-A") is True
+    assert resume("run-2", "owner-A") is False
+
+
+def test_g20_stop_terminates_execution():
+    """G20。前置：run_owner.claim + stop。步骤：claim 后 stop。
+    预期：stop 返回 True（实际终止），随后 release 允许重新 claim。"""
+    claim = _phase_e_fn("app.services.bioflow.run_owner", "claim")
+    stop = _phase_e_fn("app.services.bioflow.run_owner", "stop")
+    release = _phase_e_fn("app.services.bioflow.run_owner", "release")
+    assert claim("run-3", "owner-A") is True
+    assert stop("run-3", "owner-A") is True
+    assert release("run-3", "owner-A") is True
+    assert claim("run-3", "owner-B") is True  # 释放后可被重新接管

bioflow_service/tests/test_phase_f.py

@@ -0,0 +1,97 @@
+"""tests/test_phase_f.py —— Phase F（交付）测试用例集。
+
+覆盖：G21 交付清单（delivery_validate/publish）、G22 终报告范围（classify_report_scope）、
+G23 资源预算门禁（check_download_budget / check_disk_available）。
+契约测试见 test_phase_f_delivery.py；本文件补契约未直接断言的点（publish / build_report）。
+分层标记 -m bioflow_unit。
+"""
+from __future__ import annotations
+
+import pytest
+
+from app.services.bioflow.delivery import (
+    build_report,
+    check_disk_available,
+    check_download_budget,
+    classify_report_scope,
+    delivery_validate,
+    publish_delivery,
+)
+
+pytestmark = pytest.mark.bioflow_unit
+
+
+def _complete() -> dict:
+    return {
+        "selected_stages": ["identify", "phylogeny"],
+        "run_id": "run-1",
+        "input_sources": ["/data/genome.pep.fa"],
+        "output_sources": ["/data/final/Ft.SPL.final_members.id"],
+        "config": {"cpu": "8"},
+        "required_results": ["final_members.id"],
+        "validation_values": {"final_members": 24},
+        "review_status": "approved",
+    }
+
+
+# G21 补充：publish 幂等/阻断
+
+def test_g21_publish_valid():
+    m = _complete()
+    r = publish_delivery(m)
+    assert r["ok"] is True and r["published"] is True
+    assert m["review_status"] == "approved"
+
+
+def test_g21_publish_invalid_blocked():
+    m = _complete()
+    m["run_id"] = ""
+    r = publish_delivery(m)
+    assert r["ok"] is False and r["published"] is False
+
+
+def test_g21_validate_checks_eight_keys():
+    r = delivery_validate(_complete())
+    assert set(r["checks"]) == {
+        "selected_stages", "run_id", "input_sources", "output_sources",
+        "config", "required_results", "validation_values", "review_status",
+    }
+
+
+# G22 补充：五分类边界
+
+def test_g22_classify_five_categories():
+    assert classify_report_scope("done", "user") == "user_provided"
+    assert classify_report_scope("done", "reuse") == "reused"
+    assert classify_report_scope("done", None) == "user_provided"
+    assert classify_report_scope("waiting", None) == "not_executed"
+    assert classify_report_scope("queued", None) == "not_executed"
+    assert classify_report_scope("skipped", None) == "skipped"
+    assert classify_report_scope("failed", None) == "failed"
+    assert classify_report_scope("partial_success", None) == "not_executed"
+
+
+# G22 补充：终报告结构
+
+def test_g22_build_report_structure():
+    m = _complete()
+    report = build_report(m, stage_sources={"identify": "reused",
+                                            "phylogeny": "failed"})
+    for k in ("execution_scope", "data_sources", "qc", "scientific_preconditions",
+              "failed_skipped_uncovered", "artifacts"):
+        assert k in report, f"缺报告段 {k}"
+    assert report["failed_skipped_uncovered"]["failed"] == ["phylogeny"]
+    assert report["artifacts"] == ["final_members.id"]
+
+
+# G23 补充
+
+def test_g23_download_budget_boundary():
+    assert check_download_budget(100, 100)["ok"] is True  # 恰好等于不超
+    assert check_download_budget(101, 100)["ok"] is False
+
+
+def test_g23_disk_available_ok(tmp_path):
+    r = check_disk_available(tmp_path, 1)
+    assert r["ok"] is True
+    assert r["free_bytes"] > 0

bioflow_service/tests/test_phase_f_delivery.py

@@ -0,0 +1,187 @@
+"""tests/test_phase_f_delivery.py —— Phase F（交付）测试用例集。
+
+覆盖（Phase F 验收）：G21 / G22 / G23。
+
+## 契约说明（开发对齐用，预期模块 + 函数签名）
+模块：`app.services.bioflow.delivery`
+
+- G21 交付清单完整性：
+    delivery_validate(manifest: dict) -> dict
+    manifest 八项：selected_stages / run_id / input_sources / output_sources /
+    config / required_results / validation_values / review_status。
+    返回 {"ok": bool, "checks": {item: bool},
+          "incomplete": [{"item": str, "reason": str, "error": {G13 对象}}]}
+    任一项缺失 → ok=False + incomplete 记录 item/reason/结构化错误（未完成原因）。
+- G22 终报告范围：
+    classify_report_scope(status: str, source: str | None = None) -> str
+    status 终态分类：failed→"failed"、skipped→"skipped"、
+    非终态(waiting/queued/created/await_*)→"not_executed"；
+    done + source="reuse"→"reused"；done + source="user"(或空)→"user_provided"。
+- G23 资源预算：
+    check_download_budget(size_bytes: int, budget_bytes: int) -> dict
+        # 超限 → {"ok": False, "code": "DOWNLOAD_BUDGET_EXCEEDED", "error": {...}}
+    check_disk_available(dest_dir, needed_bytes: int) -> dict
+        # 不足 → {"ok": False, "code": "DISK_FULL", "error": {...}}
+    两者阻断（ok=False）并返回结构化错误。
+
+未实现函数用 `_phase_f_fn` 动态导入，缺失则 skip（开发完成后须全部存在、无 skip）。
+"""
+from __future__ import annotations
+
+import importlib
+
+import pytest
+
+pytestmark = pytest.mark.bioflow_unit
+
+
+def _phase_f_fn(module: str, name: str):
+    """动态取 Phase F 函数；未实现则 skip（开发完成后须全部存在）。"""
+    try:
+        mod = importlib.import_module(module)
+        return getattr(mod, name)
+    except (ImportError, AttributeError) as exc:
+        pytest.skip(f"Phase F 未实现 {module}.{name}: {exc}")
+
+
+def _complete_manifest() -> dict:
+    return {
+        "selected_stages": ["identify", "phylogeny"],
+        "run_id": "run-1",
+        "input_sources": ["/data/genome.pep.fa"],
+        "output_sources": ["/data/final/Ft.SPL.final_members.id"],
+        "config": {"cpu": "8"},
+        "required_results": ["final_members.id"],
+        "validation_values": {"final_members": 24},
+        "review_status": "approved",
+    }
+
+
+def _g13_fields():
+    return ("error_id", "category", "code", "summary", "diagnosis_status")
+
+
+# ===========================================================================
+# G21 交付清单完整性（delivery validate）
+# ===========================================================================
+
+def test_g21_delivery_validate_complete():
+    """G21。前置：八项齐备 manifest。步骤：delivery_validate。预期：ok=True，incomplete 空。"""
+    delivery_validate = _phase_f_fn("app.services.bioflow.delivery", "delivery_validate")
+    r = delivery_validate(_complete_manifest())
+    assert r["ok"] is True
+    assert r.get("incomplete") == []
+
+
+def test_g21_delivery_validate_missing_run_id():
+    """G21。前置：缺 run_id。步骤：delivery_validate。预期：ok=False，incomplete 含 run_id + 结构化错误。"""
+    delivery_validate = _phase_f_fn("app.services.bioflow.delivery", "delivery_validate")
+    m = _complete_manifest()
+    m["run_id"] = ""
+    r = delivery_validate(m)
+    assert r["ok"] is False
+    items = {i["item"]: i for i in r["incomplete"]}
+    assert "run_id" in items
+    err = items["run_id"].get("error")
+    assert err is not None
+    for f in _g13_fields():
+        assert f in err, f"缺字段 {f}"
+
+
+def test_g21_delivery_validate_missing_required_results():
+    """G21。前置：缺 required_results。步骤：delivery_validate。预期：ok=False，未完成原因含 required_results。"""
+    delivery_validate = _phase_f_fn("app.services.bioflow.delivery", "delivery_validate")
+    m = _complete_manifest()
+    m["required_results"] = []
+    r = delivery_validate(m)
+    assert r["ok"] is False
+    items = {i["item"]: i for i in r["incomplete"]}
+    assert "required_results" in items
+    assert items["required_results"].get("reason")
+
+
+def test_g21_delivery_validate_checks_eight_items():
+    """G21。前置：完整 manifest。步骤：delivery_validate。预期：checks 覆盖八项。"""
+    delivery_validate = _phase_f_fn("app.services.bioflow.delivery", "delivery_validate")
+    r = delivery_validate(_complete_manifest())
+    checks = r.get("checks")
+    assert checks is not None, "应返回 checks 覆盖八项"
+    for k in ("selected_stages", "run_id", "input_sources", "output_sources",
+              "config", "required_results", "validation_values", "review_status"):
+        assert k in checks, f"checks 缺项 {k}"
+
+
+# ===========================================================================
+# G22 终报告范围（用户提供 / 历史复用 / 未执行 / 跳过 / 失败）
+# ===========================================================================
+
+def test_g22_report_scope_user_provided():
+    """G22。前置：done + source=user。步骤：classify_report_scope。预期：user_provided。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "classify_report_scope")
+    assert fn("done", source="user") == "user_provided"
+
+
+def test_g22_report_scope_reused():
+    """G22。前置：done + source=reuse。步骤：classify_report_scope。预期：reused。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "classify_report_scope")
+    assert fn("done", source="reuse") == "reused"
+
+
+def test_g22_report_scope_not_executed():
+    """G22。前置：非终态 waiting。步骤：classify_report_scope。预期：not_executed。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "classify_report_scope")
+    assert fn("waiting", source=None) == "not_executed"
+
+
+def test_g22_report_scope_skipped():
+    """G22。前置：skipped。步骤：classify_report_scope。预期：skipped。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "classify_report_scope")
+    assert fn("skipped", source=None) == "skipped"
+
+
+def test_g22_report_scope_failed():
+    """G22。前置：failed。步骤：classify_report_scope。预期：failed。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "classify_report_scope")
+    assert fn("failed", source=None) == "failed"
+
+
+# ===========================================================================
+# G23 资源预算（下载预算超限 / 磁盘不足阻断，结构化错误）
+# ===========================================================================
+
+def test_g23_download_budget_exceeded():
+    """G23。前置：下载超预算。步骤：check_download_budget。预期：ok=False + 结构化错误阻断。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "check_download_budget")
+    r = fn(size_bytes=1024 * 1024 * 1024, budget_bytes=100)
+    assert r["ok"] is False
+    assert r["code"] == "DOWNLOAD_BUDGET_EXCEEDED"
+    err = r.get("error")
+    assert err is not None
+    for f in _g13_fields():
+        assert f in err, f"缺字段 {f}"
+
+
+def test_g23_download_budget_ok():
+    """G23。前置：下载未超预算。步骤：check_download_budget。预期：ok=True。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "check_download_budget")
+    r = fn(size_bytes=100, budget_bytes=1024)
+    assert r["ok"] is True
+
+
+def test_g23_disk_insufficient_blocks(tmp_path):
+    """G23。前置：磁盘不足（1EB）。步骤：check_disk_available。预期：ok=False + 结构化错误。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "check_disk_available")
+    r = fn(tmp_path, needed_bytes=10 ** 18)
+    assert r["ok"] is False
+    assert r["code"] == "DISK_FULL"
+    err = r.get("error")
+    assert err is not None
+    for f in _g13_fields():
+        assert f in err, f"缺字段 {f}"
+
+
+def test_g23_disk_sufficient_ok(tmp_path):
+    """G23。前置：磁盘充足（1 字节）。步骤：check_disk_available。预期：ok=True。"""
+    fn = _phase_f_fn("app.services.bioflow.delivery", "check_disk_available")
+    r = fn(tmp_path, needed_bytes=1)
+    assert r["ok"] is True

bioflow_service/tests/test_source_fetcher.py

@@ -0,0 +1,455 @@
+"""tests/test_source_fetcher.py —— 源文件拉取（web/OSS/局域网）+ 磁盘余量 + provenance。
+
+分层标记 -m bioflow_unit。覆盖（S0 验收）：
+- web http 流式下载（本地 http.server 实测 httpx 通道）+ provenance 落盘。
+- 协议白名单（ftp:// 拒绝 BAD_SCHEME）。
+- oss:// 无 endpoint 拒绝 / 预签名 URL 直通 web / endpoint 解析。
+- 局域网本机路径直读；远端 host:/path 解析。
+- 磁盘余量不足 DISK_FULL（check_disk_space 纯函数）。
+"""
+from __future__ import annotations
+
+import asyncio
+import functools
+import http.server
+import threading
+from pathlib import Path
+
+import pytest
+
+from app.services.bioflow.source_fetcher import (
+    FetchError,
+    _parse_lan_remote,
+    _resolve_oss_url,
+    check_disk_space,
+    fetch_lan,
+    fetch_source,
+    fetch_web,
+)
+
+
+def _run(coro):
+    return asyncio.new_event_loop().run_until_complete(coro)
+
+
+# ---------------------------------------------------------------------------
+# 本地 http 服务器（测 httpx 通道，不依赖外网）
+# ---------------------------------------------------------------------------
+
+@pytest.fixture()
+def http_url(tmp_path):
+    content = b">seq1\nACGTACGT\n>seq2\nTGCATGCA\n"
+    (tmp_path / "test.fa").write_bytes(content)
+    handler = functools.partial(http.server.SimpleHTTPRequestHandler, directory=str(tmp_path))
+    server = http.server.HTTPServer(("127.0.0.1", 0), handler)
+    thread = threading.Thread(target=server.serve_forever, daemon=True)
+    thread.start()
+    yield f"http://127.0.0.1:{server.server_address[1]}/test.fa"
+    server.shutdown()
+
+
+def test_fetch_web_download_and_provenance(http_url, tmp_path):
+    out = tmp_path / "out"
+    r = _run(fetch_web(http_url, out))
+    assert r["ok"] is True
+    assert r["name"] == "test.fa"
+    assert r["size"] > 0
+    assert r["kind"] == "web"
+    assert r["provenance"]["source"] == http_url
+    assert len(r["provenance"]["sha256"]) == 64
+    assert (out / "test.fa").read_text().startswith(">seq1")
+    # sidecar provenance
+    assert (out / "test.fa.provenance.json").is_file()
+
+
+def test_fetch_web_http_error(http_url, tmp_path):
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_web(http_url + "/missing", tmp_path / "out"))
+    assert ei.value.code == "HTTP_ERROR"
+
+
+def test_fetch_source_bad_scheme(tmp_path):
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_source("ftp://host/x.fa", tmp_path))
+    assert ei.value.code == "BAD_SCHEME"
+
+
+# ---------------------------------------------------------------------------
+# OSS
+# ---------------------------------------------------------------------------
+
+def test_oss_url_no_endpoint_rejected():
+    with pytest.raises(FetchError) as ei:
+        _resolve_oss_url("oss://bucket/key.fa")
+    assert ei.value.code == "OSS_UNCONFIGURED"
+
+
+def test_oss_url_endpoint_resolve(monkeypatch):
+    monkeypatch.setenv("BIOFLOW_OSS_ENDPOINT", "oss-cn-hangzhou.aliyuncs.com")
+    url = _resolve_oss_url("oss://seq-bucket/data/x.fa")
+    assert url == "https://seq-bucket.oss-cn-hangzhou.aliyuncs.com/data/x.fa"
+
+
+def test_oss_presigned_passthrough():
+    url = _resolve_oss_url("https://bucket.oss-cn-hangzhou.aliyuncs.com/x.fa?sig=abc")
+    assert url.startswith("https://")
+
+
+# ---------------------------------------------------------------------------
+# 局域网 / 本机路径
+# ---------------------------------------------------------------------------
+
+def test_parse_lan_remote():
+    assert _parse_lan_remote("192.168.1.5:/data/x.fa") == ("192.168.1.5", "/data/x.fa")
+    assert _parse_lan_remote("xzq@192.168.1.5:/data/x.fa") == ("xzq@192.168.1.5", "/data/x.fa")
+    assert _parse_lan_remote("/local/path/x.fa") is None
+    assert _parse_lan_remote("http://x/y") is None
+
+
+def test_fetch_lan_local_path(tmp_path):
+    f = tmp_path / "genome.fa"
+    f.write_text(">g1\nACGT\n")
+    r = _run(fetch_lan(str(f), tmp_path / "out"))
+    assert r["ok"] is True
+    assert r["kind"] == "lan"
+    assert r["path"] == str(f)
+    assert r["provenance"]["sha256"]
+
+
+def test_fetch_lan_missing_path(tmp_path):
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan("/no/such/path.fa", tmp_path))
+    assert ei.value.code == "PATH_NOT_EXIST"
+
+
+# ---------------------------------------------------------------------------
+# 磁盘余量
+# ---------------------------------------------------------------------------
+
+def test_check_disk_space_insufficient(tmp_path):
+    ok, free = check_disk_space(tmp_path, 10 ** 18)  # 1EB，必不足
+    assert ok is False
+    assert free < 10 ** 18
+
+
+def test_check_disk_space_sufficient(tmp_path):
+    ok, _free = check_disk_space(tmp_path, 1)  # 1 字节
+    assert ok is True
+
+
+# ===========================================================================
+# S0 补强（1）web：BAD_SCHEME / 磁盘满 DISK_FULL / 断点 TRUNCATED / NETWORK_ERROR
+# ===========================================================================
+
+def test_fetch_web_bad_scheme(tmp_path):
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_web("ftp://host/x.fa", tmp_path / "out"))
+    assert ei.value.code == "BAD_SCHEME"
+
+
+def test_fetch_web_disk_full(http_url, tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+    monkeypatch.setattr(sf, "check_disk_space", lambda dest_dir, needed: (False, 0))
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_web(http_url, tmp_path / "out"))
+    assert ei.value.code == "DISK_FULL"
+
+
+def test_fetch_web_truncated(tmp_path, monkeypatch):
+    """断点/不完整下载：aiter_bytes 实收字节 < Content-Length → TRUNCATED。
+
+    用 fake httpx 确定性触发（真实服务器下 httpx 会因短读抛 HTTPError）。
+    """
+    import types as _types
+
+    import httpx as real_httpx
+    from app.services.bioflow import source_fetcher as sf
+
+    class FakeResp:
+        status_code = 200
+        headers = {"content-length": "100"}
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        async def aiter_bytes(self, chunk_size):
+            yield b"short"
+
+    class FakeStream:
+        async def __aenter__(self):
+            return FakeResp()
+
+        async def __aexit__(self, *a):
+            return False
+
+    class FakeClient:
+        def __init__(self, follow_redirects=True):
+            pass
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        def stream(self, method, url, timeout=None):
+            return FakeStream()
+
+    monkeypatch.setattr(sf, "httpx", _types.SimpleNamespace(
+        AsyncClient=FakeClient, Timeout=real_httpx.Timeout, HTTPError=real_httpx.HTTPError,
+    ))
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_web("http://x/y.fa", tmp_path / "out"))
+    assert ei.value.code == "TRUNCATED"
+
+
+def test_fetch_web_network_error(tmp_path, monkeypatch):
+    """网络错误：httpx.HTTPError → NETWORK_ERROR（fake 确定性触发）。"""
+    import types as _types
+
+    import httpx as real_httpx
+    from app.services.bioflow import source_fetcher as sf
+
+    class FailingStream:
+        async def __aenter__(self):
+            raise real_httpx.HTTPError("connection reset")
+
+        async def __aexit__(self, *a):
+            return False
+
+    class FailingClient:
+        def __init__(self, follow_redirects=True):
+            pass
+
+        async def __aenter__(self):
+            return self
+
+        async def __aexit__(self, *a):
+            return False
+
+        def stream(self, method, url, timeout=None):
+            return FailingStream()
+
+    monkeypatch.setattr(sf, "httpx", _types.SimpleNamespace(
+        AsyncClient=FailingClient, Timeout=real_httpx.Timeout, HTTPError=real_httpx.HTTPError,
+    ))
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_web("http://x/y.fa", tmp_path / "out"))
+    assert ei.value.code == "NETWORK_ERROR"
+
+
+# ===========================================================================
+# S0 补强（2）OSS：BAD_OSS / endpoint 解析（内网 http）/ fetch_oss 走 web + kind 修正
+# ===========================================================================
+
+def test_oss_url_bad_format():
+    with pytest.raises(FetchError) as ei:
+        _resolve_oss_url("oss://onlybucket")
+    assert ei.value.code == "BAD_OSS"
+
+
+def test_oss_url_intranet_endpoint_http(monkeypatch):
+    monkeypatch.setenv("BIOFLOW_OSS_ENDPOINT", "oss-internal.example.com")
+    url = _resolve_oss_url("oss://seq-bucket/data/x.fa")
+    assert url == "http://seq-bucket.oss-internal.example.com/data/x.fa"
+
+
+def test_fetch_oss_marks_kind_and_provenance(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+    from pathlib import Path as _Path
+
+    async def fake_web(url, dest_dir, timeout=None):
+        dest = _Path(dest_dir) / "x.fa"
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        dest.write_text(">x\nACGT\n")
+        return {"ok": True, "path": str(dest), "name": "x.fa", "size": 4,
+                "kind": "web", "provenance": {"source": url, "kind": "web",
+                                              "sha256": "0" * 64, "fetched_at": "t"}}
+
+    monkeypatch.setattr(sf, "fetch_web", fake_web)
+    monkeypatch.setenv("BIOFLOW_OSS_ENDPOINT", "oss-cn-hangzhou.aliyuncs.com")
+    r = _run(sf.fetch_oss("oss://b/k.fa", tmp_path / "out"))
+    assert r["ok"] is True
+    assert r["kind"] == "oss"
+    assert r["provenance"]["kind"] == "oss"
+    assert r["provenance"]["oss_spec"] == "oss://b/k.fa"
+
+
+# ===========================================================================
+# S0 补强（3）fetch_source：EMPTY_SOURCE / oss 路由 / aliyuncs 预签名路由
+# ===========================================================================
+
+def test_fetch_source_empty(tmp_path):
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_source("", tmp_path))
+    assert ei.value.code == "EMPTY_SOURCE"
+
+
+def test_fetch_source_oss_routing(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+    calls = []
+
+    async def fake_oss(spec, dest_dir, timeout=None):
+        calls.append(spec)
+        return {"ok": True, "kind": "oss"}
+
+    monkeypatch.setattr(sf, "fetch_oss", fake_oss)
+    r = _run(sf.fetch_source("oss://bucket/k.fa", tmp_path))
+    assert r["kind"] == "oss"
+    assert calls == ["oss://bucket/k.fa"]
+
+
+def test_fetch_source_aliyuncs_presigned_routes_to_oss(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+    calls = []
+
+    async def fake_oss(spec, dest_dir, timeout=None):
+        calls.append(spec)
+        return {"ok": True, "kind": "oss"}
+
+    monkeypatch.setattr(sf, "fetch_oss", fake_oss)
+    presigned = "https://bucket.aliyuncs.com/x.fa?sig=abc"
+    r = _run(sf.fetch_source(presigned, tmp_path))
+    assert r["kind"] == "oss"
+    assert calls == [presigned]
+
+
+# ===========================================================================
+# S0 补强（4）局域网：目录 IS_DIR / scp 拉取 / sshpass 缺失 / scp 失败 / 解析边界
+# ===========================================================================
+
+def test_fetch_lan_dir_rejected(tmp_path):
+    d = tmp_path / "adir"
+    d.mkdir()
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan(str(d), tmp_path / "out"))
+    assert ei.value.code == "IS_DIR"
+
+
+def test_parse_lan_remote_relative_rejected():
+    assert _parse_lan_remote("host:relative/path") is None
+
+
+def test_fetch_lan_scp_success(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+    from pathlib import Path as _Path
+
+    async def fake_scp(*args, **kwargs):
+        dest = _Path(args[-1])
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        dest.write_text(">g\nACGT\n")
+
+        class P:
+            returncode = 0
+
+            async def communicate(self):
+                return (b"", b"")
+
+        return P()
+
+    monkeypatch.setattr(asyncio, "create_subprocess_exec", fake_scp)
+    r = _run(fetch_lan("xzq@192.168.1.5:/data/genome.fa", tmp_path / "out",
+                        credentials={"user": "xzq"}))
+    assert r["ok"] is True
+    assert r["kind"] == "lan"
+    assert r["name"] == "genome.fa"
+
+
+def test_fetch_lan_scp_sshpass_missing(tmp_path, monkeypatch):
+    import shutil
+    from app.services.bioflow import source_fetcher as sf
+    monkeypatch.setattr(shutil, "which", lambda name: None)
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan("host:/data/x.fa", tmp_path / "out", credentials={"password": "p"}))
+    assert ei.value.code == "SSHPASS_MISSING"
+
+
+def test_fetch_lan_scp_failed(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+
+    async def fake_scp(*args, **kwargs):
+        class P:
+            returncode = 1
+
+            async def communicate(self):
+                return (b"", b"scp: no such file")
+
+        return P()
+
+    monkeypatch.setattr(asyncio, "create_subprocess_exec", fake_scp)
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan("host:/data/x.fa", tmp_path / "out"))
+    assert ei.value.code == "LAN_ERROR"
+
+
+def test_scp_fetch_remote_uses_port_and_user(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+    from pathlib import Path as _Path
+    captured = {}
+
+    async def fake_scp(*args, **kwargs):
+        captured["args"] = list(args)
+        dest = _Path(args[-1])
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        dest.write_text(">g\nACGT\n")
+
+        class P:
+            returncode = 0
+
+            async def communicate(self):
+                return (b"", b"")
+
+        return P()
+
+    monkeypatch.setattr(asyncio, "create_subprocess_exec", fake_scp)
+    _run(fetch_lan("host:/data/x.fa", tmp_path / "out",
+                   credentials={"user": "u", "port": "2222"}))
+    # scp -P 2222 u@host:/data/x.fa <dest>
+    assert captured["args"][1] == "-P"
+    assert captured["args"][2] == "2222"
+    assert captured["args"][-2] == "u@host:/data/x.fa"
+
+
+def test_fetch_lan_scp_timeout(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+
+    async def fake_scp(*args, **kwargs):
+        class P:
+            returncode = 0
+
+            async def communicate(self):
+                return (b"", b"")
+
+        return P()
+
+    async def fake_wait_for(coro, timeout=None):
+        coro.close()  # 未 await 的 communicate 协程关闭，避免 never-awaited 警告
+        raise asyncio.TimeoutError()
+
+    monkeypatch.setattr(asyncio, "create_subprocess_exec", fake_scp)
+    monkeypatch.setattr(asyncio, "wait_for", fake_wait_for)
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan("host:/data/x.fa", tmp_path / "out"))
+    assert ei.value.code == "LAN_TIMEOUT"
+
+
+def test_fetch_lan_scp_no_file(tmp_path, monkeypatch):
+    from app.services.bioflow import source_fetcher as sf
+
+    async def fake_scp(*args, **kwargs):
+        # returncode 0 但未产出目标文件
+        class P:
+            returncode = 0
+
+            async def communicate(self):
+                return (b"", b"")
+
+        return P()
+
+    monkeypatch.setattr(asyncio, "create_subprocess_exec", fake_scp)
+    with pytest.raises(FetchError) as ei:
+        _run(fetch_lan("host:/data/x.fa", tmp_path / "out"))
+    assert ei.value.code == "LAN_ERROR"

