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plan/2026-05-20_add_two_node.md
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576
plan/2026-05-20_add_two_node.md
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# Peptide Station 新增三个节点：等待订单完成 + 下料确认 + take-out 同步
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> 日期: 2026-05-20
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> 目标文件: [peptide_station.py](../unilabos/devices/workstation/bioyond_studio/peptide_station/peptide_station.py)
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> 参考实现:
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> - [bioyond_cell_workstation.py](/Users/dp/python/yxz/unilabos/devices/workstation/bioyond_studio/bioyond_cell/bioyond_cell_workstation.py)（`wait_for_order_finish`、`get_material_info`）
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> - [bioyond_rpc.py L782-824](../unilabos/devices/workstation/bioyond_studio/bioyond_rpc.py)（`take_out`）
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> - [workstation_architecture.md](../docs/developer_guide/examples/workstation_architecture.md)（HTTP 报送进入 workstation，运行态记录保存在 workstation 内存）
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> 状态: 仅需求草稿，不写代码
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---
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## 一、需求背景
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`BioyondPeptideStation` 当前实验流程在 `start_experiment`（manual_confirm 启动调度器）之后即结束，缺少：
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1. **等待奔耀回报实验完成**：调度器跑完后，奔耀通过 LIMS 推送 `POST /report/order_finish` 回调；目前 peptide_station 没有把这条推送封装成 action 节点，下游无法在工作流图上等待结果，也拿不到 `usedMaterials` 等下游所需信息。
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2. **下料引导**：实验完成后操作员需要把样品/产物从仓位里取出，下料前需要看到每个物料对应的 **仓库 / 位置 / 物料名称 / 数量**；下料完成后还需要回写奔耀（调用 `take-out` 接口），让奔耀清空相应库位状态。
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本轮新增三个 action 节点，串在 `start_experiment` 之后：
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```text
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submit_experiment_dayN
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-> start_experiment(manual_confirm 上料)
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-> wait_for_order_finish (等回调 + 生成 unloadTable)
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-> confirm_unload_materials (manual_confirm 下料确认)
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-> take_out_materials (调用 take-out 同步奔耀)
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```
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---
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## 二、关键设计决策
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### D1. 本轮只支持单订单，`order_ids` 只做占位
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当前不实现多订单等待、乱序回调缓存、并发 wait 隔离。节点输入以 `order_id` 为主，`order_code` 可作为调试兜底。
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`order_ids` 可在 handle/返回值中保留为占位字段，但实现只处理第一笔或直接忽略多订单列表。多订单、乱序回调、跨节点重跑复用缓存放到后续迭代。
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### D2. `start_experiment` 需要显式透传订单字段
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当前 `start_experiment` 只有输入 handles，缺少输出 handles；如果下游 wait 节点要接在 `start_experiment` 之后，必须让 `start_experiment` 透传：
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- `order_id`
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- `order_ids`（占位）
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- `order_code`
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- `resultTable`
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实现时给 `start_experiment` 增加对应 `ActionOutputHandle`，并在返回值里保留这些字段。`submit_experiment_dayN` 的 `start_experiment` 嵌套字典也应包含 `order_code`，便于工作流编辑器连线。
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### D3. `unloadTable` 必须与 `resultTable` 字段一致
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`unloadTable` 不新增 `posX/posY/posZ/unit` 列，直接复用现有 `RESULT_TABLE_COLUMNS` 的四列：
