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S0: bioflow_service 三 MCP 端点(gene-family/rnaseq/extension) + 源文件获取/预处理 S1: QA bioflow_agent 前门 router + capabilities.yaml 三条目 + 熔断 S2: card_result 回填 + 多轮记忆 + session↔job 绑定 S3: 前端 TAB 双信号 + 卡片辅助化 + 进度块只读 + 删除直连 S4: 扩展子系统对话化(第三能力单元) S5: toggle_bioflow.sh 装卸 + SettingsPanel 三开关 S6: 多配置回归 + 对话剧本测试手册
142 lines
5.1 KiB
Bash
Executable File
142 lines
5.1 KiB
Bash
Executable File
#!/usr/bin/env bash
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# 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。
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#
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# 用法：
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# bash deploy/toggle_bioflow.sh <gene-family|rnaseq|extension|all> <on|off>
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#
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# 原理：
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# - 能力装卸经 BFF POST /api/capabilities/install（透传 QA install_manager，热加载生效不重启 QA）
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# - on = register（manifest 校验 + 原子写 capabilities.yaml + registry 差分刷新）
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# - off = unregister（按 name 移除能力段，其余能力不受影响）
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# - 自检 = GET /api/capabilities 的 installed 数组是否含对应能力
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# - bioflow_service 启停：全部能力关闭时停 8098；任一开启时启动 8098
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# - 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
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set -uo pipefail
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BFF="http://127.0.0.1:8090"
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BIOFLOW_SERVICE_DIR="/home/xzq/5090/teamWorkspace/zh/PlantAI-rag-new/bioflow_service"
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PY="/home/xzq/5090/teamWorkspace/zh/plantai-rag-new-venv/bin/python"
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BIOFLOW_PORT="${BIOFLOW_PORT:-8098}"
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CAP="${1:-}"
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ACTION="${2:-}"
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CAPS=(gene-family rnaseq extension)
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usage() {
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echo "用法: $0 <gene-family|rnaseq|extension|all> <on|off>" >&2
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exit 2
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}
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# capability key -> registry 能力名
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cap_name() {
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case "$1" in
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gene-family) echo "bioflow-gene-family" ;;
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rnaseq) echo "bioflow-rnaseq" ;;
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extension) echo "bioflow-extension" ;;
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*) usage ;;
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esac
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}
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# capability key -> register manifest YAML（与 agent/qa/configs/capabilities.yaml 一致）
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manifest() {
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case "$1" in
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gene-family) cat <<'YAML'
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capabilities:
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- name: bioflow-gene-family
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provider: mcp
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permission: read_only
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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
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session_default: true
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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]
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mcp:
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url: http://127.0.0.1:8098/mcp/gene-family/
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prompt_pack:
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file: bioflow_gene_family_agent_rules.md
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YAML
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;;
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rnaseq) cat <<'YAML'
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capabilities:
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- name: bioflow-rnaseq
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provider: mcp
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permission: read_only
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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
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session_default: true
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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]
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mcp:
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url: http://127.0.0.1:8098/mcp/rnaseq/
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prompt_pack:
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file: bioflow_rnaseq_agent_rules.md
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YAML
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;;
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extension) cat <<'YAML'
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capabilities:
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- name: bioflow-extension
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provider: mcp
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permission: read_only
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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
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session_default: true
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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]
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mcp:
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url: http://127.0.0.1:8098/mcp/extension/
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prompt_pack:
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file: bioflow_extension_agent_rules.md
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YAML
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;;
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*) usage ;;
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esac
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}
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[ -n "$CAP" ] && [ -n "$ACTION" ] || usage
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[ "$ACTION" = "on" ] || [ "$ACTION" = "off" ] || usage
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if [ "$CAP" != "all" ]; then
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cap_name "$CAP" >/dev/null 2>&1 || usage
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fi
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# 1. 逐能力 register/unregister（热加载不重启 QA）
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targets=("$CAP")
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[ "$CAP" = "all" ] && targets=("${CAPS[@]}")
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for key in "${targets[@]}"; do
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name="$(cap_name "$key")"
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if [ "$ACTION" = "on" ]; then
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body="$(manifest "$key")"
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resp=$(curl -s -m 30 -X POST "$BFF/api/capabilities/install" \
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-H 'Content-Type: application/json' \
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-d "$(python3 -c 'import json,sys; print(json.dumps({"action":"register","manifest":sys.stdin.read()}))' <<<"$body")")
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else
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resp=$(curl -s -m 30 -X POST "$BFF/api/capabilities/install" \
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-H 'Content-Type: application/json' \
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-d "{\"action\":\"unregister\",\"name\":\"$name\"}")
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fi
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echo "[$ACTION] $name -> $(echo "$resp" | head -c 300)"
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done
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# 2. 自检：GET /api/capabilities 的 installed 数组
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installed=$(curl -s -m 10 "$BFF/api/capabilities")
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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')"
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# 3. bioflow_service 按需启停：任一能力开启则启动，全部关闭则停止
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any_on=false
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for key in "${CAPS[@]}"; do
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name="$(cap_name "$key")"
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if echo "$installed" | grep -q "\"$name\""; then
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any_on=true
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fi
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done
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if [ "$any_on" = true ]; then
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if ! lsof -ti tcp:$BIOFLOW_PORT -sTCP:LISTEN >/dev/null 2>&1; then
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echo "启动 bioflow_service :$BIOFLOW_PORT"
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( cd "$BIOFLOW_SERVICE_DIR" && setsid "$PY" -m uvicorn app.main:app --host 127.0.0.1 --port "$BIOFLOW_PORT" \
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> /tmp/plantai-bioflow.log 2>&1 < /dev/null & ) && disown -a
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sleep 2
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fi
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curl -s -m 8 "http://127.0.0.1:$BIOFLOW_PORT/api/bioflow/health" | head -c 150
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echo
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else
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echo "全部能力已卸载：停止 bioflow_service :$BIOFLOW_PORT"
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kill $(lsof -ti tcp:$BIOFLOW_PORT -sTCP:LISTEN) 2>/dev/null || true
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fi
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echo "DONE"
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