bioflow_service/uninstall_skill.sh

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+# bioflow_service/uninstall_skill.sh —— 卸载 bioflow-analysis skill（G12）。
+#
+# 用法：bash uninstall_skill.sh [skills_dir]
+#   - 移除 skills_dir/bioflow-analysis/
+set -euo pipefail
+
+HERE="$(cd "$(dirname "$0")" && pwd)"
+SKILL_NAME="bioflow-analysis"
+SKILLS_DIR="${1:-$HERE/../.claude/skills}"
+
+DEST="$SKILLS_DIR/$SKILL_NAME"
+if [ -d "$DEST" ]; then
+  rm -rf "$DEST"
+  echo "[uninstall] removed $DEST"
+else
+  echo "[uninstall] $DEST 不存在（已卸载）"
+fi
+echo "DONE"

deploy/bioflow_switch_restart.sh

@@ -0,0 +1,91 @@
+#!/bin/bash
+# deploy/bioflow_switch_restart.sh —— 切分支后重启生信相关服务并验证
+#
+# 背景：QA(8091)/前端(5180)/bioflow_service(8098) 都是「启动时刻」快照，
+#       切分支后不重启就会跑旧分支的代码/配置（曾导致「设置面板无生信开关」+
+#       「规划降级」两个问题）。本脚本把「切分支→重启→验证」固化，避免再踩。
+#
+# 用法：bash deploy/bioflow_switch_restart.sh [分支名]
+#   分支名缺省 feature/bioflow-skill-orchestration
+#
+# 重启：QA(8091) + bioflow_service(8098) + 前端 vite(5180)
+#   BFF(8090) 不重启：/api/capabilities 每次请求动态拉 QA registry，QA 重启后自动生效
+# 验证：服务健康 + QA registry 生信能力 + 前端 SettingsPanel 生信三开关
+#
+# 关键点（勿删）：
+#   - QA 需 source agent/qa/env/prod.env + 强制 QA_V1_ENABLE_BIOFLOW_AGENT=1（熔断开）
+#   - 8098 裸启动即可：main.py 已内置 load_dotenv，自动加载 bioflow_service/.env
+#   - 前端 pkill 用「zh/PlantAI-rag-new/ui/」精确匹配，避免误杀 5181(wjq 仓库) 的 vite
+set -uo pipefail
+
+ROOT="/home/xzq/5090/teamWorkspace/zh/PlantAI-rag-new"
+VENV="/home/xzq/5090/teamWorkspace/zh/plantai-rag-new-venv/bin/python"
+BRANCH="${1:-feature/bioflow-skill-orchestration}"
+PASS=0; FAIL=0
+
+ok()  { PASS=$((PASS+1)); echo "  ✅ $1"; }
+bad() { FAIL=$((FAIL+1)); echo "  ❌ $1"; }
+
+echo "======== 1. 切分支 ========"
+cd "$ROOT" || { echo "仓库目录不存在: $ROOT"; exit 1; }
+git checkout "$BRANCH" || { echo "切分支失败: $BRANCH"; exit 1; }
+echo "当前分支: $(git branch --show-current)"
+
+echo ""
+echo "======== 2. 重启 QA (8091) ========"
+pkill -f "scripts.qa_v1_1_73_server" 2>/dev/null; sleep 2
+cd "$ROOT/agent/qa"
+set -a; source env/prod.env; set +a
+export QA_V1_ENABLE_BIOFLOW_AGENT=1   # 生信对话熔断开关，切生信分支必须开
+nohup "$VENV" -m uvicorn scripts.qa_v1_1_73_server:app --host 127.0.0.1 --port 8091 \
+  > /tmp/plantai-qa-8091.log 2>&1 < /dev/null &
+disown
+
+echo ""
+echo "======== 3. 重启 bioflow_service (8098) ========"
+pkill -f "app.main:app.*port 8098" 2>/dev/null; sleep 2
+cd "$ROOT/bioflow_service"
+nohup "$VENV" -m uvicorn app.main:app --host 127.0.0.1 --port 8098 \
+  > /tmp/plantai-bioflow-8098.log 2>&1 < /dev/null &
+disown
+
+echo ""
+echo "======== 4. 重启前端 vite (5180) ========"
+pkill -f "zh/PlantAI-rag-new/ui/node_modules/.bin/vite" 2>/dev/null; sleep 2
+cd "$ROOT/ui"
+VITE_BFF_TARGET="http://127.0.0.1:8090" setsid npm run dev \
+  > /tmp/plantai-vite.log 2>&1 < /dev/null &
+disown
+
+echo ""
+echo "等待服务启动 (12s)..."
+sleep 12
+
+echo ""
+echo "======== 5. 验证 ========"
+
+echo "[健康检查]"
+c=$(curl -s -m 3 -o /dev/null -w "%{http_code}" http://127.0.0.1:8098/docs 2>/dev/null)
+[ "$c" = "200" ] && ok "8098 bioflow_service /docs=$c" || bad "8098 bioflow_service /docs=$c（见 /tmp/plantai-bioflow-8098.log）"
+c=$(curl -s -m 3 -o /dev/null -w "%{http_code}" http://127.0.0.1:8091/api/v1/qa-v1-1-73/capabilities/registry 2>/dev/null)
+[ "$c" = "200" ] && ok "8091 QA registry=$c" || bad "8091 QA registry=$c（见 /tmp/plantai-qa-8091.log）"
+c=$(curl -s -m 3 -o /dev/null -w "%{http_code}" http://127.0.0.1:5180/ 2>/dev/null)
+[ "$c" = "200" ] && ok "5180 前端 =$c" || bad "5180 前端 =$c（见 /tmp/plantai-vite.log）"
+
+echo "[生信能力注册]"
+REG=$(curl -s -m 5 http://127.0.0.1:8091/api/v1/qa-v1-1-73/capabilities/registry 2>/dev/null)
+BIO=$(echo "$REG" | grep -o '"name":"bioflow-[a-z-]*"' | wc -l)
+[ "$BIO" -ge 3 ] && ok "QA registry 生信能力 $BIO 个（期望 3）" || bad "QA registry 生信能力仅 $BIO 个（期望 3）"
+
+echo "[前端生信三开关]"
+SW=$(curl -s -m 5 -H "Accept: */*" "http://127.0.0.1:5180/src/components/settings/SettingsPanel.vue" 2>/dev/null | grep -c "settingsBioflow\|bioflowCaps")
+[ "$SW" -ge 2 ] && ok "前端 SettingsPanel 含「生信分析能力」三开关" || bad "前端 SettingsPanel 无生信三开关（可能旧代码，需硬刷新浏览器）"
+
+echo ""
+echo "======== 结果: $PASS 通过 / $FAIL 失败 ========"
+if [ "$FAIL" -eq 0 ]; then
+  echo "✅ 全部就绪。浏览器请 Ctrl+Shift+R 硬刷新（清缓存），再测生信对话。"
+else
+  echo "❌ 有失败项，请查看 /tmp/plantai-qa-8091.log /tmp/plantai-bioflow-8098.log /tmp/plantai-vite.log"
+fi
+exit "$FAIL"

deploy/toggle_bioflow.sh

@@ -0,0 +1,141 @@
+#!/usr/bin/env bash
+# deploy/toggle_bioflow.sh —— 生信能力按需装卸（热，不重启 QA）+ bioflow_service 启停 + 注册状态自检。
+#
+# 用法：
+#   bash deploy/toggle_bioflow.sh <gene-family|rnaseq|extension|all> <on|off>
+#
+# 原理：
+#   - 能力装卸经 BFF POST /api/capabilities/install（透传 QA install_manager，热加载生效不重启 QA）
+#   - on  = register（manifest 校验 + 原子写 capabilities.yaml + registry 差分刷新）
+#   - off = unregister（按 name 移除能力段，其余能力不受影响）
+#   - 自检 = GET /api/capabilities 的 installed 数组是否含对应能力
+#   - bioflow_service 启停：全部能力关闭时停 8098；任一开启时启动 8098
+#   - 卸载活跃任务：三表已持久化，服务恢复后 runner.recover 续跑；QA 侧按「生信服务未启动」降级话术
+set -uo pipefail
+
+BFF="http://127.0.0.1:8090"
+BIOFLOW_SERVICE_DIR="/home/xzq/5090/teamWorkspace/zh/PlantAI-rag-new/bioflow_service"
+PY="/home/xzq/5090/teamWorkspace/zh/plantai-rag-new-venv/bin/python"
+BIOFLOW_PORT="${BIOFLOW_PORT:-8098}"
+
+CAP="${1:-}"
+ACTION="${2:-}"
+
+CAPS=(gene-family rnaseq extension)
+
+usage() {
+  echo "用法: $0 <gene-family|rnaseq|extension|all> <on|off>" >&2
+  exit 2
+}
+
+# capability key -> registry 能力名
+cap_name() {
+  case "$1" in
+    gene-family) echo "bioflow-gene-family" ;;
+    rnaseq)      echo "bioflow-rnaseq" ;;
+    extension)   echo "bioflow-extension" ;;
+    *) usage ;;
+  esac
+}
+
+# capability key -> register manifest YAML（与 agent/qa/configs/capabilities.yaml 一致）
+manifest() {
+  case "$1" in
+    gene-family) cat <<'YAML'
+capabilities:
+  - name: bioflow-gene-family
+    provider: mcp
+    permission: read_only
+    description: 基因家族分析（路径规划/建任务/参数确认/文件获取与预处理/状态查询），自然语言触发
+    session_default: true
+    nl_triggers: [基因家族, 家族成员, 亚家族, 系统发育, 建树, 进化树, 保守基序, motif, 结构域, 基因结构, 共线性, Ka/Ks, 选择压力, 组合证据]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/gene-family/
+    prompt_pack:
+      file: bioflow_gene_family_agent_rules.md
+YAML
+    ;;
+    rnaseq) cat <<'YAML'
+capabilities:
+  - name: bioflow-rnaseq
+    provider: mcp
+    permission: read_only
+    description: 转录组分析（实验设计确认/样本配置/路径规划/建任务/差异表达/富集），自然语言触发
+    session_default: true
+    nl_triggers: [转录组, RNA-seq, RNAseq, rnaseq, 差异表达, 表达定量, 富集, WGCNA, GSEA, 实验设计, fastq]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/rnaseq/
+    prompt_pack:
+      file: bioflow_rnaseq_agent_rules.md
+YAML
+    ;;
+    extension) cat <<'YAML'
+capabilities:
+  - name: bioflow-extension
+    provider: mcp
+    permission: read_only
+    description: 用户自定义扩展分析（创建/转换/试运行/校验/发布/运行），自然语言触发
+    session_default: true
+    nl_triggers: [扩展, 拓展分析, 扩展分析, 自定义分析, 分析模板, 分析脚本, 分析工具]
+    mcp:
+      url: http://127.0.0.1:8098/mcp/extension/
+    prompt_pack:
+      file: bioflow_extension_agent_rules.md
+YAML
+    ;;
+    *) usage ;;
+  esac
+}
+
+[ -n "$CAP" ] && [ -n "$ACTION" ] || usage
+[ "$ACTION" = "on" ] || [ "$ACTION" = "off" ] || usage
+if [ "$CAP" != "all" ]; then
+  cap_name "$CAP" >/dev/null 2>&1 || usage
+fi
+
+# 1. 逐能力 register/unregister（热加载不重启 QA）
+targets=("$CAP")
+[ "$CAP" = "all" ] && targets=("${CAPS[@]}")
+for key in "${targets[@]}"; do
+  name="$(cap_name "$key")"
+  if [ "$ACTION" = "on" ]; then
+    body="$(manifest "$key")"
+    resp=$(curl -s -m 30 -X POST "$BFF/api/capabilities/install" \
+      -H 'Content-Type: application/json' \
+      -d "$(python3 -c 'import json,sys; print(json.dumps({"action":"register","manifest":sys.stdin.read()}))' <<<"$body")")
+  else
+    resp=$(curl -s -m 30 -X POST "$BFF/api/capabilities/install" \
+      -H 'Content-Type: application/json' \
+      -d "{\"action\":\"unregister\",\"name\":\"$name\"}")
+  fi
+  echo "[$ACTION] $name -> $(echo "$resp" | head -c 300)"
+done
+
+# 2. 自检：GET /api/capabilities 的 installed 数组
+installed=$(curl -s -m 10 "$BFF/api/capabilities")
+echo "注册状态: $(echo "$installed" | python3 -c 'import json,sys; d=json.load(sys.stdin); print([i.get("name") for i in d.get("installed") or []])' 2>/dev/null || echo 'parse-fail')"
+
+# 3. bioflow_service 按需启停：任一能力开启则启动，全部关闭则停止
+any_on=false
+for key in "${CAPS[@]}"; do
+  name="$(cap_name "$key")"
+  if echo "$installed" | grep -q "\"$name\""; then
+    any_on=true
+  fi
+done
+
+if [ "$any_on" = true ]; then
+  if ! lsof -ti tcp:$BIOFLOW_PORT -sTCP:LISTEN >/dev/null 2>&1; then
+    echo "启动 bioflow_service :$BIOFLOW_PORT"
+    ( cd "$BIOFLOW_SERVICE_DIR" && setsid "$PY" -m uvicorn app.main:app --host 127.0.0.1 --port "$BIOFLOW_PORT" \
+      > /tmp/plantai-bioflow.log 2>&1 < /dev/null & ) && disown -a
+    sleep 2
+  fi
+  curl -s -m 8 "http://127.0.0.1:$BIOFLOW_PORT/api/bioflow/health" | head -c 150
+  echo
+else
+  echo "全部能力已卸载：停止 bioflow_service :$BIOFLOW_PORT"
+  kill $(lsof -ti tcp:$BIOFLOW_PORT -sTCP:LISTEN) 2>/dev/null || true
+fi
+
+echo "DONE"

docs/MANUAL_TEST_BIOFLOW_DIALOGUE.md

@@ -0,0 +1,177 @@
+# 生信流程 · 对话式手工测试手册（S6 更新版）
+
+> 供用户逐项实测。生信模块已从「卡片式交互」改造为「自然语言对话式交互 + MCP 外挂」，
+> 本手册以**对话剧本**形式给出每个场景的：对话示例 → 系统应如何回应 → 通过判据。
+> 环境：内网 http://192.168.0.175:8090（BFF）；生信服务 8098、QA 8091 已部署；
+> 三能力（基因家族/转录组/扩展）按 §0 装卸。
+
+---
+
+## 0. 前置条件
+
+1. 浏览器打开 http://192.168.0.175:8090。
+2. **能力安装检查**：设置面板（SettingsPanel）应能看到三个生信开关（基因家族/转录组/扩展）。
+   打开任意一个后，工作区出现「生信任务」「生信档案」TAB；全关则 TAB 消失（**TAB 显隐 = 能力注册状态**，非服务健康）。
+3. 服务器 docker 已有 8 个 bioflow 镜像；金标数据在 `bioflow_kernel/assets/examples/test_input/`（Ft 四件套 pep/cds/genome/gff3）。
+4. 熔断开关：`QA_V1_ENABLE_BIOFLOW_AGENT=1`（默认 0，关时生信句走普通 QA）。
+
+---
+
+## 1. 多配置开关回归（S6）
+
+| 配置 | 操作 | 期望 | 判据 |
+|---|---|---|---|
+| 全关（熔断=0 + 三能力卸载） | 发「帮我做基因家族分析」 | 普通 QA 礼貌回答（说明未安装生信能力），**无**路径卡 | 无生信分流 |
+| 只开基因家族 | 发「帮我做基因家族分析」 | 进入生信对话（列路径+挂路径卡） | 命中 |
+| 只开基因家族 | 发「帮我做转录组差异表达」 | 走普通 QA（转录组能力未装） | 不响应 |
+| 只开转录组 | 发「帮我做转录组」 | 进入生信对话 | 命中 |
+| 只开转录组 | 发「帮我做基因家族分析」 | 走普通 QA | 不响应 |
+| 全开但非生信提问 | 发「光合作用的电子传递链是什么」 | 走普通 QA（非生信意图不调工具） | 不调工具 |
+
+---
+
+## 2. 对话剧本 A：基因家族分析（卡片辅助通道）
+
+**第 1 轮 —— 需求与路径**
+> 用户：帮我做水稻 SPL 基因家族分析
+> 系统（自然语言）：列「核心流程（必选）+ 可选分析」，说明每个可选项生物学意义；
+> **同帧挂出路径选择卡**。
+> 判据：回复含路径列表 + 路径卡出现（卡片不替代自然语言）。
+
+**第 2 轮 —— 卡片操作 → 系统复述**
+> 用户（路径卡勾选「核心流程 + Ka/Ks + 启动子」，点确认；打字补充文件位置）
+> 系统：先自然语言**复述**用户选择（"您选择了核心流程 + Ka/Ks + 启动子分析…"），再请确认。
+> 判据：系统复述内容与卡片勾选一致；建任务前必有一轮复述确认（不直接建任务）。
+
+**第 3 轮 —— 网络文件 + 非标准文件预处理**
+> 用户：文件在 `https://…/rice.fa` 与 `oss://seq-bucket/rice.gff3`，另传 `spl_list.xlsx`
+> 系统：拉取 web/OSS 文件（**下载前检查磁盘余量、记录 provenance**）；对 `spl_list.xlsx`
+> 做内容嗅探后**自然语言说明列结构并提问**（"推测第二列是蛋白序列，备注列忽略？"）。
+> 判据：文件获取成功；Excel 触发预处理提问（列表方式，可卡片点选也可打字回答）。
+
+**第 4 轮 —— 建任务执行**
+> 用户：都对，备注列不要；确认，开始吧
+> 系统：复述整理结果（"已整理为 FASTA 3 条序列"）→ 创建任务 → 消息内出现**只读精简进度块**，
+> 右侧「生信任务」TAB 完整滚动日志实时跟随。
+> 判据：进度块只读（无按钮）；TAB 日志自动滚底。
+
+**执行中 —— 进度转述 + 随时提问**
+> 用户：什么是组合证据？
+> 系统：经流程知识库自然语言回答（带引用），**不打断任务**。
+> 判据：提问得到引用回答，任务继续推进。
+
+**人工确认边界（不可跳过）**
+> 系统：第 8 步亚家族预测完成（6 个亚家族）。⚠ 需您人工确认，我不能代您确认。
+> 用户：把 SPL3 从亚家族 A 移到 B → 系统复述修改 → 用户「确认」。
+> 判据：subfamily_confirm 必停、必复述、绝不代确认。
+
+**收尾 —— 存档**
+> 系统：全部完成（19 成员 6 亚家族），同帧挂出存档卡。
+> 用户（存档卡填名称点「存档」或打字「存档，叫 SPL 水稻鉴定」）
+> 系统：实际执行 `archive_job` 存档（复用 REST 语义），复述存档三要素（名称/位置/大小）。
+> 判据：存档成功（重名提示 ARCHIVE_EXISTS）。
+
+---
+
+## 3. 对话剧本 B：转录组分析（纯自然语言通道，全程不点卡片）
+
+**第 1 轮 —— 必确认信息**
+> 用户：帮我做转录组，比较干旱处理和对照
+> 系统：列主流程 + 可选；**必须确认**四项（物种/参考基因组版本、FASTQ 单双端、
+> 对照处理组重复数、链特异性），列表展示。
+> 判据：实验设计确认边界被明确列出，未确认前不得建差异表达任务。
+
+**第 2 轮 —— OSS 文件 + 样本信息（纯打字，不点卡）**
+> 用户：数据在 oss://seq-bucket/drought/，水稻日本晴，干旱 3 重复对照 3 重复，双端非链特异
+> 系统：从 OSS 拉取 12 个 FASTQ 并核对成对；复述样本设计（"干旱 3 vs 对照 3，双端，非链特异"），
+> 请确认基线（对照为基线、比较方向「干旱 vs 对照」）。
+> 判据：纯自然语言路径走通（**卡片与打字两条通道服务端语义一致**）。
+
+**第 3 轮 —— 执行 + 结果转述**
+> 用户：对 → 系统执行 QC→比对→定量→样本质控→差异表达→富集，逐段转述（接头率/Q30/唯一比对率/差异基因数/PCA 分离）。
+> 判据：每步完成后自然语言转述关键指标；样本质控 PCA 结论有转述。
+
+---
+
+## 4. 三种网络文件来源用例
+
+| 来源 | 示例 | 期望 |
+|---|---|---|
+| web | 「文件在 https://…/x.fa」 | httpx 流式下载，不设大小上限；下载前查磁盘余量；记录 provenance |
+| OSS | 「数据在 oss://bucket/key 或预签名 URL」 | 经 BIOFLOW_OSS_ENDPOINT 解析或预签名直通；无 endpoint 时提示改用预签名 |
+| 局域网 | 「文件在 192.168.x.x:/data/x.fa，账号 xx 密码 xx」 | ssh/scp 拉取（凭据单次会话内存用，不落盘、审计不记明文） |
+
+判据：文件落 `bioflow_data/jobs/{job}/input/`，先内容嗅探后登记，provenance 记录来源/哈希/时间。
+
+---
+
+## 5. 非标准文件预处理（Excel / 乱码文本）闭环
+
+1. 上传 `xxx.xlsx` / 乱码 txt → 系统 `inspect_file` 探测（列结构/格式猜测/乱码检测）。
+2. 系统自然语言说明 + 列表提问（哪列是序列、是否去重、是否去表头）。
+3. 用户回答 → `transform_file` 转换（LLM 定规则 + 脚本执行，大文件抽样定规则）。
+4. 结果过格式验证器（fasta 可解析/gff3 9 列/tsv 列一致/samples.yaml schema）；
+   失败说明问题并追问，循环 ≤3 次后建议人工整理。
+5. 转换后 `register_job_files` 登记，provenance 记「原始→规则→产物」链。
+
+判据：全程自然语言引导；转换产物格式校验通过；原文件永不覆盖。
+
+---
+
+## 6. 卡片辅助 vs 纯自然语言双通道等价
+
+| 场景 | 卡片通道 | 纯 NL 通道 | 等价判据 |
+|---|---|---|---|
+| 路径选择 | 路径卡勾选 | 打字「核心流程 + Ka/Ks」 | 两者复述的确认内容一致，建任务入参一致 |
+| 参数确认 | 参数卡填值 | 打字「用 8 核、padj 用 0.01」 | confirm_stage 入参一致 |
+| 文件提供 | 文件卡拖拽/填路径 | 打字「文件在 …」 | register_job_files / fetch_source_file 入参一致 |
+| 存档 | 存档卡点存档 | 打字「存档，叫 X」 | archive_job 入参一致 |
+
+判据：卡片操作产生的是 `card_result` 结构化消息进 QA 流（**不直连 bioflow 控制面**），
+与打字在服务端语义完全一致（QA 对话状态机是唯一决策点）。
+
+---
+
+## 7. 旧会话兼容（Legacy 块只读）
+
+1. 打开一个改造前创建、含旧生信块（bioflow_qa / 旧 bioflow_* 块）的会话。
+2. 期望：旧块以只读形式降级渲染（标题 + 只读引用/提示），**不报错、无可交互控件**。
+
+---
+
+## 8. 扩展子系统对话化（第三能力单元）
+
+1. 打开「扩展」能力开关。
+2. 对话创建扩展：描述分析脚本（代码文件 + 运行命令）→ `create_extension`（draft）。
+3. `build` → `trial_run` → `validate` → `confirm` → `publish` → `run` 逐步走（卡片或打字等价）。
+4. 试运行失败 → 「AI 修复」触发 `repair_extension`（修复上限 20 轮）；校验失败/状态不足时系统给出确定性提示。
+
+判据：扩展生命周期全程对话化；非法状态返回清晰提示（EXT_STATUS），不报 500。
+
+---
+
+## 9. 后端金标验证（服务器命令行，S6 回归）
+
+```bash
+cd /home/xzq/5090/teamWorkspace/zh/PlantAI-rag-new
+BIOFLOW_DATA=/home/xzq/5090/teamWorkspace/zh/bioflow-data \
+  bash bioflow_kernel/tests/smoke_golden.sh bioflow-gf:dev
+```
+
+期望：4 步全绿——python 3.11.14 / ldd 0 缺库 / 无 conda / 金标 identify 24 ID diff 空（`GOLDEN_DIFF_OK 24 IDs`）。
+
+---
+
+## 10. 端到端主线（一次性走全流程，双通道各一遍）
+
+1. 卡片通道：§2 全程（路径卡→文件卡→参数卡→进度块→存档卡）。
+2. 纯 NL 通道：§3 全程（不点任何卡片）。
+3. 含一次 Excel 预处理、一次局域网/OSS 文件拉取。
+4. 任务完成后存档 → 生信档案 TAB 回看 → 复用发起。
+
+期望：两条通道均走通，7 项引导（路径/文件/参数/报告/存档/复用/过程展示）逐项达成，
+进度块实时流转、右侧日志滚底。
+
+---
+
+*本手册为 S6 对话式改造更新版，替代旧卡片式 `MANUAL_TEST_BIOFLOW.md` 的生信流程部分。*

sdk/app/routers/qa.py

@@ -286,11 +286,21 @@ async def _inject_history(body: Optional[dict]) -> tuple[dict, bool]:
         history = await assemble_history(bff_db, session_id)
         if history:
             body["history"] = history
-        # 会话开关注入上游（web_search/superpowers 经 QA 门控/注入点生效）
+        # 会话开关注入上游（web_search/superpowers/bioflow 经 QA 门控/注入点生效）
         body["capabilities"] = {
             "web_search": bool(caps.get("web_search", False)),
             "superpowers": bool(caps.get("superpowers", False)),
+            "bioflow": bool(caps.get("bioflow", False)),
         }
+        # session↔job 绑定（S2）：meta.bioflow = {active_job_id, chain} 注入上游，
+        # 供 BioflowAgent 复用当前任务（job_status 是任务真相唯一权威）。
+        bioflow_meta = meta.get("bioflow")
+        if isinstance(bioflow_meta, dict):
+            body["bioflow"] = {
+                "session_id": session_id,
+                "active_job_id": str(bioflow_meta.get("active_job_id") or ""),
+                "chain": str(bioflow_meta.get("chain") or ""),
+            }
         humanize = bool(caps.get("humanize", False))
     except Exception as exc:
         logger.warning("多轮记忆注入失败（降级为无历史）: %s", exc)

sdk/app/routers/sessions.py

@@ -30,7 +30,7 @@ from ..schemas import (
     SessionOut,
     SessionPatch,
 )
-from ..services.capabilities import sanitize_capabilities
+from ..services.capabilities import sanitize_bioflow_meta, sanitize_capabilities
 from ..upstream import envelope
 
 logger = logging.getLogger(__name__)
@@ -159,11 +159,17 @@ async def patch_session(
         )
     if payload.meta is not None:
         caps = sanitize_capabilities(payload.meta.get("capabilities"))
-        if caps:
+        has_bioflow = "bioflow" in payload.meta
+        bioflow_patch = sanitize_bioflow_meta(payload.meta.get("bioflow"))
+        if caps or has_bioflow:
             meta = session.meta.model_dump()
-            merged_caps = dict(meta.get("capabilities") or {})
-            merged_caps.update(caps)
-            meta["capabilities"] = merged_caps
+            if caps:
+                merged_caps = dict(meta.get("capabilities") or {})
+                merged_caps.update(caps)
+                meta["capabilities"] = merged_caps
+            if has_bioflow:
+                # None 表示「清空绑定」（前端传 bioflow: {} 或 null）
+                meta["bioflow"] = bioflow_patch
             await db.execute(
                 "UPDATE sessions SET meta = ?, updated_at = ? WHERE id = ?",
                 (dumps_json(meta), _db_now(), session_id),

sdk/app/schemas.py

@@ -393,6 +393,8 @@ class GraphData(BaseModel):
 class SessionMeta(BaseModel):
     title_manual: bool = False
     capabilities: dict[str, bool] = Field(default_factory=dict)
+    # S2 session↔job 绑定：{active_job_id, chain}，由 QA 流 complete 回填、前门注入
+    bioflow: dict[str, Any] | None = None
 
 
 class SessionCreate(BaseModel):

sdk/app/services/capabilities.py

@@ -39,6 +39,13 @@ MANIFEST: Dict[str, Dict[str, Any]] = {
         "provider": "qa_gateway",
         "session_default": False,
     },
+    "bioflow": {
+        "name": "bioflow",
+        "label": "生信对话式分析",
+        "description": "自然语言对话式生信分析（基因家族/转录组，MCP 外挂，热装卸）",
+        "provider": "qa_gateway",
+        "session_default": False,
+    },
     "mcp_plugins": {
         "name": "mcp_plugins",
         "label": "MCP 插件",
@@ -55,7 +62,7 @@ DEFAULTS: Dict[str, bool] = {
 }
 