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```python
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RESULT_TABLE_COLUMNS = [
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{"name": "设备", "key": "whName"},
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{"name": "位置", "key": "locationCode"},
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{"name": "物料名称", "key": "materialName"},
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{"name": "数量", "key": "quantity"},
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]
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```
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`submit_experiment_dayN` 现有上料确认表 `resultTable` 形状如下；`unloadTable` 也必须保持同一 shape，只改 `tableName` 和行数据来源：
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```json
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{
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"data": [
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{
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"whName": "自动化堆栈",
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"locationCode": "A1",
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"materialName": "96孔板",
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"quantity": "1"
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}
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],
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"columns": [
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{"name": "设备", "key": "whName"},
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{"name": "位置", "key": "locationCode"},
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{"name": "物料名称", "key": "materialName"},
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{"name": "数量", "key": "quantity"}
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],
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"tableName": "resultTable"
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}
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```
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`material-info` 官方 schema 中位置坐标字段是 `locations[].x/y/z`，不是 `posX/posY/posZ`。本轮下料表不展示坐标。
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### D4. manual_confirm 只做人确认，take-out 放到普通 action
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`confirm_unload_materials` 只负责展示下料表、等待操作员确认并透传数据；真正的 `take-out` 调用放到后续普通 action `take_out_materials`。
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这样更接近 UniLab manual_confirm 的推荐模式：manual_confirm 是人机确认检查点，副作用由独立普通 action 执行。
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### D5. 本轮不做 unload context 缓存
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虽然 workstation architecture 文档支持在 workstation 内存保存 HTTP 报送记录，但本轮暂不实现 `unload_context_cache` 或 order report 缓存。
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因此本轮限制如下：
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- `wait_for_order_finish` 只等待本次进入节点之后到达的 `/report/order_finish`。
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- 如果 push 早于 wait 节点到达，本轮不自动补救。
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- 如果用户在 `confirm_unload_materials` approve 时忘记勾选，节点失败；当前架构不支持原地重新弹出同一个 manual_confirm，也不在本轮实现失败节点重跑。
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- 后续若要支持重跑复用，应在 `BioyondPeptideStation` 实例上新增 station runtime 的 `unload_context_cache`，按 `orderCode` 缓存 `unloadTable/material_ids/order_id` 等上下文。
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---
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## 三、节点 1：`wait_for_order_finish`（等推送 + 生成 unloadTable）
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### 行为
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1. 解析单订单目标：
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- 首选 `order_id`。
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- 如果没有 `order_code`，通过 `self.hardware_interface.order_report(order_id)` 取返回数据中的 `code` 作为 `orderCode`。