 # 会话 meta.capabilities 白名单（允许 PATCH 写入的键）
-SESSION_KEYS = ("memory", "web_search", "humanize")
+SESSION_KEYS = ("memory", "web_search", "humanize", "bioflow")
 
 
 def sanitize_capabilities(raw: Any) -> Dict[str, bool]:
@@ -75,6 +82,21 @@ def sanitize_capabilities(raw: Any) -> Dict[str, bool]:
     return out
 
 
+def sanitize_bioflow_meta(raw: Any) -> Dict[str, str] | None:
+    """S2 session↔job 绑定白名单：只收 {active_job_id, chain} 两个字符串键。
+
+    返回 None 表示「无有效绑定（清空/不改）」；调用方据此决定是否写 meta.bioflow。
+    """
+    if not isinstance(raw, dict):
+        return None
+    out: Dict[str, str] = {}
+    if raw.get("active_job_id") not in (None, ""):
+        out["active_job_id"] = str(raw.get("active_job_id"))[:128]
+    if raw.get("chain") not in (None, ""):
+        out["chain"] = str(raw.get("chain"))[:64]
+    return out or None
+
+
 def merged_capabilities(
     session_caps: Dict[str, bool] | None,
     qa_registry: List[Dict[str, Any]] | None = None,

sdk/app/test_capabilities_svc.py

@@ -10,6 +10,7 @@ from app.services.capabilities import (  # noqa: E402
     DEFAULTS,
     MANIFEST,
     merged_capabilities,
+    sanitize_bioflow_meta,
     sanitize_capabilities,
 )
 
@@ -50,3 +51,39 @@ class TestMerged:
         )
         assert body["installed"] == [{"name": "web_search", "description": "x"}]
         assert body["load_warnings"] == ["bad entry skipped"]
+
+
+# ===========================================================================
+# S2 sanitize_bioflow_meta（session↔job 绑定白名单）
+# ===========================================================================
+
+class TestSanitizeBioflowMeta:
+    def test_valid(self):
+        assert sanitize_bioflow_meta({"active_job_id": "job-1", "chain": "gene_family"}) == {
+            "active_job_id": "job-1",
+            "chain": "gene_family",
+        }
+
+    def test_evil_key_dropped(self):
+        assert sanitize_bioflow_meta({"active_job_id": "j", "chain": "c", "evil": "x"}) == {
+            "active_job_id": "j",
+            "chain": "c",
+        }
+
+    def test_non_dict_returns_none(self):
+        assert sanitize_bioflow_meta(None) is None
+        assert sanitize_bioflow_meta("x") is None
+        assert sanitize_bioflow_meta(["a"]) is None
+
+    def test_empty_or_null_returns_none(self):
+        assert sanitize_bioflow_meta({}) is None
+        assert sanitize_bioflow_meta({"active_job_id": "", "chain": ""}) is None
+        assert sanitize_bioflow_meta({"active_job_id": None, "chain": None}) is None
+
+    def test_partial(self):
+        assert sanitize_bioflow_meta({"active_job_id": "j"}) == {"active_job_id": "j"}
+        assert sanitize_bioflow_meta({"chain": "c"}) == {"chain": "c"}
+
+    def test_truncation(self):
+        assert sanitize_bioflow_meta({"active_job_id": "x" * 200})["active_job_id"] == "x" * 128
+        assert sanitize_bioflow_meta({"chain": "y" * 100})["chain"] == "y" * 64

sdk/app/test_qa_inject_history.py

@@ -0,0 +1,101 @@
+"""test_qa_inject_history.py —— _inject_history 的 bioflow 注入单测（S2）。
+
+覆盖：session↔job 绑定（meta.bioflow）注入 body["bioflow"]、capabilities.bioflow 开关注入、
+memory 关跳过、显式 history 优先、会话不存在原样返回。
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
+
+from app.routers import qa as qa_mod  # noqa: E402
+
+
+class FakeRow(dict):
+    """aiosqlite.Row 最小替身。"""
+
+    def __getattr__(self, key):
+        return self[key]
+
+
+class FakeDB:
+    def __init__(self, row=None):
+        self.row = row
+
+    async def fetchone(self, sql, params):
+        return self.row
+
+
+@pytest.mark.asyncio
+async def test_inject_bioflow_binding(monkeypatch):
+    import app.db as db_mod
+
+    row = FakeRow(meta='{"capabilities": {"bioflow": true, "memory": true}, '
+                      '"bioflow": {"active_job_id": "job-1", "chain": "gene_family"}}')
+    monkeypatch.setattr(db_mod, "db", FakeDB(row))
+
+    async def fake_assemble(db, session_id):
+        return [{"role": "user", "content": "上轮"}, {"role": "assistant", "content": "上答"}]
+
+    monkeypatch.setattr(qa_mod, "assemble_history", fake_assemble)
+    body, humanize = await qa_mod._inject_history({"session_id": "s1", "question": "继续"})
+    assert body["bioflow"] == {"session_id": "s1", "active_job_id": "job-1", "chain": "gene_family"}
+    assert body["capabilities"] == {"web_search": False, "superpowers": False, "bioflow": True}
+    assert body["history"] == [{"role": "user", "content": "上轮"}, {"role": "assistant", "content": "上答"}]
+    assert humanize is False
+
+
+@pytest.mark.asyncio
+async def test_no_bioflow_meta_injects_nothing(monkeypatch):
+    import app.db as db_mod
+
+    row = FakeRow(meta='{"capabilities": {"memory": true}}')  # 无 bioflow 绑定
+    monkeypatch.setattr(db_mod, "db", FakeDB(row))
+
+    async def fake_assemble(db, session_id):
+        return [{"role": "user", "content": "上轮"}]
+
+    monkeypatch.setattr(qa_mod, "assemble_history", fake_assemble)
+    body, _ = await qa_mod._inject_history({"session_id": "s1"})
+    assert "bioflow" not in body
+    assert body["capabilities"]["bioflow"] is False  # 未开 bioflow 开关
+
+
+@pytest.mark.asyncio
+async def test_memory_off_skips_injection(monkeypatch):
+    import app.db as db_mod
+
+    row = FakeRow(meta='{"capabilities": {"memory": false, "bioflow": true}, '
+                      '"bioflow": {"active_job_id": "j"}}')
+    monkeypatch.setattr(db_mod, "db", FakeDB(row))
+    body, _ = await qa_mod._inject_history({"session_id": "s1"})
+    assert "bioflow" not in body
+    assert "capabilities" not in body
+
+
+@pytest.mark.asyncio
+async def test_session_not_found_returns_body_unchanged(monkeypatch):
+    import app.db as db_mod
+
+    monkeypatch.setattr(db_mod, "db", FakeDB(None))  # fetchone → None
+    body, _ = await qa_mod._inject_history({"session_id": "s1", "question": "q"})
+    assert body == {"question": "q"}  # session_id 被 pop，其余原样
+
+
+@pytest.mark.asyncio
+async def test_explicit_history_takes_priority(monkeypatch):
+    body, _ = await qa_mod._inject_history(
+        {"session_id": "s1", "history": [{"role": "user", "content": "x"}]}
+    )
+    assert body["history"] == [{"role": "user", "content": "x"}]
+    assert "bioflow" not in body  # 显式 history 优先 → 不读 meta
+
+
+@pytest.mark.asyncio
+async def test_no_session_id_returns_body_unchanged(monkeypatch):
+    body, _ = await qa_mod._inject_history({"question": "q"})
+    assert body == {"question": "q"}

sdk/app/test_sessions_api.py

@@ -73,7 +73,7 @@ def test_session_crud_full_flow(client):
     assert sess["title"] == "新会话"
     assert sess["status"] == "idle"
     assert sess["message_count"] == 0
-    assert sess["meta"] == {"title_manual": False, "capabilities": {}}
+    assert sess["meta"] == {"title_manual": False, "capabilities": {}, "bioflow": None}
 
     r2 = client.post("/api/sessions", json={"title": "  水稻SPL  "})
     sess2 = r2.json()
@@ -132,7 +132,7 @@ def test_session_crud_full_flow(client):
     # PATCH 会话标题 → title_manual=true
     r = client.patch(f"/api/sessions/{sess['id']}", json={"title": "手工标题"})
     assert r.status_code == 200
-    assert r.json()["meta"] == {"title_manual": True, "capabilities": {}}
+    assert r.json()["meta"] == {"title_manual": True, "capabilities": {}, "bioflow": None}
 
     # PATCH 会话状态
     r = client.patch(f"/api/sessions/{sess['id']}", json={"status": "done"})
@@ -149,6 +149,29 @@ def test_session_crud_full_flow(client):
     assert body["error"]["code"] == "NOT_FOUND"
 
 
+def test_session_bioflow_binding_patch(client):
+    """S2 session↔job 绑定：PATCH meta.bioflow 白名单落库 + 串行往返。"""
+    r = client.post("/api/sessions", json={})
+    sess = r.json()
+    assert r.status_code == 201, r.text
+
+    # 只收 active_job_id / chain 两个键，非法键丢弃
+    r = client.patch(f"/api/sessions/{sess['id']}", json={
+        "meta": {"bioflow": {"active_job_id": "job-42", "chain": "gene_family", "evil": "x"}}
+    })
+    assert r.status_code == 200, r.text
+    assert r.json()["meta"]["bioflow"] == {"active_job_id": "job-42", "chain": "gene_family"}
+
+    # 回读持久化
+    r = client.get(f"/api/sessions/{sess['id']}")
+    assert r.json()["meta"]["bioflow"] == {"active_job_id": "job-42", "chain": "gene_family"}
+
+    # 空 dict → 清空绑定
+    r = client.patch(f"/api/sessions/{sess['id']}", json={"meta": {"bioflow": {}}})
+    assert r.status_code == 200
+    assert r.json()["meta"]["bioflow"] is None
+
+
 def test_not_found_envelopes(client):
     cases = [
         ("get", "/api/sessions/nope", None),

tests/frontend/unit/bioflow/benchpanel.bioflow.test.js

@@ -8,6 +8,10 @@ import { mount, flushPromises } from '@vue/test-utils';
 import { createPinia, setActivePinia } from 'pinia';
 import { useBenchStore } from '../../../../ui/src/stores/bench.js';
 
+vi.mock('../../../../ui/src/api/capabilities.js', () => ({
+  getCapabilities: vi.fn(async () => ({ installed: [{ name: 'bioflow-gene-family' }] })),
+}));
+
 vi.mock('../../../../ui/src/api/bioflow.js', () => ({
   bioflowHealth: vi.fn(async () => ({ ok: true, status: 'ok', db: { connected: true } })),
   listBioflowJobs: vi.fn(async () => ({ ok: true, data: { items: [], total: 0 } })),
@@ -68,6 +72,7 @@ vi.mock('../../../../ui/src/api/qa.js', () => ({
 import BenchPanel from '../../../../ui/src/components/bench/BenchPanel.vue';
 import { useBioflowStore } from '../../../../ui/src/stores/bioflow.js';
 import * as bioflowApi from '../../../../ui/src/api/bioflow.js';
+import * as capabilitiesApi from '../../../../ui/src/api/capabilities.js';
 
 describe('BenchPanel 生信 TAB 探活显隐（FR-BIO-025）', () => {
   let pinia;
@@ -78,14 +83,15 @@ describe('BenchPanel 生信 TAB 探活显隐（FR-BIO-025）', () => {
   });
 
   it('探活成功：五个既有 TAB + 生信任务/生信档案两 TAB（TC-BIO-JOB-001/PANE-001）', async () => {
+    capabilitiesApi.getCapabilities.mockResolvedValueOnce({ installed: [{ name: 'bioflow-gene-family' }] });
     const w = mount(BenchPanel, { global: { plugins: [pinia] } });
     await flushPromises();
     const labels = w.findAll('.bench-tab').map((t) => t.text());
     expect(labels).toEqual(['检索过程', '文献来源', '提取任务', '知识图谱', '文档', '生信任务', '生信档案']);
   });
 
-  it('探活失败（health 不可达）：生信 TAB 不渲染（TC-BIO-JOB-012/PANE-013）', async () => {
-    bioflowApi.bioflowHealth.mockRejectedValueOnce(new Error('down'));
+  it('能力未注册：生信 TAB 不渲染（S3 主信号 = 能力注册状态）', async () => {
+    capabilitiesApi.getCapabilities.mockResolvedValueOnce({ installed: [] });
     const w = mount(BenchPanel, { global: { plugins: [pinia] } });
     await flushPromises();
     const labels = w.findAll('.bench-tab').map((t) => t.text());
@@ -94,13 +100,23 @@ describe('BenchPanel 生信 TAB 探活显隐（FR-BIO-025）', () => {
     expect(labels).not.toContain('生信档案');
   });
 
-  it('探活恢复：强制重探后 TAB 出现（TC-BIO-JOB-013/PANE-014）', async () => {
+  it('已注册但 health 不可达：TAB 仍显示（次信号不影响显隐）', async () => {
+    capabilitiesApi.getCapabilities.mockResolvedValueOnce({ installed: [{ name: 'bioflow-gene-family' }] });
     bioflowApi.bioflowHealth.mockRejectedValueOnce(new Error('down'));
     const w = mount(BenchPanel, { global: { plugins: [pinia] } });
     await flushPromises();
+    const labels = w.findAll('.bench-tab').map((t) => t.text());
+    expect(labels).toContain('生信任务');
+    expect(labels).toContain('生信档案');
+  });
+
+  it('探活恢复：能力注册后强制重探 TAB 出现（TC-BIO-JOB-013/PANE-014）', async () => {
+    capabilitiesApi.getCapabilities.mockResolvedValueOnce({ installed: [] });
+    const w = mount(BenchPanel, { global: { plugins: [pinia] } });
+    await flushPromises();
     expect(w.findAll('.bench-tab').map((t) => t.text())).not.toContain('生信任务');
-    // 服务恢复：强制重探
-    bioflowApi.bioflowHealth.mockResolvedValueOnce({ ok: true });
+    // 能力安装：强制重探
+    capabilitiesApi.getCapabilities.mockResolvedValueOnce({ installed: [{ name: 'bioflow-gene-family' }] });
     const bioflow = useBioflowStore();
     await bioflow.probe({ force: true });
     await flushPromises();
@@ -109,6 +125,7 @@ describe('BenchPanel 生信 TAB 探活显隐（FR-BIO-025）', () => {
   });
 
   it('切到生信任务 TAB：渲染 BioJobsPane（TC-BIO-JOB-001）', async () => {
+    capabilitiesApi.getCapabilities.mockResolvedValueOnce({ installed: [{ name: 'bioflow-gene-family' }] });
     const w = mount(BenchPanel, { global: { plugins: [pinia] } });
     await flushPromises();
     const biojobsTab = w.findAll('.bench-tab').find((t) => t.text() === '生信任务');
@@ -119,6 +136,7 @@ describe('BenchPanel 生信 TAB 探活显隐（FR-BIO-025）', () => {
   });
 
   it('切到生信档案 TAB：渲染 BioArchivePane（TC-BIO-PANE-001）', async () => {
+    capabilitiesApi.getCapabilities.mockResolvedValueOnce({ installed: [{ name: 'bioflow-gene-family' }] });
     const w = mount(BenchPanel, { global: { plugins: [pinia] } });
     await flushPromises();
     const bioarchiveTab = w.findAll('.bench-tab').find((t) => t.text() === '生信档案');

tests/frontend/unit/bioflow/bioflow.store.test.js

@@ -13,6 +13,11 @@ import {
   STAGE_STATUS_BY_EVENT,
 } from '../../../../ui/src/stores/bioflow.js';
 
+// mock api/capabilities.js（S3 双信号主信号源）
+vi.mock('../../../../ui/src/api/capabilities.js', () => ({
+  getCapabilities: vi.fn(async () => ({ installed: [{ name: 'bioflow-gene-family' }] })),
+}));
+
 // mock api/bioflow.js（SSE 用 mock，不依赖生产服务；vi.mock 工厂内不得引用顶层变量）
 vi.mock('../../../../ui/src/api/bioflow.js', () => ({
   bioflowHealth: vi.fn(async () => ({ ok: true, status: 'ok', db: { connected: true } })),
@@ -176,20 +181,36 @@ describe('bioflow store —— 探活 / 动作 / 面板 / 复用', () => {
     vi.restoreAllMocks();
   });
 
-  it('探活 200 → online；失败 → offline（TC-BIO-STORE-016）', async () => {
+  it('探活 能力注册 → online；未注册 → offline（TC-BIO-STORE-016 / S3 双信号）', async () => {
+    const capsApi = await import('../../../../ui/src/api/capabilities.js');
     const store = useBioflowStore();
+    capsApi.getCapabilities.mockResolvedValueOnce({ installed: [{ name: 'bioflow-gene-family' }] });
     bioflowApi.bioflowHealth.mockResolvedValueOnce({ ok: true });
     await store.probe({ force: true });
+    expect(store.capabilityInstalled).toBe(true);
     expect(store.bioflowAvailable).toBe(true);
 
     const s2 = useBioflowStore();
     s2.availability = 'unknown';
+    capsApi.getCapabilities.mockResolvedValueOnce({ installed: [] });
     bioflowApi.bioflowHealth.mockRejectedValueOnce(new Error('down'));
     await s2.probe({ force: true });
+    expect(s2.capabilityInstalled).toBe(false);
     expect(s2.availability).toBe('offline');
     expect(s2.bioflowAvailable).toBe(false);
   });
 
+  it('探活 已注册但服务不可达 → TAB 仍显示（次信号不影响显隐）', async () => {
+    const capsApi = await import('../../../../ui/src/api/capabilities.js');
+    const store = useBioflowStore();
+    capsApi.getCapabilities.mockResolvedValueOnce({ installed: [{ name: 'bioflow-rnaseq' }] });
+    bioflowApi.bioflowHealth.mockRejectedValueOnce(new Error('down'));
+    await store.probe({ force: true });
+    expect(store.capabilityInstalled).toBe(true);
+    expect(store.healthOnline).toBe(false);
+    expect(store.bioflowAvailable).toBe(true); // 已注册 → TAB 仍显示
+  });
+
   it('applyChatEvent plan_ready 装载候选路径（TC-BIO-STORE-003）', () => {
     const store = useBioflowStore();
     store.applyChatEvent('plan_ready', {

tests/frontend/unit/bioflow/cards.phaseG.test.js

@@ -0,0 +1,232 @@
+// @vitest-environment jsdom
+// tests/frontend/unit/bioflow/cards.phaseG.test.js —— Phase G 四卡片组件测试（L4）
+// 覆盖：ReadinessCard（就绪检查）/ DiagnosisCard（诊断）/ VersioningCard（版本化修改）/
+// DeliveryCard（交付清单）的渲染、状态徽标、按钮交互、块类型接线。
+// SSE/API 用 mock，不依赖生产服务。
+//
+// ============================================================================
+// 契约说明（开发对齐用）
+// 组件路径（ui/src/components/chat/）：
+//   ReadinessCard.vue  —— block.type = 'bioflow_readiness'
+//   DiagnosisCard.vue  —— block.type = 'bioflow_diagnosis'
+//   VersioningCard.vue —— block.type = 'bioflow_versioning'
+//   DeliveryCard.vue   —— block.type = 'bioflow_delivery'
+// 根类名 / 标题关键词 / 徽标类 / 按钮类：
+//   ReadinessCard  —— .readiness-card   / 「就绪检查」 / .rc-badge  / .rc-recheck
+//   DiagnosisCard  —— .diagnosis-card   / 「诊断」     / .dc-badge  / .dc-action
+//   VersioningCard —— .versioning-card  / 「版本」     / .vc-badge  / .vc-apply
+//   DeliveryCard   —— .delivery-card    / 「交付」     / .dlc-badge / .dlc-publish
+// 按钮交互经 chat store sendCardResult 进 QA 流（card_result），卡片类型：
+//   readiness_check / diagnosis / apply_change / delivery_publish
+// ============================================================================
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { mount, flushPromises } from '@vue/test-utils';
+import { createPinia, setActivePinia } from 'pinia';
+
+vi.mock('../../../../ui/src/api/bioflow.js', () => ({
+  bioflowCatalog: vi.fn(async () => ({ ok: true, data: { data: { stage: { params: [] } } } })),
+  createBioflowJob: vi.fn(async () => ({ ok: true, data: {} })),
+  bioflowHealth: vi.fn(async () => ({ ok: true })),
+  listBioflowJobs: vi.fn(async () => ({ ok: true, data: { items: [], total: 0 } })),
+  listBioflowArchives: vi.fn(async () => ({ ok: true, data: { items: [], total: 0 } })),
+  getBioflowJob: vi.fn(async () => ({ ok: true, data: {} })),
+  checkBioflowReadiness: vi.fn(async () => ({ ok: true, data: { ready: true } })),
+  getBioflowDiagnosis: vi.fn(async () => ({ ok: true, data: {} })),
+  applyBioflowChange: vi.fn(async () => ({ ok: true, data: {} })),
+  publishBioflowDelivery: vi.fn(async () => ({ ok: true, data: {} })),
+  bioflowChatStream: vi.fn(async () => { throw new Error('unused'); }),
+  bioflowJobEvents: vi.fn(async () => { throw new Error('unused'); }),
+}));
+
+vi.mock('../../../../ui/src/api/sessions.js', () => ({
+  createMessage: vi.fn(async () => ({ id: 'm1' })),
+  createSession: vi.fn(async () => ({ id: 'sess-1' })),
+  listSessions: vi.fn(async () => []),
+  getSession: vi.fn(),
+}));
+
+import ReadinessCard from '../../../../ui/src/components/chat/ReadinessCard.vue';
+import DiagnosisCard from '../../../../ui/src/components/chat/DiagnosisCard.vue';
+import VersioningCard from '../../../../ui/src/components/chat/VersioningCard.vue';
+import DeliveryCard from '../../../../ui/src/components/chat/DeliveryCard.vue';
+import { useChatStore } from '../../../../ui/src/stores/chat.js';
+
+function setup() {
+  setActivePinia(createPinia());
+  const chat = useChatStore();
+  chat.sessionId = 'sess-1';
+  vi.spyOn(chat, 'sendCardResult').mockImplementation(() => new Promise(() => {}));
+  return { chat };
+}
+
+function sendCardSpy() {
+  return useChatStore().sendCardResult;
+}
+
+const READINESS_BLOCK = () => ({
+  type: 'bioflow_readiness',
+  ready: true,
+  quadrants: [
+    { name: 'environment', ok: true },
+    { name: 'reference', ok: true },
+    { name: 'space', ok: true },
+    { name: 'budget', ok: true },
+  ],
+});
+
+const DIAGNOSIS_BLOCK = () => ({
+  type: 'bioflow_diagnosis',
+  category: 'resource',
+  code: 'DISK_FULL',
+  summary: '磁盘不足',
+  suggested_actions: ['清理磁盘空间后重试'],
+  retryable_without_change: false,
+});
+
+const VERSIONING_BLOCK = () => ({
+  type: 'bioflow_versioning',
+  plan_revision: '1',
+  run_id: 'run-1',
+  affected_stages: ['phylogeny', 'motif'],
+  based_on_revision: null,
+});
+
+const DELIVERY_BLOCK = () => ({
+  type: 'bioflow_delivery',
+  ok: true,
+  checks: { selected_stages: true, run_id: true, required_results: true },
+  incomplete: [],
+});
+
+describe('ReadinessCard（就绪检查）', () => {
+  beforeEach(() => { setup(); vi.clearAllMocks(); });
+
+  it('卡体渲染 + 标题「就绪检查」+ 四象限（环境/参考/空间/预算）', () => {
+    const w = mount(ReadinessCard, { props: { block: READINESS_BLOCK() } });
+    expect(w.find('.readiness-card').exists()).toBe(true);
+    expect(w.find('.rc-title').text()).toContain('就绪检查');
+    expect(w.findAll('.rc-quadrant').length).toBe(4);
+  });
+
+  it('状态徽标：ready 显示「就绪」，未就绪显示「未就绪」', async () => {
+    const w = mount(ReadinessCard, { props: { block: READINESS_BLOCK() } });
+    expect(w.find('.rc-badge').text()).toContain('就绪');
+    const blk = READINESS_BLOCK();
+    blk.ready = false;
+    await w.setProps({ block: blk });
+    expect(w.find('.rc-badge').text()).toContain('未就绪');
+  });
+
+  it('按钮「重新检查」点击发出 readiness_check card_result', async () => {
+    const w = mount(ReadinessCard, { props: { block: READINESS_BLOCK() } });
+    await w.find('.rc-recheck').trigger('click');
+    await flushPromises();
+    expect(sendCardSpy()).toHaveBeenCalledTimes(1);
+    const [card] = sendCardSpy().mock.calls[0];
+    expect(card).toBe('readiness_check');
+  });
+
+  it('块类型接线：block.type=bioflow_readiness 时渲染 readiness 卡', () => {
+    const w = mount(ReadinessCard, { props: { block: READINESS_BLOCK() } });
+    expect(w.props('block').type).toBe('bioflow_readiness');
+    expect(w.find('.readiness-card').exists()).toBe(true);
+  });
+});
+
+describe('DiagnosisCard（诊断）', () => {
+  beforeEach(() => { setup(); vi.clearAllMocks(); });
+
+  it('卡体渲染 + 标题「诊断」+ 错误摘要', () => {
+    const w = mount(DiagnosisCard, { props: { block: DIAGNOSIS_BLOCK() } });
+    expect(w.find('.diagnosis-card').exists()).toBe(true);
+    expect(w.find('.dc-title').text()).toContain('诊断');
+    expect(w.find('.dc-summary').text()).toContain('磁盘不足');
+  });
+
+  it('状态徽标：显示分类（resource）', () => {
+    const w = mount(DiagnosisCard, { props: { block: DIAGNOSIS_BLOCK() } });
+    expect(w.find('.dc-badge').text()).toContain('resource');
+  });
+
+  it('建议动作渲染 + 按钮「应用建议」点击发出 diagnosis card_result', async () => {
+    const w = mount(DiagnosisCard, { props: { block: DIAGNOSIS_BLOCK() } });
+    expect(w.find('.dc-actions').text()).toContain('清理磁盘空间后重试');
+    await w.find('.dc-action').trigger('click');
+    await flushPromises();
+    const [card] = sendCardSpy().mock.calls[0];
+    expect(card).toBe('diagnosis');
+  });
+
+  it('块类型接线：block.type=bioflow_diagnosis 时渲染 diagnosis 卡', () => {
+    const w = mount(DiagnosisCard, { props: { block: DIAGNOSIS_BLOCK() } });
+    expect(w.props('block').type).toBe('bioflow_diagnosis');
+  });
+});
+
+describe('VersioningCard（版本化修改）', () => {
+  beforeEach(() => { setup(); vi.clearAllMocks(); });
+
+  it('卡体渲染 + 标题「版本」+ 修订号 + 受影响下游阶段', () => {
+    const w = mount(VersioningCard, { props: { block: VERSIONING_BLOCK() } });
+    expect(w.find('.versioning-card').exists()).toBe(true);
+    expect(w.find('.vc-title').text()).toContain('版本');
+    expect(w.find('.vc-revision').text()).toContain('1');
+    expect(w.find('.vc-affected').text()).toContain('phylogeny');
+  });
+
+  it('状态徽标：显示 run_id', () => {
+    const w = mount(VersioningCard, { props: { block: VERSIONING_BLOCK() } });
+    expect(w.find('.vc-badge').text()).toContain('run-1');
+  });
+
+  it('按钮「应用修改」点击发出 apply_change card_result', async () => {
+    const w = mount(VersioningCard, { props: { block: VERSIONING_BLOCK() } });
+    await w.find('.vc-apply').trigger('click');
+    await flushPromises();
+    const [card] = sendCardSpy().mock.calls[0];
+    expect(card).toBe('apply_change');
+  });
+
+  it('块类型接线：block.type=bioflow_versioning 时渲染 versioning 卡', () => {
+    const w = mount(VersioningCard, { props: { block: VERSIONING_BLOCK() } });
+    expect(w.props('block').type).toBe('bioflow_versioning');
+  });
+});
+
+describe('DeliveryCard（交付清单）', () => {
+  beforeEach(() => { setup(); vi.clearAllMocks(); });
+
+  it('卡体渲染 + 标题「交付」+ 清单项', () => {
+    const w = mount(DeliveryCard, { props: { block: DELIVERY_BLOCK() } });
+    expect(w.find('.delivery-card').exists()).toBe(true);
+    expect(w.find('.dlc-title').text()).toContain('交付');
+    expect(w.findAll('.dlc-item').length).toBeGreaterThan(0);
+  });
+
+  it('状态徽标：完整显示「已通过」，不完整显示「待完善」', async () => {
+    const w = mount(DeliveryCard, { props: { block: DELIVERY_BLOCK() } });
+    expect(w.find('.dlc-badge').text()).toContain('已通过');
+    const blk = DELIVERY_BLOCK();
+    blk.ok = false;
+    blk.incomplete = [{ item: 'run_id', reason: '缺运行身份' }];
+    await w.setProps({ block: blk });
+    expect(w.find('.dlc-badge').text()).toContain('待完善');
+  });
+
+  it('未完成原因显示 + 按钮「发布交付」点击发出 delivery_publish card_result', async () => {
+    const blk = DELIVERY_BLOCK();
+    blk.ok = false;
+    blk.incomplete = [{ item: 'run_id', reason: '缺运行身份' }];
+    const w = mount(DeliveryCard, { props: { block: blk } });
+    expect(w.find('.dlc-incomplete').text()).toContain('缺运行身份');
+    await w.find('.dlc-publish').trigger('click');
+    await flushPromises();
+    const [card] = sendCardSpy().mock.calls[0];
+    expect(card).toBe('delivery_publish');
+  });
+
+  it('块类型接线：block.type=bioflow_delivery 时渲染 delivery 卡', () => {
+    const w = mount(DeliveryCard, { props: { block: DELIVERY_BLOCK() } });
+    expect(w.props('block').type).toBe('bioflow_delivery');
+  });
+});

tests/frontend/unit/bioflow/cards.test.js

@@ -82,9 +82,18 @@ function setup() {
   bioflow.currentJob.jobId = 'job-1';
   const chat = useChatStore();
   chat.sessionId = 'sess-1';
+  // S3：卡片操作改走 card_result 进 QA 流——单测把 sendCardResult 打桩为「挂起中」
+  //（模拟真实 QA 流在 complete 前不 resolve），断言其被以正确 card/payload 调用；
+  // 挂起态也保证 confirming 防双击守卫在测试里不被 finally 提前复位。
+  vi.spyOn(chat, 'sendCardResult').mockImplementation(() => new Promise(() => {}));
   return { bioflow, chat };
 }
 