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- `order_ids` 仅占位，本轮不实现多订单循环。
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2. 设置 `self.last_order_code = order_code`、`self.last_order_report = None`，并 `self.order_finish_event.clear()`。
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3. 阻塞在 `self.order_finish_event.wait(timeout=timeout_seconds)` 等 LIMS 推送。
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4. peptide_station override `process_order_finish_report(report_request, used_materials)`：
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- 先调用 `super().process_order_finish_report(...)` 保留父类行为（状态发布、物料同步等）。
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- 当 `report_request.data.orderCode == self.last_order_code` 时，把 `report_request.data` 存入 `self.last_order_report`，并 `set()` event。
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- 非当前订单推送只记录日志，本轮不缓存。
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5. 解除阻塞后解析 `status`：
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- `"30"` -> `success`
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- `"-11"` -> `abnormal_stop`
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- `"-12"` -> `manual_stop`
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- 其它 -> `unknown_<status>`
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- 超时 -> `timeout`
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6. 对 `report.usedMaterials[].materialId` 调用 `self.hardware_interface.material_info(material_id)`，带本地函数级 `material_info_cache` 避免重复请求。
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7. 组装 `unloadTable`、`material_ids`、`preintake_ids`、`unload_summary` 并作为输出 handles 暴露。
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### 入参（goal_default）
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| 参数 | 类型 | 说明 |
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|------|------|------|
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| `order_id` | `str` | 来自 `start_experiment` 透传输出，必填优先 |
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| `order_code` | `str` | 调试兜底；若已知 orderCode 可跳过 `order_report` 反查 |
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| `order_ids` | `List[str]` | 占位字段；本轮不实现多订单 |
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| `timeout_seconds` | `int` | 默认 `36000`（10h） |
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| `poll_mode` | `bool` | 默认 `False`；如需要可沿用 bioyond_cell 的轮询等待风格 |
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### 输出 handles
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| key | data_type | 说明 |
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|-----|-----------|------|
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| `order_finish_status` | `str` | `success` / `abnormal_stop` / `manual_stop` / `timeout` / `unknown_*` |
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| `order_finish_report` | `json` | 完整 `report_request.data` |
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| `used_materials` | `json` | JSON 化后的 `usedMaterials` 列表 |
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| `material_ids` | `json` | 从 `used_materials` 抽出的 `materialId` 列表，可为空 |
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| `preintake_ids` | `json` | 本轮默认 `[]`，保留扩展点 |
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| `unloadTable` | `table` | 下料表，字段与 `resultTable` 一致 |
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| `unload_summary` | `json` | `{ "order_code": ..., "total_items": N, "missing_material_info": [...] }` |
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| `order_id` | `str` | 透传给后续节点 |
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| `order_code` | `str` | 透传给后续节点 |
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| `order_ids` | `json` | 占位透传 |
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### `unloadTable` 组装规则
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返回结构：
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||||