+/** 当前活跃 chat store 的 sendCardResult spy（setup 已打桩）。 */
+function sendCardSpy() {
+  return useChatStore().sendCardResult;
+}
+
 const PATH_BLOCK = () => ({
   type: 'bioflow_path',
   status: 'done',
@@ -169,9 +178,11 @@ describe('FlowPathCard —— TC-BIO-PATH-001~022（L4）', () => {
     await w.find('.fpc-confirm').trigger('click'); // 进确认视图
     await w.findAll('.fpc-confirm')[0].trigger('click'); // 确认创建
     await flushPromises();
-    expect(bioflowApi.createBioflowJob).toHaveBeenCalledTimes(1);
-    const body = bioflowApi.createBioflowJob.mock.calls[0][0];
-    expect(body.stages).toEqual(['identify', 'align', 'phylogeny']);
+    expect(sendCardSpy()).toHaveBeenCalledTimes(1);
+    const [card, payload] = sendCardSpy().mock.calls[0];
+    expect(card).toBe('path_selection');
+    expect(payload.chain).toBe('gene_family');
+    expect(payload.stages).toEqual(['identify', 'align', 'phylogeny']);
   });
 
   it('确认按钮双击只触发一次创建（TC-BIO-ACT-008 防重复）', async () => {
@@ -182,7 +193,7 @@ describe('FlowPathCard —— TC-BIO-PATH-001~022（L4）', () => {
     await confirmBtn.trigger('click');
     await confirmBtn.trigger('click');
     await flushPromises();
-    expect(bioflowApi.createBioflowJob).toHaveBeenCalledTimes(1);
+    expect(sendCardSpy()).toHaveBeenCalledTimes(1);
   });
 
   it('键盘 Enter 触发确认（TC-BIO-ACT-010）', async () => {
@@ -272,11 +283,12 @@ describe('FlowFormCard —— TC-BIO-FORM-001~024（L4）', () => {
     await w.findAll('.ffc-input')[0].setValue('8');
     await w.find('.ffc-continue').trigger('click');
     await flushPromises();
-    expect(bioflowApi.confirmBioflowStage).toHaveBeenCalledTimes(1);
-    const [jobId, stage, params] = bioflowApi.confirmBioflowStage.mock.calls[0];
-    expect(jobId).toBe('job-1');
-    expect(stage).toBe('identify');
-    expect(params.cpu).toBe(8);
+    expect(sendCardSpy()).toHaveBeenCalledTimes(1);
+    const [card, payload] = sendCardSpy().mock.calls[0];
+    expect(card).toBe('form_confirm');
+    expect(payload.job_id).toBe('job-1');
+    expect(payload.stage).toBe('identify');
+    expect(payload.params.cpu).toBe(8);
   });
 
   it('继续按钮双击仅一次请求（TC-BIO-ACT-021 提交中禁用）', async () => {
@@ -285,7 +297,7 @@ describe('FlowFormCard —— TC-BIO-FORM-001~024（L4）', () => {
     await btn.trigger('click');
     await btn.trigger('click');
     await flushPromises();
-    expect(bioflowApi.confirmBioflowStage).toHaveBeenCalledTimes(1);
+    expect(sendCardSpy()).toHaveBeenCalledTimes(1);
   });
 
   it('数字类型校验：输入 abc 拦截（TC-BIO-FORM-014）', async () => {
@@ -293,7 +305,7 @@ describe('FlowFormCard —— TC-BIO-FORM-001~024（L4）', () => {
     await w.findAll('.ffc-input')[0].setValue('abc');
     await w.find('.ffc-continue').trigger('click');
     await flushPromises();
-    expect(bioflowApi.confirmBioflowStage).not.toHaveBeenCalled();
+    expect(sendCardSpy()).not.toHaveBeenCalled();
     expect(w.find('.ffc-err').text()).toContain('类型');
   });
 
@@ -303,7 +315,7 @@ describe('FlowFormCard —— TC-BIO-FORM-001~024（L4）', () => {
     const w = mount(FlowFormCard, { props: { block: blk } });
     await w.findAll('.ffc-input')[0].setValue('999');
     await w.find('.ffc-continue').trigger('click');
-    expect(bioflowApi.confirmBioflowStage).not.toHaveBeenCalled();
+    expect(sendCardSpy()).not.toHaveBeenCalled();
     expect(w.find('.ffc-err').text()).toContain('1 ~ 64');
   });
 
@@ -312,15 +324,15 @@ describe('FlowFormCard —— TC-BIO-FORM-001~024（L4）', () => {
     // species 默认空字符串
     await w.find('.ffc-continue').trigger('click');
     await flushPromises();
-    const [, , params] = bioflowApi.confirmBioflowStage.mock.calls[0];
-    expect(params.species).toBeUndefined();
+    const [, payload] = sendCardSpy().mock.calls[0];
+    expect(payload.params.species).toBeUndefined();
   });
 
   it('键盘 Enter 提交（TC-BIO-FORM-023/ACT-016）', async () => {
     const w = mount(FlowFormCard, { props: { block: FORM_BLOCK() } });
     await w.findAll('.ffc-input')[0].trigger('keydown', { key: 'Enter' });
     await flushPromises();
-    expect(bioflowApi.confirmBioflowStage).toHaveBeenCalledTimes(1);
+    expect(sendCardSpy()).toHaveBeenCalledTimes(1);
   });
 
   it('键盘 Esc 恢复默认值（TC-BIO-FORM-024/ACT-017）', async () => {
@@ -432,7 +444,7 @@ describe('FlowFileCard —— TC-BIO-FILE-001~022（L4）', () => {
     await w.find('.ffile-path-input').setValue('/data/examples/SPL.fa');
     await w.find('.ffile-path-row .pane-btn').trigger('click');
     await flushPromises();
-    expect(bioflowApi.uploadBioflowFile).toHaveBeenCalledWith('job-1', { server_path: '/data/examples/SPL.fa' });
+    expect(sendCardSpy()).toHaveBeenCalledWith('file_upload', expect.objectContaining({ job_id: 'job-1', paths: ['/data/examples/SPL.fa'] }));
   });
 
   it('登记路径按钮空 input 禁用（TC-BIO-ACT-048）', () => {
@@ -445,7 +457,7 @@ describe('FlowFileCard —— TC-BIO-FILE-001~022（L4）', () => {
     await w.find('.ffile-path-input').setValue('/data/SPL.fa');
     await w.find('.ffile-path-input').trigger('keydown', { key: 'Enter' });
     await flushPromises();
-    expect(bioflowApi.uploadBioflowFile).toHaveBeenCalled();
+    expect(sendCardSpy()).toHaveBeenCalledWith('file_upload', expect.objectContaining({ job_id: 'job-1', paths: ['/data/SPL.fa'] }));
   });
 
   it('路径输入 Esc 清空（TC-BIO-ACT-044）', async () => {
@@ -524,46 +536,15 @@ describe('FlowProgressCard —— TC-BIO-PROG-001~024（L4）', () => {
     expect(w.find('.pc-log-body').exists()).toBe(true);
   });
 
-  it('失败标红 ✕ + 状态文字 error 色 + 三选一按钮出现（TC-BIO-PROG-006/007）', () => {
+  it('失败标红 ✕ + 状态文字 error 色（TC-BIO-PROG-006/007；S3 无三选一按钮）', () => {
     const blk = PROG_BLOCK();
     blk.stages[1] = { stage: 'align', status: 'failed', log_tail: 'error', error: 'manifest_failed' };
     const w = mount(FlowProgressCard, { props: { block: blk } });
     const failedStep = w.findAll('.p-step')[1];
     expect(failedStep.classes()).toContain('failed');
     expect(failedStep.find('.p-dot').text()).toBe('✕');
-    const actions = failedStep ? w.findAll('.pc-actions')[0] : null;
-    expect(actions.text()).toContain('重跑');
-    expect(actions.text()).toContain('跳过');
-    expect(actions.text()).toContain('改参数重跑');
-  });
-
-  it('重跑：发出 rerun 请求（TC-BIO-PROG-008/ACT-050）', async () => {
-    const blk = PROG_BLOCK();
-    blk.stages[1] = { stage: 'align', status: 'failed', log_tail: '', error: 'x' };
-    const w = mount(FlowProgressCard, { props: { block: blk } });
-    const btn = w.findAll('.pc-actions .pane-btn')[0];
-    await btn.trigger('click');
-    await flushPromises();
-    expect(bioflowApi.rerunBioflowStage).toHaveBeenCalledWith('job-1', 'align', null);
-  });
-
-  it('跳过：发出 skip 请求（TC-BIO-PROG-009/ACT-051）', async () => {
-    const blk = PROG_BLOCK();
-    blk.stages[1] = { stage: 'align', status: 'failed', log_tail: '', error: 'x' };
-    const w = mount(FlowProgressCard, { props: { block: blk } });
-    await w.findAll('.pc-actions .pane-btn')[1].trigger('click');
-    await flushPromises();
-    expect(bioflowApi.skipBioflowStage).toHaveBeenCalledWith('job-1', 'align');
-  });
-
-  it('改参数重跑：弹出参数表单（TC-BIO-PROG-010/ACT-052）', async () => {
-    const blk = PROG_BLOCK();
-    blk.stages[1] = { stage: 'align', status: 'failed', log_tail: '', error: 'x' };
-    const w = mount(FlowProgressCard, { props: { block: blk } });
-    await w.findAll('.pc-actions .pane-btn')[2].trigger('click');
-    await flushPromises();
-    expect(w.find('.pc-rerun-form').exists()).toBe(true);
-    expect(bioflowApi.bioflowCatalog).toHaveBeenCalledWith({ stage: 'align' });
+    // S3 精简：失败态不再渲染直连控制按钮（重跑/跳过/改参数重跑）
+    expect(w.findAll('.pc-actions').length).toBe(0);
   });
 
   it('skipped 态视觉（TC-BIO-PROG-011）', () => {
@@ -604,24 +585,6 @@ describe('FlowProgressCard —— TC-BIO-PROG-001~024（L4）', () => {
     expect(w.findAll('.p-step').length).toBe(10);
   });
 
-  it('暂停/恢复按钮随任务状态显隐；点击发请求（TC-BIO-PROG-017/018）', async () => {
-    const w = mount(FlowProgressCard, { props: { block: PROG_BLOCK() } });
-    // running → 暂停按钮
-    let pauseBtn = w.findAll('.pc-head-right .pane-btn').find((b) => b.text().includes('暂停'));
-    expect(pauseBtn).toBeTruthy();
-    await pauseBtn.trigger('click');
-    await flushPromises();
-    expect(bioflowApi.pauseBioflowJob).toHaveBeenCalledWith('job-1');
-    // paused → 恢复按钮
-    const blk = { ...PROG_BLOCK(), jobStatus: 'paused' };
-    const w2 = mount(FlowProgressCard, { props: { block: blk } });
-    const resumeBtn = w2.findAll('.pc-head-right .pane-btn').find((b) => b.text().includes('继续'));
-    expect(resumeBtn).toBeTruthy();
-    await resumeBtn.trigger('click');
-    await flushPromises();
-    expect(bioflowApi.resumeBioflowJob).toHaveBeenCalledWith('job-1');
-  });
-
   it('快照整体替换：块 stages 引用变化后自动整体刷新（TC-BIO-PROG-015）', async () => {
     const w = mount(FlowProgressCard, { props: { block: PROG_BLOCK() } });
     const before = w.findAll('.p-step').length;

tests/frontend/unit/bioflow/chat.bioflow.test.js

@@ -190,141 +190,3 @@ describe('消息更新器 —— 五类块 patch', () => {
     expect(blk.citations).toHaveLength(1);
   });
 });
-
-describe('sendBioflow —— 全流程（SSE 用 mock，不依赖生产服务）', () => {
-  beforeEach(() => {
-    setActivePinia(createPinia());
-    vi.restoreAllMocks();
-  });
-  afterEach(() => {
-    chatFrames = [];
-  });
-
-  it('plan_ready + job_created + stage_await_confirm + job_done 事件流 patch 消息 blocks（TC-BIO-STORE-003/004/005）', async () => {
-    const { chat } = await setupChat();
-    chatFrames = [
-      frame('plan_ready', { candidates: [{ purpose: '标准流程', stages: ['identify', 'align'] }], source: 'llm_rag', auto_filled: [], reuse_archive: null, reuse_name: null, fallback: null }),
-      frame('job_created', { job_id: 'j1', session_id: 'sess-1', title: 'SPL', stages: [{ stage: 'identify', status: 'waiting' }, { stage: 'align', status: 'waiting' }], auto_continue: false }),
-      frame('stage_started', { job_id: 'j1', stage: 'identify', attempt: 1 }),
-      frame('stage_await_confirm', { job_id: 'j1', stage: 'align', form_defaults: [{ name: 'cpu', default: 4, source: 'contract' }] }),
-      frame('job_done', { job_id: 'j1', progress: 100 }),
-    ];
-    await chat.sendBioflow('帮我跑水稻 SPL 家族鉴定');
-    expect(chat.messages).toHaveLength(2);
-    expect(chat.messages[0].role).toBe('user');
-    expect(chat.messages[0].kind).toBe('bioflow');
-    const aMsg = chat.messages[1];
-    expect(aMsg.kind).toBe('bioflow');
-    expect(aMsg.status).toBe('done');
-    const types = aMsg.blocks.map((b) => b.type);
-    expect(types).toContain('bioflow_path');
-    expect(types).toContain('bioflow_progress');
-    expect(types).toContain('bioflow_form');
-    expect(types).toContain('bioflow_archive');
-    const path = aMsg.blocks.find((b) => b.type === 'bioflow_path');
-    expect(path.candidates).toHaveLength(1);
-    const prog = aMsg.blocks.find((b) => b.type === 'bioflow_progress');
-    expect(prog.jobId).toBe('j1');
-    expect(prog.stages.map((s) => s.status)).toEqual(['running', 'waiting_confirm']);
-    // 用户消息落库（骨架 + 终态 patch）
-    expect(sessionCalls.messages.length).toBeGreaterThanOrEqual(2);
-    expect(sessionCalls.messages[0].body.role).toBe('user');
-  });
-
-  it('plan_ready 后心跳流断连（无任务事件）：path 卡保留，消息收口 done', async () => {
-    const { chat } = await setupChat();
-    chatFrames = [
-      frame('plan_ready', { candidates: [{ purpose: 'p', stages: ['identify'] }], source: 'llm_only', auto_filled: [], reuse_archive: null, reuse_name: null, fallback: null }),
-    ];
-    await chat.sendBioflow('跑 SPL 家族');
-    const aMsg = chat.messages[1];
-    expect(aMsg.status).toBe('done');
-    expect(aMsg.blocks.find((b) => b.type === 'bioflow_path').candidates).toHaveLength(1);
-    expect(aMsg.blocks.some((b) => b.type === 'bioflow_progress')).toBe(false);
-  });
-
-  it('message_done flow_qa 分支：引用块渲染（FR-BIO-026 不新建任务）', async () => {
-    const { chat } = await setupChat();
-    chatFrames = [
-      frame('message_done', { kind: 'flow_qa', citations: [{ source: 'flow_docs', title_path: 'identify.md', text: '输入 fasta 与 hmm' }], degraded: false }),
-    ];
-    await chat.sendBioflow('identify 需要什么输入');
-    const aMsg = chat.messages[1];
-    expect(aMsg.status).toBe('done');
-    const qa = aMsg.blocks.find((b) => b.type === 'bioflow_qa');
-    expect(qa.citations).toHaveLength(1);
-    expect(aMsg.blocks.some((b) => b.type === 'bioflow_progress')).toBe(false);
-  });
-
-  it('错误帧（统一信封）：标注 error + 可重试', async () => {
-    const { chat } = await setupChat();
-    chatFrames = [
-      frame('error', { code: 'UPSTREAM_DOWN', message: '生信服务当前不可用' }),
-    ];
-    await chat.sendBioflow('帮我跑水稻 SPL 家族鉴定');
-    const aMsg = chat.messages[1];
-    expect(aMsg.status).toBe('error');
-    expect(aMsg.errText).toBe('生信服务当前不可用');
-    expect(chat.lastResult.ok).toBe(false);
-    expect(chat.lastResult.error.code).toBe('UPSTREAM_DOWN');
-  });
-
-  it('网络中断：标注 disconnected；任务状态保留（快照兜底不丢进度）', async () => {
-    const { chat } = await setupChat();
-    chatFrames = [
-      frame('plan_ready', { candidates: [{ purpose: 'p', stages: ['identify'] }], source: 'llm_only', auto_filled: [], reuse_archive: null, reuse_name: null, fallback: null }),
-      frame('job_created', { job_id: 'j1', stages: [{ stage: 'identify', status: 'waiting' }], auto_continue: false }),
-      frame('stage_started', { job_id: 'j1', stage: 'identify', attempt: 1 }),
-    ];
-    // 让 fetch 在流消费中途失败：mock 抛网络错误
-    bioflowApi.bioflowChatStream.mockRejectedValueOnce(new Error('network'));
-    await chat.sendBioflow('帮我跑水稻 SPL 家族鉴定');
-    const aMsg = chat.messages[1];
-    expect(aMsg.status).toBe('error');
-    expect(aMsg.streamErr).toBe('disconnected');
-    expect(chat.lastResult.ok).toBe(false);
-    expect(chat.lastResult.error.retryable).toBe(true);
-  });
-
-  it('retry：bioflow 失败消息同位置替换走生信路径（TC-BIO-STORE-022 语义）', async () => {
-    const { chat } = await setupChat();
-    chatFrames = [frame('error', { code: 'UPSTREAM_DOWN', message: 'x' })];
-    await chat.sendBioflow('跑 SPL 家族');
-    expect(chat.messages).toHaveLength(2);
-    // 重试成功路径
-    chatFrames = [
-      frame('plan_ready', { candidates: [{ purpose: 'p', stages: ['identify'] }], source: 'llm_only', auto_filled: [], reuse_archive: null, reuse_name: null, fallback: null }),
-    ];
-    await chat.retry();
-    expect(chat.messages).toHaveLength(2); // 同位置替换不新增
-    const aMsg = chat.messages[1];
-    expect(aMsg.status).toBe('done');
-    expect(aMsg.kind).toBe('bioflow');
-  });
-});
-
-describe('分流纪律（漏判安全）', () => {
-  beforeEach(() => {
-    setActivePinia(createPinia());
-    vi.clearAllMocks();
-  });
-
-  it('sendBioflow 不经过 qa 流（bioflowChatStream 独立端点）', async () => {
-    const { chat } = await setupChat();
-    chatFrames = [frame('plan_ready', { candidates: [], source: 'llm_only', auto_filled: [], reuse_archive: null, reuse_name: null, fallback: null })];
-    await chat.sendBioflow('跑 SPL 家族');
-    expect(bioflowApi.bioflowChatStream).toHaveBeenCalledTimes(1);
-    const body = bioflowApi.bioflowChatStream.mock.calls[0][0];
-    expect(body.session_id).toBe('sess-1');
-    expect(body.message).toBe('跑 SPL 家族');
-    expect(body).toHaveProperty('has_bioflow_context');
-  });
-
-  it('busy 时不重复发起（并发防护）', async () => {
-    const { chat } = await setupChat();
-    vi.clearAllMocks();
-    chat.streamCtx['sess-1'] = { busy: true };
-    await chat.sendBioflow('跑 SPL 家族');
-    expect(bioflowApi.bioflowChatStream).not.toHaveBeenCalled();
-  });
-});

tests/frontend/unit/bioflow/composer.bioflow.test.js

@@ -100,18 +100,12 @@ describe('Composer 生信分流（漏判安全）', () => {
     vi.clearAllMocks();
   });
 
-  it('bioflow 意图：走 chat.sendBioflow（用户消息 kind=bioflow + path 块）', async () => {
-    chatFrames = [{
-      event: 'plan_ready',
-      data: { candidates: [{ purpose: 'p', stages: ['identify'] }], source: 'llm_only', auto_filled: [], reuse_archive: null, reuse_name: null, fallback: null },
-    }];
+  it('生信意图：统一走 QA 流（emit send，不产生 bioflow 直连请求；S3）', async () => {
     const w = mount(Composer, { props: { mode: 'ask', busy: false, disabled: false } });
     await submit(w, '帮我跑水稻 SPL 家族鉴定');
-    expect(bioflowApi.bioflowChatStream).toHaveBeenCalledTimes(1);
-    const chat = useChatStore();
-    expect(chat.messages).toHaveLength(2);
-    expect(chat.messages[0].kind).toBe('bioflow');
-    expect(chat.messages[1].blocks[0].type).toBe('bioflow_path');
+    expect(w.emitted('send')).toBeTruthy();
+    expect(w.emitted('send')[0][0]).toContain('帮我跑水稻 SPL 家族鉴定');
+    expect(bioflowApi.bioflowChatStream).not.toHaveBeenCalled();
   });
 
   it('未命中词典：走原 send 路径（不产生 bioflow 请求；TC-BIO-STORE-002）', async () => {

tests/frontend/unit/bioflow/intent.test.js

@@ -1,118 +1,57 @@
 // @vitest-environment jsdom
-// tests/frontend/unit/bioflow/intent.test.js —— 生信意图分流（L3）
-// 与 docs/team/cases_bioflow_intent.md 冻结词典 40 用例表同表双跑
-// （TC-BIO-INTENT-001~047；后端 intent.py 同词典同规则，L2 侧由 T 执行同表校验）。
+// tests/frontend/unit/bioflow/intent.test.js —— 意图分流（S3：生信词典删除后等价语义）
+// S3 起生信分析意图统一走 QA 流（bioflow_agent 服务端 nl_triggers 判定），
+// 前端 route() 不再产生 bioflow/bioflow_qa——本测试锁定该等价语义：
+//   生信句 → qa；文档意图（docgen/export/edit）不变；扩展创建意图保留。
 import { describe, expect, it } from 'vitest';
-import { route, extractReuseName, hasAnyWord } from '../../../../ui/src/utils/intent.js';
+import { route, hasAnyWord, isExtensionCreateIntent } from '../../../../ui/src/utils/intent.js';
 
-/** 词典用例表（cases_bioflow_intent.md §4）：[text, attachments, activeArtifact, bioflowContext, expected] */
-const DICT_CASES = [
-  // #  text 附件 活动文档 生信上下文 期望
-  ['帮我跑水稻 SPL 家族鉴定', false, false, false, 'bioflow'],
-  ['跑一下拟南芥 MADS-box 家族分析', false, false, false, 'bioflow'],
-  ['请帮我鉴定水稻 SPL 家族', false, false, false, 'bioflow'],
-  ['识别玉米 bZIP 家族成员', false, false, false, 'bioflow'],
-  ['帮我研究一下水稻 SPL 基因家族', false, false, false, 'bioflow'],
-  ['分析小麦 WRKY 转录因子家族', false, false, false, 'bioflow'],
-  ['做个大豆 NAC 家族分析', false, false, false, 'bioflow'],
-  ['跑 SPL 家族', false, false, false, 'bioflow'],
-  ['水稻 SPL 家族，帮我跑', false, false, false, 'bioflow'],
-  ['基因家族鉴定：水稻 SPL', false, false, false, 'bioflow'],
-  ['帮我跑水稻叶片 RNA-seq 差异表达分析', false, false, false, 'bioflow'],
-  ['帮我做水稻全基因组变异检测', false, false, false, 'bioflow'],
-  ['帮我跑水稻产量性状 GWAS 关联分析', false, false, false, 'bioflow'],
-  ['什么是基因家族？', false, false, false, 'qa'],
-  ['帮我跑一下', false, false, false, 'qa'],
-  ['SPL 家族', false, false, false, 'qa'],
-  ['今天天气不错', false, false, false, 'qa'],
-  ['跑 SPL 家族鉴定需要准备什么输入？', false, false, false, 'qa'], // 无生信上下文漏判安全
-  ['帮我跑一个数据分析', false, false, false, 'qa'],
-  ['你好呀', false, false, false, 'qa'],
-  ['', false, false, false, 'qa'], // 空字符串
-  ['帮我跑香蕉 XYK 家族鉴定', false, false, false, 'qa'], // XYK 不在家族词典
-  ['跑水稻 spl 家族鉴定', false, false, false, 'bioflow'], // 家族名大小写不敏感
-  ['Please run rice SPL family identification', false, false, false, 'bioflow'],
-  ['帮我跑（水稻 SPL 家族）鉴定！', false, false, false, 'bioflow'],
-  ['用 XXX 存档任务的方法帮我跑水稻 SPL 家族鉴定', false, false, false, 'bioflow'], // 复用意图
-  ['根据 XXX 存档任务的方法帮我跑一下玉米 bZIP', false, false, false, 'bioflow'],
-  ['参考 XXX 存档的方法再跑一个水稻 SPL', false, false, false, 'bioflow'],
-  ['用《XXX》存档任务的方法帮我跑小麦 WRKY 家族', false, false, false, 'bioflow'],
-  ['用 XXX 存档任务的方法', false, false, false, 'qa'], // 无目标任务词
-  ['用 XXX 存档任务的方法帮我跑 yyy', false, false, false, 'qa'], // yyy 无家族/对象匹配
-  ['帮我生成一份水稻 SPL 家族分析报告', false, false, false, 'docgen'], // docgen 优先于 bioflow
-  ['帮我写一篇水稻基因家族研究论文', false, false, false, 'docgen'],
-  ['导出成 PDF', false, true, false, 'export'],
-  ['把这句话改成红色', false, true, false, 'edit'], // 无图表词
-  ['xxx 图表颜色换成红色', false, true, false, 'bioflow'], // 图表词走 FR-BIO-019
-  ['identify 需要什么输入', false, false, true, 'bioflow_qa'], // 不新建任务
-  ['帮我总结一下这个问题的要点', false, false, false, 'qa'],
-  ['写一段水稻基因的介绍', false, false, false, 'qa'], // 介绍在 docgen 排除表
-  ['跑水稻 SPL 家族鉴定', false, true, false, 'bioflow'], // 活动文档不改判定
-];
-
-describe('intent route —— 词典 40 用例同表双跑', () => {
-  DICT_CASES.forEach(([text, att, artifact, ctx, expected], i) => {
-    const label = text ? text.slice(0, 24) : '（空字符串）';
-    it(`#${i + 1} 「${label}」 → ${expected}`, () => {
-      const { intent } = route(text, att, artifact, ctx);
-      expect(intent).toBe(expected);
-    });
+describe('route —— S3 生信意图一律 qa（漏判安全）', () => {
+  it('生信分析句 → qa（不再产生 bioflow 分流）', () => {
+    for (const t of [
+      '帮我跑水稻 SPL 家族鉴定',
+      '跑一下拟南芥 MADS-box 家族分析',
+      '帮我跑水稻叶片 RNA-seq 差异表达分析',
+      '帮我做水稻全基因组变异检测',
+      '识别玉米 bZIP 家族成员',
+      '用 XXX 存档任务的方法帮我跑水稻 SPL 家族鉴定',
+      'xxx 图表颜色换成红色',
+    ]) {
+      expect(route(t, false, false, false).intent).toBe('qa');
+    }
   });
-});
 
-describe('intent route —— 边界与实现注意（词典 §5）', () => {
-  it('文本长度 ≤1 或纯空白 → qa', () => {
+  it('生信流程咨询句 → qa（bioflow_qa 已删除）', () => {
+    expect(route('identify 需要什么输入', false, false, true).intent).toBe('qa');
+  });
+
+  it('文档意图 docgen 不变', () => {
+    expect(route('帮我写一份水稻分析报告').intent).toBe('docgen');
+    expect(route('帮我整理一下', true, false, false).intent).toBe('docgen');
+  });
+
+  it('导出/编辑需活动文档才生效（docgen 语义不变）', () => {
+    expect(route('导出成 PDF', false, true, false).intent).toBe('export');
+    expect(route('导出成 PDF', false, false, false).intent).toBe('qa');
+    expect(route('把这句话改成红色', false, true, false).intent).toBe('edit');
+  });
+
+  it('边界：长度 ≤1/空/纯空白 → qa', () => {
     expect(route('a').intent).toBe('qa');
     expect(route('   ').intent).toBe('qa');
     expect(route(null).intent).toBe('qa');
     expect(route(undefined).intent).toBe('qa');
   });
-  it('>2000 字符按截断前 2000 判定（长前缀不淹没意图）', () => {
-    const long = '啊'.repeat(3000) + ' 帮我跑水稻 SPL 家族鉴定';
-    expect(route(long).intent).toBe('qa'); // 意图词在 2000 之后被截掉
-    const short = '帮我跑水稻 SPL 家族鉴定' + '啊'.repeat(3000);
-    expect(route(short).intent).toBe('bioflow');
-  });
-  it('bioflow_qa 仅在 has_bioflow_context=true 生效', () => {
-    expect(route('identify 需要什么输入', false, false, true).intent).toBe('bioflow_qa');
-    expect(route('identify 需要什么输入', false, false, false).intent).toBe('qa');
-  });
-  it('家族名后须跟语境词或位于句尾（SPL 会议不命中）', () => {
-    expect(route('跑 SPL 会议').intent).toBe('qa');
-    expect(route('帮我跑玉米 bZIP').intent).toBe('bioflow'); // 句尾命中
-  });
-  it('「做」动词需对象组合（分析对象词命中）', () => {
-    expect(route('帮我做水稻全基因组变异检测').intent).toBe('bioflow');
-    expect(route('帮我做个分析').intent).toBe('qa'); // 无对象词
-  });
-  it('附件 + 写类动词 → docgen（兜底信号，词典规则 4）', () => {
-    expect(route('帮我整理一下', true, false, false).intent).toBe('docgen');
-  });
-  it('导出需 has_active_artifact 才生效', () => {
-    expect(route('导出成 PDF', false, false, false).intent).toBe('qa');
-  });
-  it('命中句不打乱后续 QA 判定（无状态残留）', () => {
-    expect(route('什么是 SPL 家族').intent).toBe('qa');
-    expect(route('帮我跑水稻 SPL 家族鉴定').intent).toBe('bioflow');
-    expect(route('什么是 SPL 家族').intent).toBe('qa');
-  });
 });
 
-describe('extractReuseName —— 复用方法名提取（词典实现注意 2）', () => {
-  it('标准句式：方法名 = REUSE_PHRASE 之前最近的 3-20 字符片段', () => {
-    expect(extractReuseName('用 XXX 存档任务的方法帮我跑水稻 SPL 家族鉴定')).toBe('XXX');
-    expect(extractReuseName('根据 XXX 存档任务的方法帮我跑一下玉米 bZIP')).toBe('XXX');
-    expect(extractReuseName('参考 XXX 存档的方法再跑一个水稻 SPL')).toBe('XXX');
-    expect(extractReuseName('用《XXX》存档任务的方法帮我跑小麦 WRKY 家族')).toBe('XXX');
+describe('isExtensionCreateIntent —— 扩展创建意图（S4 保留）', () => {
+  it('创建/上传 扩展句式命中', () => {
+    expect(isExtensionCreateIntent('帮我创建一个分析扩展')).toBe(true);
+    expect(isExtensionCreateIntent('上传一个自定义分析工具')).toBe(true);
   });
-  it('非复用句式返回 null', () => {
-    expect(extractReuseName('帮我跑水稻 SPL 家族鉴定')).toBeNull();
-    expect(extractReuseName('')).toBeNull();
-  });
-  it('片段长度不足 3 或超 20 返回 null', () => {
-    expect(extractReuseName('用 AB 存档任务的方法帮我跑水稻 SPL 家族鉴定')).toBeNull();
-    // 21 字符片段超上限
-    expect(extractReuseName('用 一二三四五六七八九十一二三四五六七八九十一 存档任务的方法帮我跑水稻 SPL')).toBeNull();
+  it('非扩展句不命中', () => {
+    expect(isExtensionCreateIntent('帮我跑水稻 SPL 家族鉴定')).toBe(false);
+    expect(isExtensionCreateIntent('')).toBe(false);
   });
 });
 

tests/frontend/unit/bioflow/legacy.block.test.js

@@ -0,0 +1,59 @@
+// @vitest-environment jsdom
+// tests/frontend/unit/bioflow/legacy.block.test.js —— S3 旧生信块只读降级（LegacyBioflowBlock）
+// 覆盖：四类旧块标题映射 / bioflow_qa 引用列表（含空态）/ 任务类块 jobId 前缀 / 只读（无可交互控件）。
+import { describe, it, expect } from 'vitest';
+import { mount } from '@vue/test-utils';
+import LegacyBioflowBlock from '../../../../ui/src/components/chat/LegacyBioflowBlock.vue';
+
+describe('LegacyBioflowBlock —— 旧生信块只读降级（S3）', () => {
+  it('bioflow_qa 渲染只读引用列表（title + citations）', () => {
+    const w = mount(LegacyBioflowBlock, {
+      props: {
+        block: {
+          type: 'bioflow_qa',
+          citations: [{ text: '引用正文', source: 's1', title_path: 't1' }],
+        },
+      },
+    });
+    expect(w.find('.legacy-bioflow-block').exists()).toBe(true);
+    expect(w.findAll('.lbf-cite')).toHaveLength(1);
+    expect(w.text()).toContain('引用正文');
+  });
+
+  it('bioflow_qa 空引用显示空态文案', () => {
+    const w = mount(LegacyBioflowBlock, {
+      props: { block: { type: 'bioflow_qa', citations: [] } },
+    });
+    expect(w.find('.lbf-empty').exists()).toBe(true);
+  });
+
+  it('任务类块（bioflow_progress）显示 jobId 前缀 + 只读提示', () => {
+    const w = mount(LegacyBioflowBlock, {
+      props: { block: { type: 'bioflow_progress', jobId: 'job-9' } },
+    });
+    expect(w.find('.lbf-job').exists()).toBe(true);
+    expect(w.text()).toContain('job-9');
+    expect(w.find('.lbf-empty').exists()).toBe(true); // 只读提示
+  });
+
+  it('各类旧块标题映射非空（path/form/file/archive/progress）', () => {
+    for (const type of ['bioflow_path', 'bioflow_form', 'bioflow_file', 'bioflow_archive', 'bioflow_progress']) {
+      const w = mount(LegacyBioflowBlock, { props: { block: { type } } });
+      expect(w.find('.lbf-title').text()).toBeTruthy();
+    }
+  });
+
+  it('未知类型回退 legacyBlockTitle 不抛错', () => {
+    const w = mount(LegacyBioflowBlock, { props: { block: { type: 'bioflow_unknown' } } });
+    expect(w.find('.lbf-title').text()).toBeTruthy();
+  });
+
+  it('只读：不渲染 button/input/a 等可交互控件（旧块 hydrate 不报错）', () => {
+    const w = mount(LegacyBioflowBlock, {
+      props: { block: { type: 'bioflow_progress', jobId: 'j1', citations: [] } },
+    });
+    expect(w.find('button').exists()).toBe(false);
+    expect(w.find('input').exists()).toBe(false);
+    expect(w.find('a').exists()).toBe(false);
+  });
+});

tests/frontend/unit/bioflow/panes.test.js

@@ -331,3 +331,27 @@ describe('BioArchivePane —— TC-BIO-PANE-001~016（L4）', () => {
     expect(sizes[0].text()).toContain('KB');
   });
 });
+
+
+// ===========================================================================
+// S3：BioJobsPane 日志自动滚底（实时跟随最新一行）
+// ===========================================================================
+describe('BioJobsPane 日志自动滚底（S3）', () => {
+  it('展开日志后追加行 → scrollTop 置为 scrollHeight（保持在最新一行）', async () => {
+    const w = mount(BioJobsPane);
+    await flushPromises();
+    await w.findAll('.bj-item')[0].trigger('click');
+    await flushPromises();
+    await w.findAll('.bj-dag-row')[0].trigger('click');
+    await flushPromises();
+    const pre = w.find('.bj-log-body').element;
+    // jsdom 不实现 scrollHeight（恒 0），此处 mock 为确定值以验证滚底赋值
+    Object.defineProperty(pre, 'scrollHeight', { configurable: true, get: () => 800 });
+    // 追加一行日志（轮询增量）→ watch 触发 → nextTick 滚底
+    const bioflow = useBioflowStore();
+    bioflow.stageLogs['job-1:identify'].lines.push('appended-log-line');
+    await flushPromises();
+    await new Promise((resolve) => setTimeout(resolve, 0)); // 放行 nextTick 链
+    expect(pre.scrollTop).toBe(800);
+  });
+});

tests/frontend/unit/bioflow/settings.test.js

@@ -0,0 +1,71 @@
+// @vitest-environment jsdom
+// tests/frontend/unit/bioflow/settings.test.js —— S5 生信能力装卸（settings store）
+// 覆盖：isInstalled 判定 / toggleInstalled register↔unregister / 未知能力抛错 / 装卸后重拉清单。
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { createPinia, setActivePinia } from 'pinia';
+
+vi.mock('../../../../ui/src/api/capabilities.js', () => ({
+  installCapability: vi.fn(async () => ({ ok: true })),
+  BIOFLOW_MANIFESTS: {
+    'bioflow-gene-family': 'capabilities:\n  - name: bioflow-gene-family',
+    'bioflow-rnaseq': 'capabilities:\n  - name: bioflow-rnaseq',
+    'bioflow-extension': 'capabilities:\n  - name: bioflow-extension',
+  },
+  getCapabilities: vi.fn(async () => ({})),
+}));
+
+vi.mock('../../../../ui/src/api/http.js', () => ({
+  get: vi.fn(async () => ({ capabilities: [], defaults: {}, installed: [], load_warnings: [] })),
+  post: vi.fn(async () => ({})),
+  patch: vi.fn(async () => ({})),
+}));
+
+import { useSettingsStore } from '../../../../ui/src/stores/settings.js';
+import * as capabilitiesApi from '../../../../ui/src/api/capabilities.js';
+
+function setup() {
+  setActivePinia(createPinia());
+  return useSettingsStore();
+}
+
+describe('SettingsStore —— 生信能力装卸（S5）', () => {
+  beforeEach(() => {
+    capabilitiesApi.installCapability.mockClear();
+  });
+
+  it('isInstalled：installed 数组含该能力名 → true，否则 false', () => {
+    const s = setup();
+    s.installed = [{ name: 'bioflow-gene-family' }];
+    expect(s.isInstalled('bioflow-gene-family')).toBe(true);
+    expect(s.isInstalled('bioflow-rnaseq')).toBe(false);
+    expect(s.isInstalled('bioflow-extension')).toBe(false);
+  });
+
+  it('toggleInstalled：未安装 → register；已安装 → unregister', async () => {
+    const s = setup();
+    s.installed = [];
+    await s.toggleInstalled('bioflow-gene-family');
+    expect(capabilitiesApi.installCapability).toHaveBeenLastCalledWith(
+      'register', expect.any(String), 'bioflow-gene-family',
+    );
+
+    s.installed = [{ name: 'bioflow-gene-family' }];
+    await s.toggleInstalled('bioflow-gene-family');
+    expect(capabilitiesApi.installCapability).toHaveBeenLastCalledWith(
+      'unregister', '', 'bioflow-gene-family',
+    );
+  });
+
+  it('toggleInstalled：未知生信能力抛错', async () => {
+    const s = setup();
+    await expect(s.toggleInstalled('bogus')).rejects.toThrow('未知生信能力');
+  });
+
+  it('toggleInstalled：装卸后重拉清单刷新 installed（load 被调用）', async () => {
+    const s = setup();
+    s.installed = [];
+    const loadSpy = vi.spyOn(s, 'load').mockResolvedValue(undefined);
+    await s.toggleInstalled('bioflow-rnaseq');
+    expect(loadSpy).toHaveBeenCalledTimes(1);
+  });
+});

ui/src/api/capabilities.js

@@ -0,0 +1,59 @@
+// api/capabilities.js —— 能力清单端点（S4 BFF；GET /api/capabilities）+ 装卸接口（S5）。
+// 生信 TAB 显隐的主信号源：installed 数组含 bioflow-* 能力即视为「生信能力已安装」。
+import { get, post } from './http.js';
+
+/** GET /api/capabilities —— 能力清单 + 默认值 + 当前会话开关 + QA 已装插件 */
+export function getCapabilities(params = {}, opts = {}) {
+  return get('/api/capabilities', params, { timeout: 5000, ...opts });
+}
+
+/** POST /api/capabilities/install —— 按能力 register/unregister（透传 QA，热加载不重启） */
+export function installCapability(action, manifest, name) {
+  return post('/api/capabilities/install', { action, manifest, name });
+}
+
+// 三个生信能力的 register manifest（与 agent/qa/configs/capabilities.yaml 一致，热装卸用）。
+export const BIOFLOW_MANIFESTS = {
+  'bioflow-gene-family': [
+    'capabilities:',
+    '  - name: bioflow-gene-family',
+    '    provider: mcp',
+    '    permission: read_only',
+    '    description: 基因家族分析（路径规划/建任务/参数确认/文件获取与预处理/状态查询），自然语言触发',
+    '    session_default: true',
+    '    nl_triggers: [基因家族, 家族成员, 亚家族, 系统发育, 建树, 进化树, 保守基序, motif, 结构域, 基因结构, 共线性, Ka/Ks, 选择压力, 组合证据]',
+    '    mcp:',
+    '      url: http://127.0.0.1:8098/mcp/gene-family/',
+    '    prompt_pack:',
+    '      file: bioflow_gene_family_agent_rules.md',
+  ].join('\n'),
+  'bioflow-rnaseq': [
+    'capabilities:',
+    '  - name: bioflow-rnaseq',
+    '    provider: mcp',
+    '    permission: read_only',
+    '    description: 转录组分析（实验设计确认/样本配置/路径规划/建任务/差异表达/富集），自然语言触发',
+    '    session_default: true',
+    '    nl_triggers: [转录组, RNA-seq, RNAseq, rnaseq, 差异表达, 表达定量, 富集, WGCNA, GSEA, 实验设计, fastq]',
+    '    mcp:',
+    '      url: http://127.0.0.1:8098/mcp/rnaseq/',
+    '    prompt_pack:',
+    '      file: bioflow_rnaseq_agent_rules.md',
+  ].join('\n'),
+  'bioflow-extension': [
+    'capabilities:',
+    '  - name: bioflow-extension',
+    '    provider: mcp',
+    '    permission: read_only',
+    '    description: 用户自定义扩展分析（创建/转换/试运行/校验/发布/运行），自然语言触发',
+    '    session_default: true',
+    '    nl_triggers: [扩展, 拓展分析, 扩展分析, 自定义分析, 分析模板, 分析脚本, 分析工具]',
+    '    mcp:',
+    '      url: http://127.0.0.1:8098/mcp/extension/',
+    '    prompt_pack:',
+    '      file: bioflow_extension_agent_rules.md',
+  ].join('\n'),
+};
+
+// 生信能力名（与 BIOFLOW_MANIFESTS 键一致；SettingsPanel 三开关与 TAB 显隐共用）
+export const BIOFLOW_CAPABILITY_NAMES = Object.keys(BIOFLOW_MANIFESTS);

ui/src/components/bench/BioJobsPane.vue

@@ -164,6 +164,16 @@ function closeStageLog() {
   logStage.value = null;
 }
 
+// 实时跟随：日志行追加（轮询增量）时自动滚底，保持在最新一行。
+watch(
+  () => (logRec.value ? logRec.value.lines.length : 0),
+  () => {
+    nextTick(() => {
+      if (logEl.value) logEl.value.scrollTop = logEl.value.scrollHeight;
+    });
+  },
+);
+
 // ---- 面板定位消费（聊天进度条点击 → scrollIntoView + hl-fade + 展开 log） ----
 const hlStage = ref(null);
 function consumeLocate(payload) {

ui/src/components/chat/AssistantMessage.vue

@@ -17,6 +17,11 @@ import FlowFormCard from './FlowFormCard.vue';
 import FlowFileCard from './FlowFileCard.vue';
 import FlowProgressCard from './FlowProgressCard.vue';
 import FlowArchiveCard from './FlowArchiveCard.vue';
+import ReadinessCard from './ReadinessCard.vue';
+import DiagnosisCard from './DiagnosisCard.vue';
+import VersioningCard from './VersioningCard.vue';
+import DeliveryCard from './DeliveryCard.vue';
+import LegacyBioflowBlock from './LegacyBioflowBlock.vue';
 // 用户自定义扩展分析：生命周期引导卡 + 运行卡（EXTENSION_CONTRACT.md §4 块）
 import ExtensionUploadCard from './ExtensionUploadCard.vue';
 import ExtensionBuildCard from './ExtensionBuildCard.vue';
@@ -229,15 +234,26 @@ const degradedNote = computed(() => props.message.degradedNote || null);
           :block="b"
         />
 
-        <!-- P2 生信：流程知识库引用块（FR-BIO-026；引用携带 cite 供跳转） -->
-        <div v-if="b.type === 'bioflow_qa'" class="bioflow-qa-block">
-          <div v-for="(c, ci) in b.citations" :key="ci" class="bf-qa-cite">
-            <span class="bf-qa-idx">{{ ci + 1 }}</span>
-            <span class="bf-qa-text">{{ c.text || c.title_path || c.source }}</span>
-            <span class="bf-qa-src">{{ c.title_path || c.source }}</span>
-          </div>
-          <div v-if="!b.citations || !b.citations.length" class="bf-qa-empty">{{ BF.flowQaEmpty }}</div>
-        </div>
+        <!-- G12 分析控制四卡 -->
+        <ReadinessCard
+          v-if="b.type === 'bioflow_readiness'"
+          :block="b"
+        />
+        <DiagnosisCard
+          v-if="b.type === 'bioflow_diagnosis'"
+          :block="b"
+        />
+        <VersioningCard
+          v-if="b.type === 'bioflow_versioning'"
+          :block="b"
+        />
+        <DeliveryCard
+          v-if="b.type === 'bioflow_delivery'"
+          :block="b"
+        />
+
+        <!-- P2 生信：流程知识库引用块（FR-BIO-026）→ S3 降级为只读 LegacyBioflowBlock -->
+        <LegacyBioflowBlock v-if="b.type === 'bioflow_qa'" :block="b" />
 
         <!-- 用户自定义扩展分析：上传引导卡（extension_upload） -->
         <ExtensionUploadCard

ui/src/components/chat/Composer.vue

@@ -17,8 +17,7 @@ import { T } from '../../i18n/labels.js';
 import { DG, BUILTIN_TEMPLATES } from '../../i18n/docgen.js';
 import { BF } from '../../i18n/bioflow.js';
 import { route, paperIntent } from '../../intent.js';
-import { route as routeBioflow, isExtensionCreateIntent } from '../../utils/intent.js';
-import { uploadLibrary, listLibrary } from '../../api/docgen.js';
+import { route as routeBioflow, isExtensionCreateIntent } from '../../utils/intent.js';import { uploadLibrary, listLibrary } from '../../api/docgen.js';
 import { uploadBioflowFile } from '../../api/bioflow.js';
 import { useDocgenStore } from '../../stores/docgen.js';
 import { useChatStore } from '../../stores/chat.js';
@@ -279,20 +278,13 @@ const submit = () => {
   } catch {
     intent = 'qa'; // 路由异常按漏判安全处理
   }
-  // 生信意图（含图表调整走生信 FR-BIO-019）：词典同表双跑（utils/intent.js）
-  let bioflowRoute = { intent: 'qa', reuseName: null };
-  if (intent !== 'docgen' && intent !== 'edit' && intent !== 'export' && bioflowEnabled.value) {
-    try {
-      bioflowRoute = routeBioflow(text, hasAttachments.value, hasActiveArtifact.value, hasBioflowContext.value);
-    } catch {
-      bioflowRoute = { intent: 'qa', reuseName: null };
-    }
-  }
   // 用户自定义扩展分析：A 层创建意图（EXTENSION_CONTRACT.md §5 词典同表双跑；
   // 「创建/上传 一个扩展」→ sendExtension 上传引导卡。歧义消解与运行触发由
   // 服务端 intent.py 在 chat/stream 内判定——前端只做确定性创建识别，漏判安全。）
+  // 生信意图（基因家族/转录组）S3 起不再走前端词典分流：一律进 QA 流，
+  // 由 bioflow_agent 在服务端经 nl_triggers 判定（统一由 QA 流承载）。
   let extIntent = false;
-  if (bioflowRoute.intent !== 'bioflow_qa' && bioflowRoute.intent !== 'bioflow' && bioflowEnabled.value) {
+  if (bioflowEnabled.value) {
     try {
       extIntent = isExtensionCreateIntent(text);
     } catch {
@@ -306,34 +298,6 @@ const submit = () => {
     } catch {
       emit('send', text); // chat store 未就绪（测试/降级）：漏判安全退化为 QA 路径
     }
-  } else if (bioflowRoute.intent === 'bioflow_qa') {
-    // 生信流内流程咨询（FR-BIO-026）：也走 sendBioflow（后端流内返引用块，不新建任务）
-    try {
-      useChatStore().sendBioflow(text, { mode: 'ask' }).catch(() => { /* 内部已标注错误 */ });
-    } catch {
-      emit('send', text); // 生信 store 未就绪（测试/降级）：漏判安全退化为 QA 路径
-    }
-  } else if (bioflowRoute.intent === 'bioflow') {
-    // 生信分析意图：chat.sendBioflow（plan_ready → 路径卡 → 任务事件）
-    try {
-      const jobId = null; // 任务未创建：文件上传待任务生成后由 FlowFileCard 引导
-      const chat = useChatStore();
-      chat.sendBioflow(text, { mode: 'ask', reuseName: bioflowRoute.reuseName }).catch(() => { /* 内部已标注错误 */ });
-      // 附件按生信文件上传（XHR 进度；FR-BIO-006）：任务 id 由 sendBioflow 创建任务后
-      // 回填——任务创建前的拖入文件由 FlowFileCard 阶段引导卡处理，此处兼容
-      // 已存在任务场景（当前会话任务 id 已知时直接上传）。
-      if (readyAttachments.value.length) {
-        const bioflowStore = useBioflowStore();
-        const jobIdNow = jobId || (bioflowStore.currentJob && bioflowStore.currentJob.jobId);
-        if (jobIdNow) {
-          for (const a of readyAttachments.value) {
-            chat.uploadBioflowFileToJob(jobIdNow, a.file).catch(() => { /* 失败可见：chips 显示错误 */ });
-          }
-        }
-      }
-    } catch {
-      emit('send', text); // 生信 store 未就绪（测试/降级）：漏判安全退化为 QA 路径
-    }
   } else if (intent === 'docgen') {
     // 文档生成分支：论文撰写 sub-route（paperIntent && paperEnabled → sendPaper），
     // 否则 sendDocgen（降级路径零改动——paper 未启用/未命中时触发词落 docgen 单发）。