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```json
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||||
{
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||||
"data": [
|
||||
{
|
||||
"whName": "自动化堆栈",
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||||
"locationCode": "A1",
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"materialName": "多肽产物",
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"quantity": "10 mg"
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}
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],
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"columns": [
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{"name": "设备", "key": "whName"},
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{"name": "位置", "key": "locationCode"},
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{"name": "物料名称", "key": "materialName"},
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{"name": "数量", "key": "quantity"}
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],
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"tableName": "unloadTable"
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}
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```
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每行字段：
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| key | 数据来源 |
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|-----|----------|
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| `whName` | `material_info.locations` 中匹配 `usedMaterials.locationId` 的 location 的 `whName`；匹配不到取第一条 location 的 `whName`；失败为空串 |
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| `locationCode` | 匹配 location 的 `code`；匹配不到取第一条 location 的 `code`；再兜底 `usedMaterials.locationId` |
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| `materialName` | `material_info.name`；失败为空串 |
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| `quantity` | `usedMaterials.usedQuantity`，若 `material_info.unit` 存在则拼成字符串（如 `"10 mg"`） |
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`material-info` 失败时不抛异常，对应行尽量保留 `locationCode` / `quantity`，`whName` 和 `materialName` 用空串，并把 `materialId` 放入 `unload_summary.missing_material_info`。
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### 接口依赖
|
||||
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||||
| 接口 | 调用方式 | 用途 |
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||||
|------|----------|------|
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| `process_order_finish_report` 钩子 | 基类 HTTP 服务已注册 | 接 LIMS push |
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| `POST /api/lims/order/order-report` | `self.hardware_interface.order_report(order_id)` | 从 `order_id` 反查 `orderCode` |
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| `POST /api/lims/storage/material-info` | `self.hardware_interface.material_info(material_id)` | 查 `whName/locationCode/materialName/unit` |
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#### `order_report(order_id)` API 形式
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请求：
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||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
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||||
"data": "<orderId UUID>"
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}
|
||||
```
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||||
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||||
响应中本节点只依赖 `data.code`：
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||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": null,
|
||||
"timestamp": 1779255000000,
|
||||
"data": {
|
||||
"id": "<orderId UUID>",
|
||||
"name": "实验260520-103000",
|
||||
"code": "EXP260520-103000",
|
||||
"status": 30,
|
||||
"statusName": "完成"
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
`BioyondV1RPC.order_report(order_id)` 已经返回响应中的 `data`，所以实现中应读取 `raw.get("code")`，不是 `raw["data"]["code"]`。
|
||||
|
||||