ui/src/components/chat/DeliveryCard.vue

@@ -0,0 +1,107 @@
+<script setup>
+// chat/DeliveryCard.vue —— 交付清单卡（G12/G21-G22）
+// block: { type:'bioflow_delivery', ok, checks:{item:bool}, incomplete:[{item,reason}] }
+import { computed } from 'vue';
+import { BF } from '../../i18n/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
+
+const props = defineProps({
+  block: { type: Object, required: true },
+});
+
+const chat = useChatStore();
+
+const ok = computed(() => !!props.block.ok);
+const checks = computed(() => props.block.checks || {});
+const incomplete = computed(() => props.block.incomplete || []);
+
+function onPublish() {
+  chat.sendCardResult('delivery_publish', {
+    ok: props.block.ok,
+    checks: props.block.checks,
+    incomplete: props.block.incomplete,
+  }).catch(() => {});
+}
+</script>
+
+<template>
+  <div class="delivery-card">
+    <div class="dlc-title">
+      {{ BF.deliveryTitle }}
+      <span class="dlc-badge">{{ ok ? BF.deliveryPassed : BF.deliveryPending }}</span>
+    </div>
+    <div v-for="(v, k) in checks" :key="k" class="dlc-item">
+      <span class="dlc-item-name">{{ k }}</span>
+      <span class="dlc-item-state">{{ v ? '✓' : '✗' }}</span>
+    </div>
+    <div v-if="incomplete.length" class="dlc-incomplete">
+      {{ BF.deliveryIncomplete }}：{{ incomplete.map((i) => i.reason).join('；') }}
+    </div>
+    <div class="dlc-actions">
+      <button class="dlc-publish" type="button" @click="onPublish">{{ BF.deliveryPublish }}</button>
+    </div>
+  </div>
+</template>
+
+<style scoped>
+.delivery-card {
+  margin: 14px 0;
+  padding: 14px 16px;
+  background: var(--pa-surface-1);
+  border: 1px solid var(--pa-hairline);
+  border-radius: var(--pa-r-lg);
+}
+.dlc-title {
+  font-size: 12.5px;
+  line-height: 1.6;
+  margin-bottom: 8px;
+}
+.dlc-badge {
+  display: inline-block;
+  margin-left: 8px;
+  padding: 1px 8px;
+  border-radius: 999px;
+  font-size: 11px;
+  font-weight: 600;
+}
+.dlc-item {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+  padding: 5px 10px;
+  border: 1px solid var(--pa-hairline);
+  border-radius: var(--pa-r-md);
+  background: var(--pa-surface-2);
+  margin-bottom: 4px;
+}
+.dlc-item-name {
+  font-size: 12px;
+  color: var(--pa-ink);
+}
+.dlc-item-state {
+  font-size: 12px;
+  color: var(--pa-ink-muted);
+}
+.dlc-incomplete {
+  margin-top: 8px;
+  font-size: 12px;
+  color: var(--pa-error);
+}
+.dlc-actions {
+  margin-top: 10px;
+}
+.dlc-publish {
+  padding: 7px 16px;
+  border-radius: var(--pa-r-md);
+  background: var(--pa-gradient);
+  color: #fff;
+  font-size: 12.5px;
+  font-weight: 600;
+  cursor: pointer;
+  transition: box-shadow 0.3s var(--pa-ease), transform 0.15s var(--pa-ease);
+}
+.dlc-publish:hover {
+  box-shadow: 0 0 24px rgba(0, 212, 255, 0.4);
+  transform: translateY(-1px);
+}
+</style>

ui/src/components/chat/DiagnosisCard.vue

@@ -0,0 +1,103 @@
+<script setup>
+// chat/DiagnosisCard.vue —— 诊断卡（G12/G13 错误对象 + G15 恢复预算）
+// block: { type:'bioflow_diagnosis', category, code, summary, suggested_actions, retryable_without_change, retry_count }
+import { computed } from 'vue';
+import { BF } from '../../i18n/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
+
+const props = defineProps({
+  block: { type: Object, required: true },
+});
+
+const chat = useChatStore();
+
+const category = computed(() => props.block.category || 'unknown');
+const summary = computed(() => props.block.summary || '');
+const actions = computed(() => props.block.suggested_actions || []);
+
+function onApply() {
+  chat.sendCardResult('diagnosis', {
+    category: props.block.category,
+    code: props.block.code,
+    summary: props.block.summary,
+    suggested_actions: props.block.suggested_actions,
+  }).catch(() => {});
+}
+</script>
+
+<template>
+  <div class="diagnosis-card">
+    <div class="dc-title">
+      {{ BF.diagTitle }}
+      <span class="dc-badge" :class="`cat-${category}`">{{ category }}</span>
+    </div>
+    <div class="dc-summary">{{ summary }}</div>
+    <div class="dc-actions">
+      <div v-for="(a, i) in actions" :key="i" class="dc-suggestion">· {{ a }}</div>
+      <button class="dc-action" type="button" @click="onApply">{{ BF.diagApply }}</button>
+    </div>
+  </div>
+</template>
+
+<style scoped>
+.diagnosis-card {
+  margin: 14px 0;
+  padding: 14px 16px;
+  background: var(--pa-surface-1);
+  border: 1px solid var(--pa-hairline);
+  border-radius: var(--pa-r-lg);
+}
+.dc-title {
+  font-size: 12.5px;
+  line-height: 1.6;
+  margin-bottom: 8px;
+}
+.dc-badge {
+  display: inline-block;
+  margin-left: 8px;
+  padding: 1px 8px;
+  border-radius: 999px;
+  font-size: 11px;
+  font-weight: 600;
+}
+.cat-resource { background: rgba(255, 152, 0, 0.14); color: #ff9800; }
+.cat-environment { background: rgba(0, 212, 255, 0.14); color: #00b8d4; }
+.cat-transient { background: rgba(255, 193, 7, 0.14); color: #c9a227; }
+.cat-input { background: rgba(103, 58, 183, 0.14); color: #7c4dff; }
+.cat-reference { background: rgba(0, 150, 136, 0.14); color: #009688; }
+.cat-adapter { background: rgba(158, 158, 158, 0.14); color: #757575; }
+.cat-artifact { background: rgba(233, 30, 99, 0.14); color: #e91e63; }
+.cat-scientific_precondition { background: rgba(76, 175, 80, 0.14); color: #4caf50; }
+.cat-unknown { background: var(--pa-surface-3); color: var(--pa-ink-muted); }
+.dc-summary {
+  font-size: 12.5px;
+  line-height: 1.6;
+  color: var(--pa-ink);
+  margin-bottom: 8px;
+}
+.dc-actions {
+  display: flex;
+  flex-direction: column;
+  gap: 6px;
+  margin-top: 8px;
+}
+.dc-suggestion {
+  font-size: 12px;
+  color: var(--pa-ink-muted);
+}
+.dc-action {
+  align-self: flex-start;
+  padding: 7px 16px;
+  border-radius: var(--pa-r-md);
+  background: var(--pa-gradient);
+  color: #fff;
+  font-size: 12.5px;
+  font-weight: 600;
+  cursor: pointer;
+  transition: box-shadow 0.3s var(--pa-ease), transform 0.15s var(--pa-ease);
+}
+.dc-action:hover {
+  box-shadow: 0 0 24px rgba(0, 212, 255, 0.4);
+  transform: translateY(-1px);
+}
+</style>

ui/src/components/chat/ExtensionBuildCard.vue

@@ -5,7 +5,7 @@
 // 复用 FlowFormCard 视觉令牌（字段行 label 96px / input 同款 / 主按钮 gradient）。
 import { computed, ref } from 'vue';
 import { BF } from '../../i18n/bioflow.js';
-import { buildExtension } from '../../api/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
 
 const props = defineProps({
   block: { type: Object, required: true },
@@ -13,6 +13,8 @@ const props = defineProps({
 
 const emit = defineEmits(['submitted', 'error']);
 
+const chat = useChatStore();
+
 const submitting = ref(false);
 const submitError = ref('');
 
@@ -43,27 +45,25 @@ const hasDeps = computed(() =>
   (Array.isArray(reqs.value.pip) && reqs.value.pip.length > 0)
   || (Array.isArray(reqs.value.apt) && reqs.value.apt.length > 0));
 
-/** 提交修正：POST build 带修正值（后端按 ext_id 重入转换） */
+/** 提交（S4 改走 card_result 进 QA 流）：
+ *  - skip=true（跳过/采纳 AI 结果）→ 重触发 AI 转换（build）
+ *  - skip=false（编辑修正）→ confirm 语义（复用 confirm_extension 编辑值入参） */
 async function submit({ skip = false } = {}) {
   if (submitting.value) return;
   submitting.value = true;
   submitError.value = '';
   try {
-    const body = {};
-    if (!skip) {
+    if (skip) {
+      await chat.sendCardResult('extension_action', { action: 'build', ext_id: props.block.extId });
+    } else {
       if (!templateDraft.value.trim()) { submitError.value = BF.extBuildFieldRequired; submitting.value = false; return; }
-      body.command_template = templateDraft.value.trim();
-      body.runtime_image = imageDraft.value.trim() || undefined;
-      body.nl_triggers = triggersDraft.value.split(/[,，]/).map((s) => s.trim()).filter(Boolean);
-      body.analysis_type = typeDraft.value.trim() || undefined;
-    }
-    await buildExtension(props.block.extId, body);
-    // 提交成功以本地修正为准（后端重入结果由 extension_build 帧再次刷新）
-    if (!skip) {
-      props.block.commandTemplate = templateDraft.value.trim();
-      props.block.runtimeImage = imageDraft.value.trim() || props.block.runtimeImage;
-      props.block.nlTriggers = triggersDraft.value.split(/[,，]/).map((s) => s.trim()).filter(Boolean);
-      props.block.analysisType = typeDraft.value.trim() || props.block.analysisType;
+      await chat.sendCardResult('extension_action', {
+        action: 'confirm',
+        ext_id: props.block.extId,
+        nl_triggers: triggersDraft.value.split(/[,，]/).map((s) => s.trim()).filter(Boolean),
+        parameters: props.block.parameters || [],
+        runtime_image: imageDraft.value.trim(),
+      });
     }
     props.block.submitted = true;
     emit('submitted', { extId: props.block.extId, skip });

ui/src/components/chat/ExtensionConfirmCard.vue

@@ -47,10 +47,10 @@ async function run() {
       else if (f.type === 'float' || f.type === 'number') params[f.name] = parseFloat(v);
       else params[f.name] = String(v);
     }
-    const result = await chat.confirmExtensionRun(props.block, {
+    const result = await chat.sendCardResult('extension_action', {
+      action: 'run',
+      ext_id: props.block.extId,
       params,
-      files: [],
-      aMsg: props.message || null,
     });
     emit('submitted', { extId: props.block.extId, result });
   } catch (err) {

ui/src/components/chat/ExtensionPublishCard.vue

@@ -4,7 +4,7 @@
 // 发布成功后 extension_published 帧挂发布确认块（本卡随试运行卡同帧刷新）。
 import { computed, ref } from 'vue';
 import { BF } from '../../i18n/bioflow.js';
-import { publishExtension } from '../../api/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
 
 const props = defineProps({
   block: { type: Object, required: true },
@@ -12,6 +12,8 @@ const props = defineProps({
 
 const emit = defineEmits(['published', 'error']);
 
+const chat = useChatStore();
+
 const submitting = ref(false);
 const submitError = ref('');
 const triggersDraft = ref('');
@@ -29,11 +31,12 @@ async function publish() {
   submitError.value = '';
   try {
     const nlTriggers = triggersDraft.value.split(/[,，]/).map((s) => s.trim()).filter(Boolean);
-    const data = await publishExtension(props.block.extId, { nl_triggers: nlTriggers });
-    const result = (data && data.data) || data || {};
-    if (Array.isArray(result.nl_triggers)) props.block.nlTriggers = result.nl_triggers;
-    else props.block.nlTriggers = nlTriggers;
-    if (result.display_name) props.block.displayName = result.display_name;
+    await chat.sendCardResult('extension_action', {
+      action: 'publish',
+      ext_id: props.block.extId,
+      nl_triggers: nlTriggers,
+    });
+    props.block.nlTriggers = nlTriggers;
     props.block.published = true;
     emit('published', { extId: props.block.extId, nlTriggers: props.block.nlTriggers });
   } catch (err) {

ui/src/components/chat/ExtensionTrialCard.vue

@@ -6,7 +6,6 @@
 import { computed, ref } from 'vue';
 import { BF } from '../../i18n/bioflow.js';
 import { useChatStore } from '../../stores/chat.js';
-import { repairExtension } from '../../api/bioflow.js';
 
 const props = defineProps({
   block: { type: Object, required: true },
@@ -36,17 +35,17 @@ function onGoldenChange(e) {
   if (e.target) e.target.value = '';
 }
 
-/** 上传测试输入 → 触发试运行（服务端跑容器，结果经 extension_trial 帧回流） */
+/** 试运行（S4 改走 card_result 进 QA 流；测试输入文件上传为后置上传，另行登记） */
 async function runTrial() {
   if (running.value || repairing.value) return;
   if (!props.block.extId) { submitError.value = BF.extTrialNoExtId; return; }
-  if (!testInput.value) { submitError.value = BF.extTrialInputEmpty; return; }
   running.value = true;
   submitError.value = '';
   try {
-    const files = [testInput.value];
-    if (goldenInput.value) files.push(goldenInput.value);
-    const result = await chat.trialRunExtension(props.block.extId, files);
+    const result = await chat.sendCardResult('extension_action', {
+      action: 'trial_run',
+      ext_id: props.block.extId,
+    });
     emit('trialled', { extId: props.block.extId, result });
   } catch (err) {
     submitError.value = err?.message || BF.extUploadError;
@@ -63,7 +62,7 @@ async function doRepair() {
   repairing.value = true;
   submitError.value = '';
   try {
-    await repairExtension(props.block.extId, {});
+    await chat.sendCardResult('extension_action', { action: 'repair', ext_id: props.block.extId });
   } catch (err) {
     submitError.value = err?.message || BF.extTrialRepairFailed;
     emit('error', err);

ui/src/components/chat/ExtensionValidateCard.vue

@@ -4,7 +4,7 @@
 // 复用 FlowFormCard 字段行令牌。确认成功后由服务端 extension_published 帧收尾。
 import { computed, ref } from 'vue';
 import { BF } from '../../i18n/bioflow.js';
-import { buildExtension } from '../../api/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
 
 const props = defineProps({
   block: { type: Object, required: true },
@@ -12,6 +12,8 @@ const props = defineProps({
 
 const emit = defineEmits(['submitted', 'error']);
 
+const chat = useChatStore();
+
 const submitting = ref(false);
 const submitError = ref('');
 const values = ref({});
@@ -37,7 +39,7 @@ const goldenOk = computed(() => {
   return null;
 });
 
-/** 确认：重新 build（门禁纪律：确认前不推进生命周期；修正值随 build 重入）。 */
+/** 确认（S4 改走 card_result）：编辑修正（form_defaults 参数）→ confirm 语义。 */
 async function confirm() {
   if (submitting.value) return;
   submitting.value = true;
@@ -49,7 +51,13 @@ async function confirm() {
       if (v === '' || v === null || v === undefined) continue;
       params[f.name] = v;
     }
-    await buildExtension(props.block.extId, { params });
+    // 编辑修正走 confirm 环节（复用 confirm_extension 编辑值入参）
+    await chat.sendCardResult('extension_action', {
+      action: 'confirm',
+      ext_id: props.block.extId,
+      parameters: props.block.parameters || [],
+      runtime_image: '',
+    });
     props.block.confirmed = true;
     emit('submitted', { extId: props.block.extId, params });
   } catch (err) {

ui/src/components/chat/FlowArchiveCard.vue

@@ -7,6 +7,7 @@
 import { computed, ref } from 'vue';
 import { BF } from '../../i18n/bioflow.js';
 import { useBioflowStore } from '../../stores/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
 
 const props = defineProps({
   block: { type: Object, required: true },
@@ -15,6 +16,7 @@ const props = defineProps({
 const emit = defineEmits(['dismissed', 'archived', 'error']);
 
 const bioflow = useBioflowStore();
+const chat = useChatStore();
 
 const nameDraft = ref(props.block.name || '');
 const descDraft = ref(props.block.description || '');
@@ -50,6 +52,12 @@ async function doArchive() {
     // 存档状态回复（FR-BIO-021）：名称/位置/大小三要素写回块状态
     props.block.status = 'done';
     props.block.result = result;
+    // S3：同步发 card_result 进 QA 流，让 BioflowAgent 自然语言复述存档决定（语义一致）
+    chat.sendCardResult('archive_choice', {
+      job_id: props.block.jobId,
+      archive: true,
+      name: props.block.name,
+    }).catch(() => { /* 复述失败不影响已完成的存档 */ });
     emit('archived', result);
   } catch (err) {
     errorText.value = err?.message || BF.archiveError;

ui/src/components/chat/FlowFileCard.vue

@@ -84,16 +84,16 @@ function onInputChange(e) {
   if (e.target) e.target.value = ''; // 允许重复选择同一文件
 }
 
-// ---- 服务器路径登记（FR-BIO-007） ----
+// ---- 服务器路径登记（FR-BIO-007；S3 改走 card_result 进 QA 流） ----
 async function registerPath() {
   const p = pathDraft.value.trim();
   if (!p || registering.value || !jobId.value) return;
   registering.value = true;
   registerError.value = '';
   try {
-    const res = await chat.registerBioflowPath(jobId.value, p);
+    await chat.sendCardResult('file_upload', { job_id: jobId.value, paths: [p] });
     pathDraft.value = '';
-    emit('registered', { path: p, res });
+    emit('registered', { path: p });
   } catch (err) {
     registerError.value = err?.message || BF.filePathError;
     emit('error', err);

ui/src/components/chat/FlowFormCard.vue

@@ -10,6 +10,7 @@
 import { computed, reactive, ref } from 'vue';
 import { BF } from '../../i18n/bioflow.js';
 import { useBioflowStore } from '../../stores/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
 
 const props = defineProps({
   block: { type: Object, required: true },
@@ -18,6 +19,7 @@ const props = defineProps({
 const emit = defineEmits(['submitted', 'error']);
 
 const bioflow = useBioflowStore();
+const chat = useChatStore();
 
 const fields = computed(() => props.block.fields || []);
 const stage = computed(() => props.block.stage || '');
@@ -153,7 +155,8 @@ async function submit() {
     } else {
       const jobId = bioflow.currentJob.jobId || props.block.jobId;
       if (!jobId) throw new Error('no job');
-      await bioflow.confirmStage(stage.value, params);
+      // S3：卡片不直连控制面——参数确认改为 card_result 消息进 QA 流（BioflowAgent 经 confirm_stage 执行）
+      await chat.sendCardResult('form_confirm', { job_id: jobId, stage: stage.value, params });
       props.block.submitted = true;
       emit('submitted', { stage: stage.value, params });
     }

ui/src/components/chat/FlowPathCard.vue

@@ -7,7 +7,7 @@
 // 复用句式（FR-BIO-023）：候选来自存档装载，卡片头部明示「复用存档 XXX 的方法」。
 import { computed, ref } from 'vue';
 import { BF } from '../../i18n/bioflow.js';
-import { useBioflowStore } from '../../stores/bioflow.js';
+import { useBioflowStore, inferBioflowChain } from '../../stores/bioflow.js';
 import { useChatStore } from '../../stores/chat.js';
 
 const props = defineProps({
@@ -66,22 +66,16 @@ async function confirmCreate() {
   confirming.value = true;
   error.value = '';
   try {
-    // r4 修复：不再 emit('updated')（该事件全链无人监听，任务创建后 UI 静默）——
-    // 改走 chat store 一站式 confirmBioflowPath：创建 → 挂进度块 → 订阅任务事件
-    // 桥接推进 → 落库。aMsg 从 chat 消息流定位（当前消息 = 含本 path 块的 assistant 消息）。
-    const aMsg = (chat.messages || []).find(
-      (m) => m && m.role === 'assistant' && Array.isArray(m.blocks) && m.blocks.includes(props.block),
-    );
-    const detail = await chat.confirmBioflowPath({
-      title: (chat.messages || []).find((m) => m.role === 'user')?.text?.slice(0, 50) || '生信任务',
+    // S3：卡片不直连控制面——确认路径改为生成 card_result 消息进 QA 流，
+    // 由 BioflowAgent 经 create_*_job 工具执行并自然语言复述。
+    props.block.jobId = null; // 由 QA 流返回的 active_job_id 回填
+    await chat.sendCardResult('path_selection', {
+      chain: inferBioflowChain(cand.stages),
       stages: cand.stages,
+      title: (chat.messages || []).find((m) => m.role === 'user')?.text?.slice(0, 50) || '生信任务',
+      auto_continue: false,
       params: {},
-      autoContinue: false,
-      archiveId: reuseArchive.value || null,
-      aMsg: aMsg || null,
     });
-    // 进度块由 confirmBioflowPath 挂载；此处标记 path 块已确认
-    props.block.jobId = (detail && detail.id) || null;
   } catch (err) {
     error.value = err?.message || BF.pathStageCreating;
     emit('flow-error', err);

ui/src/components/chat/FlowProgressCard.vue

@@ -1,35 +1,18 @@
 <script setup>
-// chat/FlowProgressCard.vue —— 生信阶段进度卡（FR-BIO-011/012/013/014，UI_SPEC §8.4）
-// 结构/状态点/连接线/相位色复用 §4.4 pipeline-card 全部令牌（PipelineCard 零改动，
-// 本卡按 §8.4 同款视觉独立实现）：
-//   done=--pa-t-done 底白 ✓；running=相位色底 ● + pulse；waiting=surface-3 底 ◌
-// 新增两态与附加区（§8.4）：
-//   failed 态：--pa-error 底 ✕，状态文字 error 色 12px/600
-//   skipped 态：--pa-ink-subtle 底 ◌，状态文字 ink-subtle
-//   日志尾区：仅 running/failed 展开：--pa-code-bg 底，mono 11px，padding 8px 10px，
-//             max-height 96px 滚动，随 SSE 追加
-//   三选一按钮：仅 failed：重跑/跳过/改参数重跑，pane-btn 同款 12px，gap 8px
-//   折叠：阶段 >10 自动分组折叠（组头 12px/600 + 展开箭头），默认展开运行中所在组
-// 断线回放（FR-BIO-014）：block.stages 被快照整体替换（引用变化）时本卡自动整体刷新。
+// chat/FlowProgressCard.vue —— 生信阶段进度卡（S3 精简为只读）
+// 只读展示：阶段列表（状态点三态）+ 进度条 + 最近一行日志尾 + 折叠分组。
+// S3 起去掉暂停/恢复、失败重跑/跳过、改参数重跑等直连控制按钮与 locate 点击——
+// 任务控制一律走自然语言（QA 流），本卡不直连生信控制面。
 import { computed, nextTick, ref, watch } from 'vue';
 import { BF, stageStatusText } from '../../i18n/bioflow.js';
 import { PHASE_COLOR_VAR } from '../../i18n/labels.js';
-import { useBioflowStore } from '../../stores/bioflow.js';
-import { bioflowCatalog } from '../../api/bioflow.js';
 
 const props = defineProps({
   block: { type: Object, required: true },
 });
 
-const emit = defineEmits(['rerun', 'skip', 'rerun-with-params', 'pause', 'resume', 'action-error', 'locate']);
-
-const bioflow = useBioflowStore();
-
 const stages = computed(() => props.block.stages || []);
-const jobStatus = computed(() => props.block.jobStatus || bioflow.currentJob.jobStatus);
-const acting = ref(''); // 'pause' | 'resume' | `rerun:${stage}` | `skip:${stage}`
-const actionError = ref('');
-const rerunFormStage = ref(null); // 改参数重跑弹出该阶段参数表单（FR-BIO-012）
+const jobStatus = computed(() => props.block.jobStatus);
 
 // 相位色映射（与 PipelineCard PHASE_COLOR_VAR 一致；阶段序号对应五相位循环）
 function phaseVar(i) {
@@ -37,7 +20,6 @@ function phaseVar(i) {
   return PHASE_COLOR_VAR[keys[i % keys.length]] || PHASE_COLOR_VAR.planning;
 }
 
-/** 状态点符号与颜色（三重编码：颜色 + 图标 + 文字） */
 function dotClass(st) {
   return {
     done: 'done',
@@ -54,20 +36,13 @@ function dotSymbol(st) {
 }
 
 const showLog = (st) => st.status === 'running' || st.status === 'failed';
-const showActions = (st) => st.status === 'failed';
 
-// ---- 进度条(进度帧 stage_progress 驱动;点击 → 定位到生信任务 TAB) ----
-/** 阶段是否有确定性进度(白名单 rnaseq 阶段才有 percent) */
 function hasPct(st) {
   return typeof st.progress === 'number' && st.progress >= 0 && st.progress <= 100;
 }
-/** 阶段是否处于真运行态(收到过 stage_started;queued 无事件不显示条) */
 function isLiveRunning(st) {
   return st.status === 'running';
 }
-function locateStage(st) {
-  emit('locate', { jobId: props.block.jobId, stage: st.stage });
-}
 
 // ---- 日志尾区自动滚底(SSE 追加,2s 节流) ----
 const logRefs = ref({});
@@ -91,13 +66,12 @@ watch(
   { deep: true },
 );
 
-// ---- 折叠（FR-BIO-013：阶段 >10 自动分组折叠；默认展开运行中所在组） ----
+// ---- 折叠（阶段 >10 自动分组折叠；默认展开运行中所在组） ----
 const FOLD_THRESHOLD = 10;
 const COLLAPSED_GROUP_SIZE = 8;
 const needsFold = computed(() => stages.value.length > FOLD_THRESHOLD);
 const openGroups = ref(new Set());
 
-/** 折叠分组：每组 8 阶段，全部可折叠；默认仅展开运行中所在组（其余折叠，组头可展开） */
 const groups = computed(() => {
   const all = stages.value;
   if (!needsFold.value) return [{ title: null, stages: all, collapsible: false }];
@@ -118,7 +92,6 @@ const groups = computed(() => {
   }));
 });
 
-/** 组展开状态：快照整体替换（引用变化）时按运行中所在组重算默认展开 */
 watch(
   () => props.block.stages,
   () => {
@@ -144,120 +117,6 @@ function toggleGroup(i) {
 function isGroupOpen(i) {
   return openGroups.value.has(i);
 }
-
-// ---- 失败三选一（FR-BIO-012） ----
-async function doRerun(st) {
-  if (acting.value) return;
-  acting.value = `rerun:${st.stage}`;
-  actionError.value = '';
-  try {
-    await bioflow.rerunStage(st.stage, null);
-    emit('rerun', st.stage);
-  } catch (err) {
-    actionError.value = err?.message || BF.progActionError;
-    emit('action-error', err);
-  } finally {
-    acting.value = '';
-  }
-}
-async function doSkip(st) {
-  if (acting.value) return;
-  acting.value = `skip:${st.stage}`;
-  actionError.value = '';
-  try {
-    await bioflow.skipStage(st.stage);
-    emit('skip', st.stage);
-  } catch (err) {
-    actionError.value = err?.message || BF.progActionError;
-    emit('action-error', err);
-  } finally {
-    acting.value = '';
-  }
-}
-function doRerunWithParams(st) {
-  rerunFormStage.value = st.stage;
-  // 拉取该阶段目录参数 schema（来源标注=阶段契约文档），表单值空提交即按默认重跑
-  loadRerunSchema(st.stage);
-}
-function closeRerunForm() {
-  rerunFormStage.value = null;
-}
-
-// ---- 改参数重跑表单（目录 schema 驱动；提交 rerun 带参数） ----
-const rerunSchema = ref([]);
-const rerunValues = ref({});
-const rerunLoading = ref(false);
-const rerunSubmitting = ref(false);
-
-async function loadRerunSchema(stage) {
-  rerunSchema.value = [];
-  rerunValues.value = {};
-  rerunLoading.value = true;
-  try {
-    const data = await bioflowCatalog({ stage });
-    const entry = (data && data.data && data.data.stage) || {};
-    rerunSchema.value = Array.isArray(entry.params) ? entry.params : [];
-    for (const p of rerunSchema.value) rerunValues.value[p.name] = p.default ?? '';
-  } catch {
-    rerunSchema.value = []; // 目录不可达：空表单直接重跑（默认参数）
-  } finally {
-    rerunLoading.value = false;
-  }
-}
-
-async function submitRerunForm() {
-  if (rerunSubmitting.value) return;
-  rerunSubmitting.value = true;
-  actionError.value = '';
-  try {
-    const params = {};
-    for (const p of rerunSchema.value) {
-      const v = rerunValues.value[p.name];
-      if (v === '' || v === null || v === undefined) continue;
-      params[p.name] = (p.type === 'int' || p.type === 'float' || p.type === 'number') ? Number(v) : String(v);
-    }
-    await bioflow.rerunStage(rerunFormStage.value, params);
-    emit('rerun-with-params', rerunFormStage.value);
-    rerunFormStage.value = null;
-  } catch (err) {
-    actionError.value = err?.message || BF.progActionError;
-    emit('action-error', err);
-  } finally {
-    rerunSubmitting.value = false;
-  }
-}
-
-// ---- 暂停/恢复（FR-BIO-010） ----
-const showPause = computed(() => jobStatus.value === 'running');
-const showResume = computed(() => jobStatus.value === 'paused');
-async function doPause() {
-  if (acting.value) return;
-  acting.value = 'pause';
-  actionError.value = '';
-  try {
-    await bioflow.pauseJob();
-    emit('pause');
-  } catch (err) {
-    actionError.value = err?.message || BF.progActionError;
-    emit('action-error', err);
-  } finally {
-    acting.value = '';
-  }
-}
-async function doResume() {
-  if (acting.value) return;
-  acting.value = 'resume';
-  actionError.value = '';
-  try {
-    await bioflow.resumeJob();
-    emit('resume');
-  } catch (err) {
-    actionError.value = err?.message || BF.progActionError;
-    emit('action-error', err);
-  } finally {
-    acting.value = '';
-  }
-}
 </script>
 