#### `material_info(material_id)` API 形式
|
||||
|
||||
请求：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": "<materialId UUID>"
|
||||
}
|
||||
```
|
||||
|
||||
响应中本节点依赖：
|
||||
|
||||
```json
|
||||
{
|
||||
"id": "<materialId UUID>",
|
||||
"name": "多肽产物",
|
||||
"unit": "mg",
|
||||
"locations": [
|
||||
{
|
||||
"id": "<locationId UUID>",
|
||||
"whid": "<warehouse UUID>",
|
||||
"whName": "自动化堆栈",
|
||||
"code": "A1",
|
||||
"x": 1,
|
||||
"y": 1,
|
||||
"z": 1,
|
||||
"quantity": 10
|
||||
}
|
||||
]
|
||||
}
|
||||
```
|
||||
|
||||
`BioyondV1RPC.material_info(material_id)` 已经返回响应中的 `data`。字段映射：
|
||||
|
||||
| unloadTable key | 来源 |
|
||||
|-----------------|------|
|
||||
| `whName` | 匹配 `locationId` 的 `locations[].whName` |
|
||||
| `locationCode` | 匹配 `locationId` 的 `locations[].code` |
|
||||
| `materialName` | `name` |
|
||||
| `quantity` | `usedMaterials[].usedQuantity` + `unit` |
|
||||
|
||||
### 实现要点
|
||||
|
||||
- `BioyondPeptideStation.__init__` 末尾追加 `self.order_finish_event = threading.Event()`、`self.last_order_code = None`、`self.last_order_report = None`。
|
||||
- 新增 `process_order_finish_report` override，先 `super()`，再做单订单匹配。
|
||||
- `used_materials` 参数是 `MaterialUsage` dataclass 列表；输出前必须转成 JSON dict。
|
||||
- `unloadTable` 复用 `RESULT_TABLE_COLUMNS`，不新增 `UNLOAD_TABLE_COLUMNS`。
|
||||
|
||||
---
|
||||
|
||||
## 四、节点 2：`confirm_unload_materials`（人工下料确认）
|
||||
|
||||
### 行为
|
||||
|
||||
1. 接收节点 1 输出的 `order_id` / `order_code` / `material_ids` / `preintake_ids` / `unloadTable`。
|
||||
2. 进入 `NodeType.MANUAL_CONFIRM` 阻塞，操作员根据 `unloadTable` 物理下料。
|
||||
3. 操作员勾选 `materials_unloaded=True` 并 approve 后，节点函数体继续。
|
||||
4. 校验 `materials_unloaded == True`：
|
||||
- 为 True：返回确认结果，并透传 `order_id/material_ids/preintake_ids/unloadTable` 给节点 3。
|
||||
- 为 False：抛 `RuntimeError("下料未确认，拒绝继续 take-out")`。
|
||||
|
||||
### 入参（goal_default）
|
||||
|
||||
| 参数 | 类型 | 说明 |
|
||||
|------|------|------|
|
||||
| `order_id` | `str` | 来自节点 1，必填 |
|
||||
| `order_code` | `str` | 来自节点 1，日志/排错用 |
|
||||
| `material_ids` | `List[str]` | 来自节点 1，可为空 |
|
||||
| `preintake_ids` | `List[str]` | 来自节点 1，默认 `[]` |
|
||||
| `unloadTable` | `table` | 来自节点 1，供人工确认展示 |
|
||||
| `materials_unloaded` | `bool` | manual_confirm 勾选字段，默认 `False` |
|
||||
| `timeout_seconds` | `int` | 默认 `3600` |
|
||||
| `assignee_user_ids` | `List[str]` | `placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"}` |
|
||||
|
||||
### 输出 handles
|
||||
|
||||
| key | data_type | 说明 |
|
||||
|-----|-----------|------|
|
||||
| `unload_confirmed` | `bool` | 是否已人工确认下料 |
|
||||
| `order_id` | `str` | 透传 |
|
||||
| `order_code` | `str` | 透传 |
|
||||
| `material_ids` | `json` | 透传 |
|
||||
| `preintake_ids` | `json` | 透传 |
|
||||
| `unloadTable` | `table` | 透传 |
|
||||
|
||||
### 实现要点
|
||||
|
||||
- 装饰器使用 `node_type=NodeType.MANUAL_CONFIRM`。
|
||||
- `always_free=True`、`placeholder_keys`、`feedback_interval=300` 与现有 `start_experiment` 保持一致。
|
||||
- 本节点不调用 `take_out`，只做确认与透传。
|
||||
- 忘记勾选后不会自动重新显示下料指引；本轮不实现缓存或失败节点原地重跑。
|
||||
|
||||
---
|
||||
|
||||
## 五、节点 3：`take_out_materials`（调用 take-out 同步奔耀）
|
||||
|
||||
### 行为
|
||||
|
||||
1. 接收节点 2 透传的 `order_id` / `material_ids` / `preintake_ids`。
|
||||
2. 校验 `order_id` 非空。
|
||||
3. 调用 `self.hardware_interface.take_out(order_id, preintake_ids=preintake_ids, material_ids=material_ids)`。
|
||||
4. 返回 `take_out_result`、`unloaded_count`、`success`。
|
||||
|
||||
### 入参
|
||||
|
||||
| 参数 | 类型 | 说明 |
|
||||
|------|------|------|
|
||||
| `order_id` | `str` | 必填 |
|
||||
| `material_ids` | `List[str]` | 可为空；为空时由奔耀按 `orderId` 处理的能力以后现场确认 |
|
||||
| `preintake_ids` | `List[str]` | 可为空，默认 `[]` |
|
||||
| `order_code` | `str` | 日志/排错用 |
|
||||
|
||||
### 输出 handles
|
||||
|
||||
| key | data_type | 说明 |
|
||||
|-----|-----------|------|
|
||||
| `take_out_result` | `json` | `take-out` 原始响应 `{code, message, timestamp, data}` |
|
||||
| `unloaded_count` | `int` | `len(material_ids)` |
|
||||