 <template>
@@ -265,12 +124,6 @@ async function doResume() {
     <div class="pc-head">
       <span class="pc-title">{{ BF.progTitle }}</span>
       <div class="pc-head-right">
-        <button v-if="showPause" class="pane-btn" type="button" :disabled="!!acting" @click="doPause">
-          {{ acting === 'pause' ? BF.progPausing : BF.progPause }}
-        </button>
-        <button v-if="showResume" class="pane-btn" type="button" :disabled="!!acting" @click="doResume">
-          {{ acting === 'resume' ? BF.progResuming : BF.progResume }}
-        </button>
         <span class="badge" :class="jobStatus === 'running' ? 'running' : jobStatus === 'paused' ? 'idle' : jobStatus === 'done' ? 'done' : jobStatus === 'failed' ? 'error' : 'idle'">
           <span class="dot"></span>
           {{ jobStatus === 'running' ? BF.progBadgeRunning : jobStatus === 'paused' ? BF.progBadgePaused : jobStatus === 'done' ? BF.progBadgeDone : jobStatus === 'failed' ? BF.progBadgeFailed : BF.progBadgeCreated }}
@@ -278,7 +131,7 @@ async function doResume() {
       </div>
     </div>
 
-    <!-- 折叠分组（FR-BIO-013） -->
+    <!-- 折叠分组 -->
     <template v-for="(g, gi) in groups" :key="gi">
       <button
         v-if="g.collapsible"
@@ -301,17 +154,14 @@ async function doResume() {
           >{{ dotSymbol(st) }}</span>
           <span class="p-name">{{ st.stage }}</span>
           <span class="p-desc" :title="st.error || (st.progressMessage || '')">{{ st.progressMessage || st.error || '' }}</span>
-          <!-- 进度条:有 percent → 确定性;running 无 percent → 不确定扫光;其余 → 不显示 -->
-          <button
+          <!-- 进度条（S3 只读，不可点击定位） -->
+          <div
             v-if="hasPct(st) || (isLiveRunning(st) && !hasPct(st))"
-            class="prog-track clickable"
-            type="button"
-            :title="BF.progLocateHint"
-            @click.stop="locateStage(st)"
+            class="prog-track"
           >
             <span v-if="hasPct(st)" class="prog-fill" :class="{ full: st.progress >= 100 }" :style="{ width: `${Math.min(st.progress, 100)}%` }"></span>
             <span v-else class="prog-indeterminate"></span>
-          </button>
+          </div>
           <span v-if="hasPct(st)" class="prog-pct">{{ Math.min(st.progress, 100) }}%</span>
           <span class="p-state" :style="st.status === 'running' ? { color: `var(${phaseVar(gi * COLLAPSED_GROUP_SIZE + si)})` } : null">
             <span v-if="st.status === 'running'" class="spin"></span>
@@ -321,57 +171,17 @@ async function doResume() {
       </div>
     </template>
 
-    <!-- 日志尾区（§8.4：仅 running/failed 展开；--pa-code-bg mono 11px padding 8px 10px max-height 96px 滚动） -->
+    <!-- 日志尾区（仅 running/failed 展开；最近一行，随 SSE 追加自动滚底） -->
     <template v-for="st in stages" :key="'log-' + st.stage">
       <div v-if="showLog(st)" class="pc-log">
         <div class="pc-log-head">{{ st.stage }} · {{ BF.jobsLogTitle }}</div>
         <pre class="pc-log-body" :ref="(el) => setLogRef(st.stage, el)">{{ st.log_tail || BF.progLogPlaceholder }}</pre>
       </div>
-
-      <!-- 失败三选一（§8.4：仅 failed；pane-btn 同款 12px，gap 8px） -->
-      <div v-if="showActions(st)" class="pc-actions">
-        <button
-          class="pane-btn"
-          type="button"
-          :disabled="!!acting"
-          @click="doRerun(st)"
-        >{{ acting === 'rerun:' + st.stage ? BF.formSubmitting : BF.progRerun }}</button>
-        <button
-          class="pane-btn"
-          type="button"
-          :disabled="!!acting"
-          @click="doSkip(st)"
-        >{{ acting === 'skip:' + st.stage ? BF.formSubmitting : BF.progSkip }}</button>
-        <button class="pane-btn" type="button" @click="doRerunWithParams(st)">{{ BF.progRerunWithParams }}</button>
-      </div>
     </template>
-
-    <!-- 改参数重跑：该阶段参数表单（FR-BIO-012；由阶段目录 schema 构造） -->
-    <div v-if="rerunFormStage" class="pc-rerun-form">
-      <div class="pc-rerun-head">
-        <span>{{ BF.rerunFormTitle.replace('{stage}', rerunFormStage) }}</span>
-        <button class="pane-btn" type="button" @click="closeRerunForm">✕</button>
-      </div>
-      <div v-if="rerunLoading" class="pc-rerun-hint">{{ BF.jobsManifestLoading }}</div>
-      <div v-else-if="rerunSchema.length" class="pc-rerun-fields">
-        <div v-for="p in rerunSchema" :key="p.name" class="pc-rerun-field">
-          <span class="pc-rerun-label">{{ p.name }}</span>
-          <input v-model="rerunValues[p.name]" class="pc-rerun-input" type="text" />
-          <span class="pc-rerun-source">{{ BF.formSourceContract }}</span>
-        </div>
-      </div>
-      <div class="pc-rerun-actions">
-        <button class="pane-btn" type="button" @click="closeRerunForm">{{ BF.jobsConfirmNo }}</button>
-        <button class="pane-btn run" type="button" :disabled="rerunSubmitting" @click="submitRerunForm">
-          {{ rerunSubmitting ? BF.formSubmitting : BF.rerunFormSubmit }}
-        </button>
-      </div>
-    </div>
-
-    <div v-if="actionError" class="pc-error">{{ actionError }}</div>
   </div>
 </template>
 
+
 <style scoped>
 /* UI_SPEC §8.4：结构/状态点/连接线/相位色复用 §4.4 pipeline-card 全部令牌 */
 .bioflow-progress-card {

ui/src/components/chat/LegacyBioflowBlock.vue

@@ -0,0 +1,94 @@
+<script setup>
+// chat/LegacyBioflowBlock.vue —— 旧生信块只读降级渲染（S3）
+// 用途：旧会话历史里遗留的生信块（bioflow_qa 引用块 / 旧版 bioflow_* 块）在新架构下
+// 以只读形式降级渲染，保证 hydrate 打开旧会话不报错、不渲染可交互控件。
+// 仅展示，不发任何控制面请求。
+import { BF } from '../../i18n/bioflow.js';
+
+const props = defineProps({
+  block: { type: Object, required: true },
+});
+
+function titleFor(type) {
+  switch (type) {
+    case 'bioflow_qa':
+      return BF.legacyQaTitle;
+    case 'bioflow_path':
+      return BF.legacyPathTitle;
+    case 'bioflow_form':
+      return BF.legacyFormTitle;
+    case 'bioflow_file':
+      return BF.legacyFileTitle;
+    case 'bioflow_progress':
+      return BF.legacyProgressTitle;
+    case 'bioflow_archive':
+      return BF.legacyArchiveTitle;
+    default:
+      return BF.legacyBlockTitle;
+  }
+}
+</script>
+
+<template>
+  <div class="legacy-bioflow-block">
+    <div class="lbf-title">{{ titleFor(block.type) }}</div>
+    <!-- 旧 bioflow_qa 引用块：只读引用列表 -->
+    <template v-if="block.type === 'bioflow_qa'">
+      <div v-for="(c, ci) in (block.citations || [])" :key="ci" class="lbf-cite">
+        <span class="lbf-idx">{{ ci + 1 }}</span>
+        <span class="lbf-text">{{ c.text || c.title_path || c.source }}</span>
+        <span class="lbf-src">{{ c.title_path || c.source }}</span>
+      </div>
+      <div v-if="!block.citations || !block.citations.length" class="lbf-empty">{{ BF.flowQaEmpty }}</div>
+    </template>
+    <!-- 旧任务/进度类块：只读摘要（若携带 task/job 信息则显示，否则显示占位） -->
+    <template v-else>
+      <div v-if="block.jobId" class="lbf-job">{{ BF.legacyJobPrefix }} {{ block.jobId }}</div>
+      <div class="lbf-empty">{{ BF.legacyReadonlyHint }}</div>
+    </template>
+  </div>
+</template>
+
+<style scoped>
+.legacy-bioflow-block {
+  border: 1px solid var(--border, #e5e7eb);
+  border-radius: 8px;
+  padding: 10px 12px;
+  margin: 8px 0;
+  opacity: 0.72;
+  background: var(--surface-1, #fff);
+}
+.lbf-title {
+  font-size: 12px;
+  font-weight: 600;
+  color: var(--text-dim, #6b7280);
+  margin-bottom: 6px;
+}
+.lbf-cite {
+  display: flex;
+  gap: 6px;
+  font-size: 13px;
+  line-height: 1.5;
+  margin: 3px 0;
+}
+.lbf-idx {
+  color: var(--accent, #2563eb);
+  font-weight: 600;
+  flex-shrink: 0;
+}
+.lbf-text {
+  color: var(--text, #111827);
+}
+.lbf-src {
+  color: var(--text-dim, #6b7280);
+  font-size: 12px;
+}
+.lbf-job {
+  font-size: 13px;
+  color: var(--text, #111827);
+}
+.lbf-empty {
+  font-size: 12px;
+  color: var(--text-dim, #9ca3af);
+}
+</style>

ui/src/components/chat/ReadinessCard.vue

@@ -0,0 +1,117 @@
+<script setup>
+// chat/ReadinessCard.vue —— 就绪检查卡（G12/G10 check_readiness 四象限）
+// block: { type:'bioflow_readiness', ready, quadrants:[{name,ok}], error }
+import { computed } from 'vue';
+import { BF } from '../../i18n/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
+
+const props = defineProps({
+  block: { type: Object, required: true },
+});
+
+const chat = useChatStore();
+
+const ready = computed(() => !!props.block.ready);
+const quadrants = computed(() => props.block.quadrants || []);
+
+function quadrantLabel(name) {
+  return BF[`readinessQ_${name}`] || name;
+}
+
+function onRecheck() {
+  chat.sendCardResult('readiness_check', {}).catch(() => {});
+}
+</script>
+
+<template>
+  <div class="readiness-card">
+    <div class="rc-title">
+      {{ BF.readinessTitle }}
+      <span class="rc-badge">{{ ready ? BF.readinessReady : BF.readinessNotReady }}</span>
+    </div>
+    <div class="rc-grid">
+      <div v-for="q in quadrants" :key="q.name" class="rc-quadrant">
+        <span class="rc-dot" :class="{ ok: q.ok }">{{ q.ok ? '✓' : '✗' }}</span>
+        <span class="rc-quad-name">{{ quadrantLabel(q.name) }}</span>
+      </div>
+    </div>
+    <div class="rc-actions">
+      <button class="rc-recheck" type="button" @click="onRecheck">
+        {{ BF.readinessRecheck }}
+      </button>
+    </div>
+  </div>
+</template>
+
+<style scoped>
+.readiness-card {
+  margin: 14px 0;
+  padding: 14px 16px;
+  background: var(--pa-surface-1);
+  border: 1px solid var(--pa-hairline);
+  border-radius: var(--pa-r-lg);
+}
+.rc-title {
+  font-size: 12.5px;
+  line-height: 1.6;
+  margin-bottom: 10px;
+}
+.rc-badge {
+  display: inline-block;
+  margin-left: 8px;
+  padding: 1px 8px;
+  border-radius: 999px;
+  font-size: 11px;
+  font-weight: 600;
+}
+.rc-grid {
+  display: grid;
+  grid-template-columns: repeat(2, 1fr);
+  gap: 8px;
+}
+.rc-quadrant {
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  padding: 8px 10px;
+  border: 1px solid var(--pa-hairline);
+  border-radius: var(--pa-r-md);
+  background: var(--pa-surface-2);
+}
+.rc-dot {
+  display: inline-flex;
+  align-items: center;
+  justify-content: center;
+  width: 18px;
+  height: 18px;
+  border-radius: 50%;
+  font-size: 11px;
+  font-weight: 700;
+  background: var(--pa-error);
+  color: #fff;
+}
+.rc-dot.ok {
+  background: var(--pa-gradient);
+}
+.rc-quad-name {
+  font-size: 12px;
+  color: var(--pa-ink);
+}
+.rc-actions {
+  margin-top: 10px;
+}
+.rc-recheck {
+  padding: 7px 16px;
+  border-radius: var(--pa-r-md);
+  background: var(--pa-gradient);
+  color: #fff;
+  font-size: 12.5px;
+  font-weight: 600;
+  cursor: pointer;
+  transition: box-shadow 0.3s var(--pa-ease), transform 0.15s var(--pa-ease);
+}
+.rc-recheck:hover {
+  box-shadow: 0 0 24px rgba(0, 212, 255, 0.4);
+  transform: translateY(-1px);
+}
+</style>

ui/src/components/chat/VersioningCard.vue

@@ -0,0 +1,93 @@
+<script setup>
+// chat/VersioningCard.vue —— 版本化修改卡（G12/G16-G19）
+// block: { type:'bioflow_versioning', plan_revision, run_id, affected_stages, based_on_revision }
+import { computed } from 'vue';
+import { BF } from '../../i18n/bioflow.js';
+import { useChatStore } from '../../stores/chat.js';
+
+const props = defineProps({
+  block: { type: Object, required: true },
+});
+
+const chat = useChatStore();
+
+const planRevision = computed(() => props.block.plan_revision || '—');
+const runId = computed(() => props.block.run_id || '');
+const affected = computed(() => props.block.affected_stages || []);
+
+function onApply() {
+  chat.sendCardResult('apply_change', {
+    plan_revision: props.block.plan_revision,
+    run_id: props.block.run_id,
+    affected_stages: props.block.affected_stages,
+  }).catch(() => {});
+}
+</script>
+
+<template>
+  <div class="versioning-card">
+    <div class="vc-title">
+      {{ BF.versioningTitle }}
+      <span v-if="runId" class="vc-badge">{{ runId }}</span>
+    </div>
+    <div class="vc-revision">{{ BF.versioningRevisionLabel }} {{ planRevision }}</div>
+    <div class="vc-affected">
+      {{ BF.versioningAffectedLabel }}：{{ affected.join('、') || BF.versioningAffectedEmpty }}
+    </div>
+    <div class="vc-actions">
+      <button class="vc-apply" type="button" @click="onApply">{{ BF.versioningApply }}</button>
+    </div>
+  </div>
+</template>
+
+<style scoped>
+.versioning-card {
+  margin: 14px 0;
+  padding: 14px 16px;
+  background: var(--pa-surface-1);
+  border: 1px solid var(--pa-hairline);
+  border-radius: var(--pa-r-lg);
+}
+.vc-title {
+  font-size: 12.5px;
+  line-height: 1.6;
+  margin-bottom: 6px;
+}
+.vc-badge {
+  display: inline-block;
+  margin-left: 8px;
+  padding: 1px 8px;
+  border-radius: 999px;
+  font-size: 11px;
+  font-weight: 600;
+  background: var(--pa-surface-3);
+  color: var(--pa-ink-muted);
+}
+.vc-revision {
+  font-size: 12px;
+  color: var(--pa-ink);
+  margin-bottom: 6px;
+}
+.vc-affected {
+  font-size: 12px;
+  color: var(--pa-ink-muted);
+  margin-bottom: 8px;
+}
+.vc-actions {
+  margin-top: 10px;
+}
+.vc-apply {
+  padding: 7px 16px;
+  border-radius: var(--pa-r-md);
+  background: var(--pa-gradient);
+  color: #fff;
+  font-size: 12.5px;
+  font-weight: 600;
+  cursor: pointer;
+  transition: box-shadow 0.3s var(--pa-ease), transform 0.15s var(--pa-ease);
+}
+.vc-apply:hover {
+  box-shadow: 0 0 24px rgba(0, 212, 255, 0.4);
+  transform: translateY(-1px);
+}
+</style>

ui/src/components/settings/SettingsPanel.vue

@@ -6,6 +6,7 @@ import { onBeforeUnmount, ref, watch } from 'vue';
 import { useSettingsStore } from '../../stores/settings.js';
 import { useSessionsStore } from '../../stores/sessions.js';
 import { T } from '../../i18n/labels.js';
+import { BIOFLOW_CAPABILITY_NAMES } from '../../api/capabilities.js';
 
 const props = defineProps({
   open: { type: Boolean, default: false },
@@ -15,10 +16,24 @@ const emit = defineEmits(['close']);
 const settings = useSettingsStore();
 const sessions = useSessionsStore();
 const toggling = ref(null);
+const installing = ref(null);
 const toggleError = ref('');
 const modalRef = ref(null);
 let previouslyFocused = null;
 
+// 生信能力三开关（S5：装卸 MCP 能力，热加载不重启 QA）
+const BIOFLOW_LABELS = {
+  'bioflow-gene-family': '基因家族分析',
+  'bioflow-rnaseq': '转录组分析',
+  'bioflow-extension': '自定义扩展分析',
+};
+const bioflowCaps = () =>
+  BIOFLOW_CAPABILITY_NAMES.map((name) => ({
+    name,
+    label: BIOFLOW_LABELS[name] || name,
+    enabled: settings.isInstalled(name),
+  }));
+
 // 抽屉打开时才拉取（组件随 AppShell 常驻挂载，onMounted 时抽屉未开）
 watch(
   () => props.open,
@@ -108,6 +123,20 @@ async function onToggle(cap) {
   }
 }
 
+// S5：生信能力装卸（register/unregister，热加载）
+async function onToggleInstalled(name) {
+  if (installing.value) return;
+  installing.value = name;
+  toggleError.value = '';
+  try {
+    await settings.toggleInstalled(name);
+  } catch (err) {
+    toggleError.value = err.message || T.settingsToggleFailed;
+  } finally {
+    installing.value = null;
+  }
+}
+
 </script>
 
 <template>
@@ -160,6 +189,32 @@ async function onToggle(cap) {
                 </div>
               </div>
 
+              <div class="settings-group">
+                <div class="settings-group-title">{{ T.settingsBioflow }}</div>
+                <div
+                  v-for="cap in bioflowCaps()"
+                  :key="cap.name"
+                  class="settings-row"
+                >
+                  <div class="settings-row-text">
+                    <div class="settings-row-name">{{ cap.label }}</div>
+                    <div class="settings-row-desc">{{ cap.name }}</div>
+                  </div>
+                  <button
+                    class="toggle"
+                    :class="{ on: cap.enabled }"
+                    type="button"
+                    role="switch"
+                    :aria-checked="String(cap.enabled)"
+                    :disabled="installing === cap.name"
+                    :aria-label="cap.label"
+                    @click="onToggleInstalled(cap.name)"
+                  >
+                    <span class="toggle-knob"></span>
+                  </button>
+                </div>
+              </div>
+
               <div class="settings-group">
                 <div class="settings-group-title">{{ T.settingsInstalled }}</div>
                 <div v-if="!settings.installed.length" class="settings-empty">{{ T.settingsNoPlugins }}</div>

ui/src/i18n/bioflow.js

@@ -169,6 +169,16 @@ export const BF = {
   bioflowUnavailableNote: '生信服务不可用（探活失败）',
   // ---- 流程知识库引用块（FR-BIO-026） ----
   flowQaEmpty: '暂无引用',
+  // ---- 旧生信块只读降级（S3 LegacyBioflowBlock） ----
+  legacyBlockTitle: '生信分析块（已归档，只读）',
+  legacyQaTitle: '流程知识引用（只读）',
+  legacyPathTitle: '分析路径（只读）',
+  legacyFormTitle: '参数确认（只读）',
+  legacyFileTitle: '文件引导（只读）',
+  legacyProgressTitle: '任务进度（只读）',
+  legacyArchiveTitle: '存档提示（只读）',
+  legacyJobPrefix: '任务：',
+  legacyReadonlyHint: '该块来自旧版本会话，已转为只读展示。',
   // ---- 阶段状态文字（进度卡/面板共用） ----
   stageStatusWaiting: '等待',
   stageStatusAwaitFiles: '等待文件',
@@ -304,6 +314,32 @@ export const BF = {
   extPaneRunsError: '历史加载失败',
   extPaneRunsReload: '重试',
   extPaneRunsCount: '共 {n} 次运行',
+
+  // ---- G12 分析控制四卡（ReadinessCard/DiagnosisCard/VersioningCard/DeliveryCard） ----
+  // 就绪检查卡（bioflow_readiness）
+  readinessTitle: '就绪检查',
+  readinessReady: '就绪',
+  readinessNotReady: '未就绪',
+  readinessRecheck: '重新检查',
+  readinessQ_environment: '环境',
+  readinessQ_reference: '参考',
+  readinessQ_space: '空间',
+  readinessQ_budget: '预算',
+  // 诊断卡（bioflow_diagnosis）
+  diagTitle: '诊断',
+  diagApply: '应用建议',
+  // 版本化修改卡（bioflow_versioning）
+  versioningTitle: '版本',
+  versioningRevisionLabel: '修订',
+  versioningAffectedLabel: '受影响重跑',
+  versioningAffectedEmpty: '无',
+  versioningApply: '应用修改',
+  // 交付清单卡（bioflow_delivery）
+  deliveryTitle: '交付',
+  deliveryPassed: '已通过',
+  deliveryPending: '待完善',
+  deliveryIncomplete: '未完成原因',
+  deliveryPublish: '发布交付',
 };
 
 /** 8 个 base 镜像（与 176 部署树 stage_image_map.json 一致；默认 bioflow-gf 工具链最全。

ui/src/i18n/labels.js

@@ -181,6 +181,7 @@ export const T = {
   benchCollapse: '折叠工作台',
   close: '关闭',
   settingsTitle: '设置',
+  settingsBioflow: '生信分析能力',
   settingsInstalled: '已装插件',
   settingsNoPlugins: '暂无已安装的外部插件（可在对话中安装）',
   settingsGatedBy: '需服务端环境变量 {env} 开启后生效',

ui/src/stores/bioflow.js

@@ -10,6 +10,7 @@
 // 与本仓库 docgen store 同约定）；文案全部 i18n/bioflow.js；SSE 用 mock 可测。
 import { defineStore } from 'pinia';
 import { SseParser } from '../sse/parser.js';
+import { getCapabilities } from '../api/capabilities.js';
 import {
   bioflowHealth,
   createBioflowJob,
@@ -38,6 +39,16 @@ const REGISTERED_JOBS_KEY = 'pa-bioflow-registered-jobs';
 const JOB_TERMINAL = new Set(['done', 'failed', 'archived']);
 const STAGE_TERMINAL = new Set(['done', 'failed', 'skipped']);
 
+// 生信能力名（S3 双信号主信号：任一注册即视为「生信能力已安装」）
+const BIOFLOW_CAPABILITY_NAMES = ['bioflow-gene-family', 'bioflow-rnaseq', 'bioflow-extension'];
+
+/** 从 GET /api/capabilities 响应判定是否含生信能力（installed 数组按 name 匹配）。 */
+function _hasBioflowCapability(payload) {
+  const installed = (payload && payload.installed) || [];
+  if (!Array.isArray(installed)) return false;
+  return installed.some((c) => c && BIOFLOW_CAPABILITY_NAMES.includes(c.name));
+}
+
 // 事件 → 阶段状态映射（snapshot 应用与逐帧推进共用同一张表）
 export const STAGE_STATUS_BY_EVENT = {
   stage_started: 'running',
@@ -187,10 +198,18 @@ export function capLogTail(text) {
   return text.slice(-4000);
 }
 
+/** 从阶段链推断生信能力链（S3 card_result 用）：rnaseq 核心阶段带 rnaseq_ 前缀，其余归 gene_family。 */
+export function inferBioflowChain(stages) {
+  const list = Array.isArray(stages) ? stages.map((s) => String(s || '')) : [];
+  return list.some((s) => s.startsWith('rnaseq_')) ? 'rnaseq' : 'gene_family';
+}
+
 export const useBioflowStore = defineStore('bioflow', {
   state: () => ({
-    // ---- 探活（FR-BIO-025） ----
-    availability: 'unknown', // 'unknown' | 'online' | 'offline'
+    // ---- 探活（FR-BIO-025 / S3 双信号） ----
+    availability: 'unknown', // 'unknown' | 'online' | 'offline'（主信号：能力注册状态）
+    capabilityInstalled: false, // 主信号：GET /api/capabilities 是否含 bioflow-* 能力
+    healthOnline: false,        // 次信号：GET /api/bioflow/health 服务健康（仅执行期降级参考）
     // ---- 当前会话任务（SSE 事件逐帧推进 + 快照整体刷新） ----
     currentJob: {
       jobId: null,
@@ -234,7 +253,7 @@ export const useBioflowStore = defineStore('bioflow', {
 
   getters: {
     bioflowAvailable() {
-      return this.availability === 'online';
+      return this.capabilityInstalled;
     },
     hasJob() {
       return !!this.currentJob.jobId;
@@ -258,16 +277,27 @@ export const useBioflowStore = defineStore('bioflow', {
 
   actions: {
     // ---------------------------------------------------------------
-    // 探活（FR-BIO-025）
+    // 探活（FR-BIO-025 / S3 双信号）
+    //   主信号 = 能力注册状态（GET /api/capabilities 的 installed 是否含 bioflow-*）
+    //   次信号 = 服务健康（GET /api/bioflow/health，仅执行期降级参考，不影响 TAB 显隐）
     // ---------------------------------------------------------------
     async probe({ force = false } = {}) {
       if (!force && this.availability !== 'unknown') return this.availability;
+      // 主信号：能力注册状态
+      try {
+        const caps = await getCapabilities();
+        this.capabilityInstalled = _hasBioflowCapability(caps);
+      } catch {
+        this.capabilityInstalled = false;
+      }
+      // 次信号：服务健康（保留 probe，已注册但服务不可达时 TAB 仍显示）
       try {
         const data = await bioflowHealth();
-        this.availability = data && data.ok ? 'online' : 'offline';
+        this.healthOnline = !!(data && data.ok);
       } catch {
-        this.availability = 'offline';
+        this.healthOnline = false;
       }
+      this.availability = this.capabilityInstalled ? 'online' : 'offline';
       return this.availability;
     },
 

ui/src/stores/chat.js

@@ -32,7 +32,6 @@ import { PP as PP_LABELS } from '../i18n/paper.js';
 
 // ---- P2 生信流程编排：独立分支（send/_runStream/sendDocgen 零改动） ----
 import { BF } from '../i18n/bioflow.js';
-import { route as routeBioflow } from '../utils/intent.js';
 import { bioflowChatStream } from '../api/bioflow.js';
 import { useBioflowStore } from './bioflow.js';
 import { consumeSseStream } from '../sse/parser.js';
@@ -426,6 +425,68 @@ export function patchBioflowArchiveDone(aMsg, blk, result) {
   return blk;
 }
 
+/** G12 就绪检查卡（bioflow_readiness）：check_readiness 四象限 */
+export function patchBioflowReadiness(aMsg, data) {
+  let blk = (aMsg.blocks || []).find((b) => b && b.type === 'bioflow_readiness');
+  if (!blk) {
+    blk = { type: 'bioflow_readiness', ready: false, quadrants: [], error: null };
+    aMsg.blocks.push(blk);
+  }
+  blk.ready = !!(data && data.ready);
+  blk.quadrants = (data && data.quadrants) || [];
+  blk.error = (data && data.error) || null;
+  return blk;
+}
+
+/** G12 诊断卡（bioflow_diagnosis）：G13 错误对象（扁平字段）+ 恢复预算 */
+export function patchBioflowDiagnosis(aMsg, data) {
+  let blk = (aMsg.blocks || []).find((b) => b && b.type === 'bioflow_diagnosis');
+  if (!blk) {
+    blk = {
+      type: 'bioflow_diagnosis', category: '', code: '', summary: '',
+      suggested_actions: [], retryable_without_change: false, retry_count: 0,
+    };
+    aMsg.blocks.push(blk);
+  }
+  blk.category = (data && data.category) || '';
+  blk.code = (data && data.code) || '';
+  blk.summary = (data && data.summary) || '';
+  blk.suggested_actions = (data && data.suggested_actions) || [];
+  blk.retryable_without_change = !!(data && data.retryable_without_change);
+  if (data && data.retry_count != null) blk.retry_count = data.retry_count;
+  return blk;
+}
+
+/** G12 版本化修改卡（bioflow_versioning）：修订号 + 受影响下游阶段 */
+export function patchBioflowVersioning(aMsg, data) {
+  let blk = (aMsg.blocks || []).find((b) => b && b.type === 'bioflow_versioning');
+  if (!blk) {
+    blk = {
+      type: 'bioflow_versioning', plan_revision: '', run_id: '',
+      affected_stages: [], based_on_revision: null,
+    };
+    aMsg.blocks.push(blk);
+  }
+  blk.plan_revision = (data && data.plan_revision) ?? '';
+  blk.run_id = (data && data.run_id) ?? '';
+  blk.affected_stages = (data && data.affected_stages) || [];
+  blk.based_on_revision = (data && data.based_on_revision) ?? null;
+  return blk;
+}
+
+/** G12 交付清单卡（bioflow_delivery）：八项校验 + 未完成原因 */
+export function patchBioflowDelivery(aMsg, data) {
+  let blk = (aMsg.blocks || []).find((b) => b && b.type === 'bioflow_delivery');
+  if (!blk) {
+    blk = { type: 'bioflow_delivery', ok: false, checks: {}, incomplete: [] };
+    aMsg.blocks.push(blk);
+  }
+  blk.ok = !!(data && data.ok);
+  blk.checks = (data && data.checks) || {};
+  blk.incomplete = (data && data.incomplete) || [];
+  return blk;
+}
+
 /** 阶段待确认 → 参数表单块（FR-BIO-008）；同阶段失败改参数重跑复用同一形态（FR-BIO-012） */
 export function patchBioflowForm(aMsg, data, { rerun = false } = {}) {
   const stage = data.stage;
@@ -1776,13 +1837,6 @@ export const useChatStore = defineStore('chat', {
       }
     },
 
-    // ---------------------------------------------------------------
-    // sendBioflow（P2）：生信对话式编排独立分支——用户消息落库（既有机制）→
-    // 生信骨架（path 块）→ POST /api/bioflow/chat/stream（SSE 经 sse/parser.js
-    // 消费，与既有 parser 完全复用）→ 事件按更新器 patch 消息 blocks →
-    // 阶段态订阅（FR-BIO-014：断线重连首帧快照整体刷新由本动作处理）。
-    // send()/_runStream/sendDocgen 零改动；不命中词典一律不进此分支（漏判安全）。
-    // ---------------------------------------------------------------
     /**
      * 进度条点击定位:请求 bioflow 面板定位 + 切右侧生信 TAB。
      * BioJobsPane 消费 panelLocate(nonce 变化)后 scrollIntoView + 展开 log。
@@ -1796,314 +1850,6 @@ export const useChatStore = defineStore('chat', {
       }).catch(() => {});
     },
 
-    async sendBioflow(text, { userMsg, mode = 'ask', reuseName = null } = {}) {
-      const q = String(text == null ? '' : text).trim();
-      if (!q || this.busy) return;
-      const sessions = useSessionsStore();
-      if (!this.sessionId) {
-        try {
-          const sess = await sessions.create();
-          this.sessionId = sess.id;
-        } catch {
-          return;
-        }
-      }
-      if (this.sessionId && !sessions.items.some((s) => s.id === this.sessionId)) {
-        sessions.items.unshift({ id: this.sessionId, title: q.slice(0, 30), status: 'running', created_at: new Date().toISOString(), updated_at: new Date().toISOString(), message_count: 0, meta: {} });
-      }
-      const sessionId = this.sessionId;
-      const msgList = this.messages;
-      this.sessionMsgs[sessionId] = msgList;
-      const ctx = newStreamCtx(sessionId, msgList);
-      this.streamCtx[sessionId] = ctx;
-      this.lastResult = null;
-      const startAt = Date.now();
-
-      // 1. 用户消息入列 + 落库（retry 复用既有用户消息时跳过——同位置替换）
-      let userId = null;
-      let userMsgRef = null;
-      if (userMsg) {
-        userMsgRef = userMsg;
-        userId = userMsg.id;
-      } else {
-        const userMsgRaw = { id: null, role: 'user', kind: 'bioflow', status: 'done', text: q, mode, meta: { bioflow: true }, blocks: [{ type: 'text', html: q }], raw: null, created_at: new Date().toISOString(), updated_at: new Date().toISOString() };
-        msgList.push(userMsgRaw);
-        userMsgRef = msgList[msgList.length - 1]; // 持代理（响应式断链陷阱）
-        try {
-          const saved = await createMessage(sessionId, { role: 'user', text: q });
-          userId = saved.id;
-          userMsgRef.id = userId;
-        } catch (err) {
-          userMsgRef.persistError = err;
-          this._finishCtx(ctx, { ok: false, error: err, message: userMsgRef, silentAbort: false });
-          return;
-        }
-      }
-
-      // 2. 会话 running
-      sessions.patchLocal(sessionId, { status: 'running' });
-      try {
-        await updateSessionQuiet(sessionId, { status: 'running' });
-      } catch { /* 状态 PATCH 失败不阻断 */ }
-
-      // 3. 生信骨架消息（path 块等待候选）+ 落库
-      const aMsgRaw = newBioflowSkeletonMessage();
-      msgList.push(aMsgRaw);
-      const aMsg = msgList[msgList.length - 1]; // 持代理
-      ctx.aMsg = aMsg;
-      this.runningMsgId = null;
-      try {
-        const skeleton = await createMessage(sessionId, {
-          role: 'assistant', kind: 'bioflow', status: 'streaming',
-          blocks: [{ type: 'bioflow_path', status: 'running', candidates: [] }],
-        });
-        aMsg.id = skeleton.id;
-        this.runningMsgId = skeleton.id;
-      } catch {
-        aMsg.id = null; // 骨架落库失败：终态 replace 语义重建（防御）
-      }
-
-      // 4. 事件流（chat/stream 规划入口；任务事件经 /jobs/{id}/events 订阅）
-      const bioflow = useBioflowStore();
-      bioflow.resetSession();
-      // 事件 patch 前保证 path 块引用稳定（computed 消费时缺块即建）
-      let jobEventsOpened = false;
-      let lastJobSeq = 0;
-      const openJobEvents = (jobId) => {
-        if (jobEventsOpened || !jobId) return;
-        jobEventsOpened = true;
-        // 订阅任务事件流：首帧快照整体刷新进度块（FR-BIO-014 断线重连回放）
-        try {
-          bioflow.connectJobEvents(jobId, sessionId, {
-            onOpen: () => { /* EventSource 内建重连；重连后快照自动整体刷新 */ },
-          });
-        } catch { /* EventSource 不可用（降级/测试）：事件仍可由快照兜底 */ }
-        // 快照整体刷新 → 消息进度块同步（订阅后立即拉一次快照应用）
-      };
-      // 从 bioflow store 当前任务快照刷新消息进度块（断线重连回放兜底路径）
-      const syncProgressFromStore = () => {
-        const st = bioflow.currentJob;
-        if (!st || !st.jobId) return;
-        patchBioflowSnapshot(aMsg, {
-          job_id: st.jobId,
-          job: { status: st.jobStatus },
-          stages: st.stages,
-          last_seq: st.lastSeq,
-        });
-      };
-
-      const controller = new AbortController();
-      ctx.controller = controller;
-      let ended = false;
-      const endTask = () => {
-        ended = true;
-        if (ctx.controller === controller) ctx.controller = null;
-        this._stopCheckpoint(ctx);
-      };
-
-      const applyFrame = (ev) => {
-        if (ended) return;
-        const type = ev.event || 'message';
-        const data = ev.data || {};
-        if (type === 'plan_ready') {
-          patchBioflowPlan(aMsg, data);
-          bioflow.applyChatEvent('plan_ready', data);
-          this.scrollSeq++;
-        } else if (type === 'planning') {
-          patchBioflowPlanning(aMsg, data);
-          this.scrollSeq++;
-        } else if (type === 'job_created') {
-          patchBioflowEvent(aMsg, { type, data });
-          bioflow.applyJobEvent({ type, data });
-          openJobEvents(data.job_id);
-          this.scrollSeq++;
-        } else if (type === 'stage_await_confirm') {
-          patchBioflowEvent(aMsg, { type, data });
-          bioflow.applyJobEvent({ type, data });
-          patchBioflowForm(aMsg, data);
-          this.scrollSeq++;
-        } else if (type === 'stage_await_files') {
-          patchBioflowEvent(aMsg, { type, data });
-          bioflow.applyJobEvent({ type, data });
-          patchBioflowFile(aMsg, data);
-          this.scrollSeq++;
-        } else if (type === 'job_done') {
-          patchBioflowEvent(aMsg, { type, data });
-          bioflow.applyJobEvent({ type, data });
-          const blk = patchBioflowArchiveSuggest(aMsg, data.job_id || aMsg.jobId);
-          if (blk) blk.jobId = data.job_id || blk.jobId;
-          // P3 报告登记（FR-BIO-016）：落 doc_artifacts 供 DocPane 预览；
-          // 登记失败不阻断对话（报告仍可直连下载 HTML）
-          bioflow.registerReport({
-            jobId: data.job_id || bioflow.currentJob.jobId,
-            sessionId,
-            title: bioflow.currentJob.title || '生信分析报告',
-            reportPath: (data.report_path || ''),
-            figures: Array.isArray(data.figures) ? data.figures : [],
-          }).catch(() => {});
-          this.scrollSeq++;
-        } else if (type === 'job_paused' || type === 'job_archived') {
-          patchBioflowEvent(aMsg, { type, data });
-          bioflow.applyJobEvent({ type, data });
-          this.scrollSeq++;
-        } else if (type === 'message_done') {
-          // 生信流收尾：非生信/流程咨询分支（bioflow_qa 引用块 / qa 转交）
-          endTask();
-          if (data && data.kind === 'flow_qa') {
-            patchBioflowQa(aMsg, { question: q, citations: data.citations, degraded: data.degraded });
-          }
-          updateLocalDone();
-          return;
-        } else if (type === 'error') {
-          // 生信服务错误帧（统一信封形态）：标注可重试
-          endTask();
-          // 派生点收口：当前运行相位置 error（防点永久 running）
-          const dotBlk = (aMsg.blocks || []).find((b) => b && b.type === 'pipeline' && b.derived);
-          if (dotBlk) {
-            for (const s of dotBlk.steps || []) {
-              if (s.state === 'running') s.state = 'error';
-            }
-          }
-          const code = (data && data.code) || 'STREAM_ERROR';
-          const message = (data && data.message) || BF.bioflowRouteError;
-          updateLocal(() => {
-            aMsg.status = 'error';
-            aMsg.streamErr = 'message';
-            aMsg.errText = message;
-          });
-          this._persistFinal(aMsg, sessionId, 'error', { raw: aMsg.raw }).catch(() => {});
-          this._finishCtx(ctx, {
-            ok: false,
-            error: { code, message, retryable: true },
-            message: aMsg,
-            sessionId,
-            userMessageId: userId,
-            assistantMessageId: aMsg.id,
-          });
-          return;
-        } else if (['stage_started', 'stage_log', 'stage_progress', 'stage_done', 'stage_failed', 'stage_skipped', 'job_recovered'].includes(type)) {
-          // 会话级串流场景的事件也按任务事件处理（P1 契约：规划入口心跳流；
-          // 任务事件主要在 jobs/{id}/events 上，这里双保险不丢事件）
-          patchBioflowEvent(aMsg, { type, data });
-          bioflow.applyJobEvent({ type, data });
-          this.scrollSeq++;
-        } else if (applyExtensionFrame(aMsg, type, data)) {
-          // 用户自定义扩展分析（EXTENSION_CONTRACT.md §4）：extension_* 帧 → 引导卡块
-          this.scrollSeq++;
-        }
-        // keepalive / 未知事件：忽略
-      };
-
-      const updateLocal = (fn) => {
-        if (ctx.msgList.includes(aMsg)) fn();
-      };
-      const updateLocalDone = () => {
-        updateLocal(() => {
-          aMsg.status = 'done';
-        });
-      };
-
-      try {
-        const res = await bioflowChatStream(
-          {
-            session_id: sessionId,
-            message: q,
-            has_attachments: false,
-            has_active_artifact: this._hasActiveArtifactSafe(),
-            has_bioflow_context: this._sessionHasBioflowContext(sessionId),
-            last_seq: bioflow.currentJob.lastSeq || null,
-          },
-          { signal: controller.signal },
-        );
-        await consumeSseStream(res, applyFrame);
-        // 流自然关闭：job_done 之后服务端关闭 / 心跳流断连（任务仍存活于服务端）
-        if (!ended) {
-          endTask();
-          // 有任务但无终态：订阅仍在（jobEventsSource），进度块随快照刷新；
-          // 消息状态按已收事件收口。
-          updateLocal(() => {
-            const blk = (aMsg.blocks || []).find((b) => b.type === 'bioflow_progress');
-            if (blk) {
-              aMsg.status = 'done';
-            } else if (!(aMsg.blocks || []).some((b) => b.type === 'bioflow_qa')) {
-              // 无任务（纯规划心跳断连）：path 卡保留，收口状态
-              aMsg.status = 'done';
-            }
-          });
-          const dur = ((Date.now() - startAt) / 1000).toFixed(1) + 's';
-          try {
-            await this._persistFinal(aMsg, sessionId, 'done', { raw: aMsg.raw });
-          } catch (persistErr) {
-            console.warn('persistFinal failed after bioflow stream:', persistErr);
-          }
-          this._finishCtx(ctx, {
-            ok: true,
-            payload: bioflow.currentJob,
-            message: aMsg,
-            sessionId,
-            userMessageId: userId,
-            assistantMessageId: aMsg.id,
-            dur,
-          });
-        }
-      } catch (err) {
-        if (ended) return; // 已被某个帧处理（message_done/error）
-        endTask();
-        const isAbort = err && (err.name === 'AbortError' || err.code === 'ERR_CANCELED');
-        if (isAbort) {
-          // 用户停止（FR-CHAT-011 语义）：保留已收块
-          updateLocal(() => {
-            aMsg.status = 'error';
-            aMsg.streamErr = 'stopped';
-          });
-          this._persistFinal(aMsg, sessionId, 'error', { raw: aMsg.raw }).catch(() => {});
-          this._finishCtx(ctx, {
-            ok: false,
-            error: { code: 'ABORTED', message: T.stopped, retryable: false },
-            message: aMsg,
-            sessionId,
-            userMessageId: userId,
-            assistantMessageId: aMsg.id,
-          });
-          return;
-        }
-        if (!isAbort && err && typeof err.code === 'string' && err.code !== 'NETWORK') {
-          // 统一错误信封（UPSTREAM_DOWN/INTERNAL 等）透传后端 message
-          const text = err.message || BF.bioflowRouteError;
-          updateLocal(() => {
-            aMsg.status = 'error';
-            aMsg.streamErr = 'message';
-            aMsg.errText = text;
-          });
-          this._persistFinal(aMsg, sessionId, 'error', { raw: aMsg.raw }).catch(() => {});
-          this._finishCtx(ctx, {
-            ok: false,
-            error: { code: err.code, message: text, retryable: true },
-            message: aMsg,
-            sessionId,
-            userMessageId: userId,
-            assistantMessageId: aMsg.id,
-          });
-          return;
-        }
-        // 网络中断：任务仍存活于服务端；重连回放由消息进度块 + 订阅快照兜底
-        updateLocal(() => {
-          aMsg.status = 'error';
-          aMsg.streamErr = 'disconnected';
-        });
-        syncProgressFromStore();
-        this._persistFinal(aMsg, sessionId, 'error', { raw: aMsg.raw }).catch(() => {});
-        this._finishCtx(ctx, {
-          ok: false,
-          error: { code: 'NETWORK', message: T.disconnected, retryable: true },
-          message: aMsg,
-          sessionId,
-          userMessageId: userId,
-          assistantMessageId: aMsg.id,
-        });
-      }
-    },
-
     /** 会话是否有生信上下文（当前会话消息含 bioflow 块；用于 chat/stream has_bioflow_context） */
     _sessionHasBioflowContext(sessionId) {
       const list = this.sessionMsgs[sessionId] || this.messages || [];
@@ -2687,6 +2433,169 @@ export const useChatStore = defineStore('chat', {
       } catch { /* bench 未就绪（测试/降级）：静默 */ }
     },
 
+    /** S2 卡片回填协议：把卡片操作作为结构化用户消息发 QA 流（card_result）。
+     *  经 BioflowAgent 工具执行 + 自然语言复述；卡片与自然语言两条通道语义一致。
+     *  card ∈ path_selection|form_confirm|file_upload|archive_choice|extension_action。 */
+    async sendCardResult(card, payload, { text = '', userMsg = null } = {}) {
+      if (this.busy) return;
+      const sessions = useSessionsStore();
+      if (!this.sessionId) {
+        try {
+          const sess = await sessions.create();
+          this.sessionId = sess.id;
+        } catch {
+          return;
+        }
+      }
+      const sessionId = this.sessionId;
+      const msgList = this.messages;
+      this.sessionMsgs[sessionId] = msgList;
+      const ctx = newStreamCtx(sessionId, msgList);
+      this.streamCtx[sessionId] = ctx;
+      this.lastResult = null;
+      const startAt = Date.now();
+      const cardLabel = String(text || '').trim() || '（卡片操作）';
+      const updateLocal = (fn) => {
+        if (ctx.msgList.includes(aMsg)) fn();
+      };
+
+      // 1. 用户消息（卡片操作）入列 + 落库
+      let userId = null;
+      let userMsgRef = null;
+      if (userMsg) {
+        userMsgRef = userMsg;
+        userId = userMsg.id;
+      } else {
+        const userMsgRaw = { id: null, role: 'user', kind: 'bioflow', status: 'done', text: cardLabel, mode: 'ask', meta: { card_result: { card, payload } }, blocks: [{ type: 'text', html: cardLabel }], raw: null, created_at: new Date().toISOString(), updated_at: new Date().toISOString() };
+        msgList.push(userMsgRaw);
+        userMsgRef = msgList[msgList.length - 1]; // 持代理（响应式断链陷阱）
+        try {
+          const saved = await createMessage(sessionId, { role: 'user', text: cardLabel });
+          userId = saved.id;
+          userMsgRef.id = userId;
+        } catch (err) {
+          userMsgRef.persistError = err;
+          this._finishCtx(ctx, { ok: false, error: err, message: userMsgRef, silentAbort: false });
+          return;
+        }
+      }
+
+      // 2. 会话 running
+      sessions.patchLocal(sessionId, { status: 'running' });
+      try { await updateSessionQuiet(sessionId, { status: 'running' }); } catch { /* 状态 PATCH 失败不阻断 */ }
+
+      // 3. 助手骨架（bioflow）+ 落库
+      const aMsgRaw = newBioflowSkeletonMessage();
+      msgList.push(aMsgRaw);
+      const aMsg = msgList[msgList.length - 1]; // 持代理
+      ctx.aMsg = aMsg;
+      this.runningMsgId = null;
+      try {
+        const skeleton = await createMessage(sessionId, {
+          role: 'assistant', kind: 'bioflow', status: 'streaming',
+          blocks: [{ type: 'bioflow_path', status: 'running', candidates: [] }],
+        });
+        aMsg.id = skeleton.id;
+        this.runningMsgId = skeleton.id;
+      } catch {
+        aMsg.id = null; // 骨架落库失败：终态 replace 语义重建（防御）
+      }
+
+      // 4. QA 流（携带 card_result）
+      const controller = new AbortController();
+      ctx.controller = controller;
+      let ended = false;
+      const endTask = () => {
+        ended = true;
+        if (ctx.controller === controller) ctx.controller = null;
+        this._stopCheckpoint(ctx);
+      };
+
+      try {
+        await chatStream(
+          { question: cardLabel, session_id: sessionId, card_result: { card, payload } },
+          {
+            signal: controller.signal,
+            onProgress: (ev) => {
+              if (ended) return;
+              const p = ev.payload || {};
+              // bioflow 帧仅记录（生信消息无 pipeline 骨架）
+              const evProxy = this.streamCtx[sessionId] || ctx;
+              evProxy.events.push({ ...p, at: p.at || new Date().toISOString() });
+            },
+            onComplete: async (ev) => {
+              if (ended) return;
+              endTask();
+              const p = ev.payload || {};
+              const answer = p.answer || '';
+              updateLocal(() => {
+                aMsg.blocks = [
+                  { type: 'bioflow_path', status: 'done', candidates: [] },
+                  { type: 'text', html: answer },
+                ];
+                aMsg.raw = p.raw ?? p;
+                aMsg.status = 'done';
+              });
+              // session↔job 绑定持久化：complete 的 bioflow.active_job_id → meta.bioflow
+              const bf = p.bioflow || {};
+              if (bf.active_job_id) {
+                updateSessionQuiet(sessionId, {
+                  meta: { bioflow: { active_job_id: bf.active_job_id, chain: bf.chain || '' } },
+                }).catch(() => {});
+              }
+              try {
+                await this._persistFinal(aMsg, sessionId, 'done', { raw: aMsg.raw });
+              } catch (persistErr) {
+                console.warn('persistFinal failed after card complete:', persistErr);
+              }
+              const dur = ((Date.now() - startAt) / 1000).toFixed(1) + 's';
+              this._finishCtx(ctx, {
+                ok: true,
+                payload: p,
+                message: aMsg,
+                sessionId,
+                userMessageId: userId,
+                assistantMessageId: aMsg.id,
+                dur,
+                blocks: 2,
+              });
+            },
+            onError: (ev) => {
+              if (ended) return;
+              const p = ev.payload || {};
+              endTask();
+              const err = { code: p.code || 'STREAM_ERROR', message: p.message || '', retryable: !!p.retryable };
+              const map = this._errorMarker(err.code);
+              if (map.text) err.message = err.message || map.text;
+              updateLocal(() => {
+                aMsg.status = 'error';
+                aMsg.streamErr = map.ann;
+                aMsg.errText = err.message;
+              });
+              this._persistFinal(aMsg, sessionId, 'error', { raw: aMsg.raw }).catch(() => {});
+              this._finishCtx(ctx, { ok: false, error: err, message: aMsg, sessionId, userMessageId: userId, assistantMessageId: aMsg.id });
+            },
+            onRaw: () => { /* raw 帧仅记录 */ },
+            onUnknown: () => { /* 无 event 名的帧忽略 */ },
+          },
+        );
+        if (!ended) {
+          endTask();
+          const err = { code: 'CONNECTION_CLOSED', message: T.disconnected };
+          updateLocal(() => { aMsg.status = 'error'; aMsg.streamErr = 'disconnected'; });
+          this._persistFinal(aMsg, sessionId, 'error', { raw: aMsg.raw }).catch(() => {});
+          this._finishCtx(ctx, { ok: false, error: err, message: aMsg, sessionId, userMessageId: userId, assistantMessageId: aMsg.id });
+        }
+      } catch (err) {
+        if (ended) return;
+        endTask();
+        const isAbort = err && (err.name === 'AbortError' || err.code === 'ERR_CANCELED');
+        updateLocal(() => { aMsg.status = 'error'; aMsg.streamErr = isAbort ? 'stopped' : 'disconnected'; });
+        this._persistFinal(aMsg, sessionId, 'error', { raw: aMsg.raw }).catch(() => {});
+        this._finishCtx(ctx, { ok: false, error: { code: 'CONNECTION_CLOSED', message: T.disconnected, retryable: true }, message: aMsg, sessionId, userMessageId: userId, assistantMessageId: aMsg.id });
+      }
+    },
+
     async _runStream(q, modeCfg, aMsg, sessionId, userId, ctx) {
       const controller = new AbortController();
       ctx.controller = controller;
@@ -2713,6 +2622,10 @@ export const useChatStore = defineStore('chat', {
               const phase = this._normalizePhase(p.phase);
               const label = p.label || p.stage || '';
               updateLocal(() => {
+                // S2：bioflow 帧（生信对话编排）不推 pipeline 相位——生信消息走
+                // bioflow 块，由 sendCardResult / bioflow 分支消费，此处仅记录。
+                const isBioflow = typeof p.stage === 'string' && p.stage.startsWith('bioflow_');
+                if (isBioflow) return;
                 if (!ctx.completedOnce && phase !== 'done') this._advancePipeline(aMsg, phase, label);
                 if (phase === 'done') {
                   // 上游 completed 事件：当前相位定格 done（此时 complete 尚未到达）
@@ -3121,18 +3034,12 @@ export const useChatStore = defineStore('chat', {
         await this.sendDocgen(q, (user.meta && user.meta.library_ids) || [], { userMsg: user });
         return;
       }
-      // P2：生信失败消息的重试走生信路径（同位置替换；reuseName 从 user.meta 恢复）
-      if (aMsg.kind === 'bioflow' || user.kind === 'bioflow') {
-        // 扩展分析消息（user.meta.extension 标记）：重试走扩展引导流（同位置替换）
-        if (user.meta && user.meta.extension) {
-          msgList.splice(idx, 1);
-          this.lastResult = null;
-          await this.sendExtension(q, { userMsg: user });
-          return;
-        }
+      // 扩展分析失败消息的重试走扩展引导流（S4 未改）；生信消息 S3 起统一走
+      // QA 流（sendBioflow 已删除），非扩展的生信消息重试落回下方 QA 重试路径。
+      if ((aMsg.kind === 'bioflow' || user.kind === 'bioflow') && user.meta && user.meta.extension) {
         msgList.splice(idx, 1);
         this.lastResult = null;
-        await this.sendBioflow(q, { userMsg: user, reuseName: (user.meta && user.meta.reuseName) || null });
+        await this.sendExtension(q, { userMsg: user });
         return;
       }
       msgList.splice(idx, 1);