| `success` | `bool` | `take_out_result.code == 1` 且 `data` 不为 False |
|
||||
|
||||
### 接口依赖
|
||||
|
||||
| 接口 | 调用方式 | 用途 |
|
||||
|------|----------|------|
|
||||
| `POST /api/lims/order/take-out` | `self.hardware_interface.take_out(order_id, preintake_ids, material_ids)` | 通知奔耀同步取出 |
|
||||
|
||||
请求体 schema（helper script 已核对）：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": {
|
||||
"orderId": "<UUID>",
|
||||
"preintakeIds": [],
|
||||
"materialIds": ["<UUID-1>", "<UUID-2>"]
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
响应 schema：
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": null,
|
||||
"timestamp": 1779255000000,
|
||||
"data": true
|
||||
}
|
||||
```
|
||||
|
||||
`BioyondV1RPC.take_out(...)` 返回完整响应包，因此 `take_out_materials` 应保留原始包到 `take_out_result`。
|
||||
|
||||
### 实现要点
|
||||
|
||||
- 本轮不修改 `sample_waste_removal`，保持 backward compatibility。
|
||||
- 新节点只调用现有完整能力的 `take_out(...)`。
|
||||
- `preintake_ids` / `material_ids` 都按可选列表处理，默认 `[]`。
|
||||
- `take-out` 返回 `code != 1` 时返回 `success=False` 并记录 warning；是否抛异常留作开放问题。
|
||||
|
||||
---
|
||||
|
||||
## 六、端到端工作流连线
|
||||
|
||||
```mermaid
|
||||
flowchart LR
|
||||
submit["submit_experiment_dayN"] --> start["start_experiment<br/>manual_confirm: 上料"]
|
||||
start -->|order_id, order_code| wait["wait_for_order_finish<br/>等 order_finish + 生成 unloadTable"]
|
||||
wait -->|order_id, material_ids,<br/>preintake_ids, unloadTable| confirm["confirm_unload_materials<br/>manual_confirm: 操作员下料确认"]
|
||||
confirm -->|order_id, material_ids,<br/>preintake_ids| takeout["take_out_materials<br/>调用 take-out 同步奔耀"]
|
||||
bioyond["奔耀 LIMS"] -.HTTP POST /report/order_finish.-> wait
|
||||
wait -.material-info.-> bioyond
|
||||
takeout -.take-out.-> bioyond
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 七、影响面与兼容性
|
||||
|
||||
- **`peptide_station.py`**
|
||||
- 修改 `start_experiment`：增加 `order_id/order_code/order_ids/resultTable` 输出 handles，并在返回值透传。
|
||||
- 增加 `wait_for_order_finish`、`confirm_unload_materials`、`take_out_materials` 三个 action。
|
||||
- 增加 `process_order_finish_report` override。
|
||||
- 增加 `_build_unload_table(...)` 等私有辅助方法。
|
||||
- **`bioyond_rpc.py` 不动**
|
||||
- `take_out` 已有完整 schema 能力。
|
||||
- `sample_waste_removal` 本轮不改，保持兼容。
|
||||
- **基类 `station.py` 不动**
|
||||
- override 中保留 `super().process_order_finish_report(...)` 调用。
|
||||
- **HTTP 服务不动**
|
||||
- `WorkstationHTTPService` 已支持 `/report/order_finish`。
|
||||
- **本轮不做缓存**
|
||||
- 不新增 `unload_context_cache`。
|
||||
- 不支持 push 早于 wait 的自动补救。
|
||||
- 不支持失败 manual_confirm 原地重跑。
|
||||
- **测试**：补在现有路径 `unilabos/devices/workstation/bioyond_studio/peptide_station/tests/test_peptide_station_contracts.py`
|
||||
1. `start_experiment` 输出 handles/返回值透传 `order_id/order_code/order_ids/resultTable`。
|
||||
2. `process_order_finish_report` orderCode 匹配 / 不匹配时 event 是否触发。
|
||||
3. `wait_for_order_finish` 单订单成功、超时、状态映射、`used_materials` JSON 化。
|
||||
4. `_build_unload_table` 列顺序严格等于 `RESULT_TABLE_COLUMNS`，且无 `posX/posY/posZ/unit` 列。
|
||||
5. `material-info` 失败时不抛异常，`missing_material_info` 正确记录。
|
||||
6. `confirm_unload_materials` 未勾选时报错，勾选后透传下游字段且不调用 `take_out`。
|
||||
7. `take_out_materials` 调用 `hardware_interface.take_out(order_id, preintake_ids, material_ids)`，不调用 `sample_waste_removal`。
|
||||
|
||||
---
|
||||
|
||||
## 八、待人类确认的开放问题
|
||||
|
||||
1. **过滤产物 vs 全量**：`usedMaterials` 同时包含试剂、耗材、样品（`typeMode` 区分），下料表是否需要默认排除试剂/耗材？当前默认全量列出。
|
||||
2. **take-out 失败是否阻塞工作流**：本计划暂定返回 `success=False` 并 warning，不抛异常；如果希望奔耀仓位状态必须一致，可改为抛 `RuntimeError`。
|
||||
3. **后续缓存/重跑能力**：如果要支持 push 早到、忘勾选后重跑复用 `unloadTable`，后续应在 `BioyondPeptideStation` station runtime 上实现 `unload_context_cache`，但本轮不做。
|
||||
4. **多订单**：本轮只保留 `order_ids` 占位，不实现多订单等待、乱序回调或并发 wait。
|
||||
|
||||
---
|
||||
|
||||
## 附录 A：API schema 核对摘要
|
||||
|
||||
使用 `temp_benyao/scripts/api_helper.py --root temp_benyao/peptide` 核对：
|
||||
|
||||
### A.1 `POST /api/lims/storage/material-info`
|
||||
|
||||
请求：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": "<materialId UUID>"
|
||||
}
|
||||
```
|
||||
|
||||
响应关键字段：
|
||||
|
||||
```json
|
||||
{
|
||||
"id": "<materialId UUID>",
|
||||
"typeName": "样品",
|
||||
"code": "MAT-001",
|
||||
"barCode": "BC-001",
|
||||
"name": "多肽产物",
|
||||
"quantity": 10,
|
||||
"lockQuantity": 0,
|
||||
"unit": "mg",
|
||||
"status": 1,
|
||||
"isUse": true,
|
||||
"locations": [
|
||||
{
|
||||
"id": "<locationId UUID>",
|
||||
"whid": "<warehouse UUID>",
|
||||
"whName": "自动化堆栈",
|
||||
"code": "A1",
|
||||
"x": 1,
|
||||
"y": 1,
|
||||
"z": 1,
|
||||
"quantity": 10
|
||||
}
|
||||
],
|
||||
"detail": []
|
||||
}
|
||||
```
|
||||
|
||||
注意：schema 没有 `posX/posY/posZ`，本轮也不展示坐标。
|
||||
|
||||
### A.2 `POST /api/lims/order/take-out`
|
||||
|
||||
请求：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": {
|
||||
"orderId": "<orderId UUID>",
|
||||
"preintakeIds": [],
|
||||
"materialIds": ["<materialId UUID>"]
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
响应：
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": null,
|
||||
"timestamp": 1779255000000,
|
||||
"data": true
|
||||
}
|
||||
```
|
||||
|
||||
源码中已有 `BioyondV1RPC.take_out(order_id, preintake_ids=None, material_ids=None)`，本轮复用它。
|
||||
|
||||
### A.3 `/report/order_finish`
|
||||
|
||||
`/report/order_finish` 不在 Peptide JSON OpenAPI specs 中；schema 依据：
|
||||
|
||||
- `unilabos/devices/workstation/workstation_http_service.py`
|
||||
- `temp_benyao/peptide/docs/reference/api_manual.md`
|
||||
|
||||
关键字段：
|
||||
|
||||
```json
|
||||
{
|
||||
"token": "token-from-lims",
|
||||
"request_time": "2026-05-20 10:50:00.123",
|
||||
"data": {
|
||||
"orderCode": "EXP260520-103000",
|
||||
"orderName": "实验260520-103000",
|
||||
"startTime": "2026-05-20 09:00:00",
|
||||
"endTime": "2026-05-20 10:50:00",
|
||||
"status": "30",
|
||||
"usedMaterials": [
|
||||
{
|
||||
"materialId": "<materialId UUID>",
|
||||
"locationId": "<locationId UUID>",
|
||||
"typeMode": "1",
|
||||
"usedQuantity": 10
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
`WorkstationHTTPService` 会把 `usedMaterials[]` 转成 `MaterialUsage` dataclass 列表传给 `process_order_finish_report(report_request, used_materials)`；peptide 输出 `used_materials` handle 前需要转回 JSON dict：
|
||||
|
||||
```json
|
||||
[
|
||||
{
|
||||
"materialId": "<materialId UUID>",
|
||||
"locationId": "<locationId UUID>",
|
||||
"typeMode": "1",
|
||||
"usedQuantity": 10
|
||||
}
|
||||
]
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 附录 B：本轮不实现的内容
|
||||
|
||||
- 不做 station runtime 的 `unload_context_cache`。
|
||||
- 不做多订单。
|
||||
- 不做 push 早到后的补救。
|
||||
- 不做 failed manual_confirm 原地重跑。
|
||||
- 不改前端。
|
||||
- 不改 `sample_waste_removal`。
|
||||
461
plan/2026-05-21_01_peptide_reset_four_checkbox_plan.md
Normal file
461
plan/2026-05-21_01_peptide_reset_four_checkbox_plan.md
Normal file
@@ -0,0 +1,461 @@
|
||||
# Peptide Four-Checkbox Reset Plan
|
||||
|
||||
Date: 2026-05-21 16:30
|
||||
Status: Proposal only / not executed
|
||||
|
||||
## Scope
|
||||
|
||||
This plan replaces `2026-05-21_1556_peptide_reset_sirna_reference_plan.md` for Peptide reset work.
|
||||
|
||||
User direction captured here:
|
||||
|
||||
- `take_out` is unnecessary for Peptide reset.
|
||||
- Do not add a material-cache refresh checkbox.
|
||||
- Change reset to four checkbox-controlled operations:
|
||||
- 调度器复位
|
||||
- 订单状态复位
|
||||
- 库位复位
|
||||
- 仪器复位
|
||||
- The first three checkboxes default to checked.
|
||||
- The fourth checkbox, 仪器复位 / `reset_devices`, defaults to unchecked.
|
||||
- Replace the current public `reset` action with:
|
||||
- `reset_auto`: normal ILab action node. This is the renamed/replaced version of the current reset implementation.
|
||||
- `reset_manual`: manual-confirm action node with a physical cleanup confirmation message.
|
||||
|
||||
## Evidence Summary
|
||||
|
||||
Current Peptide source:
|
||||
|
||||
- Reset action code is currently in `unilabos/devices/workstation/bioyond_studio/peptide_station/peptide_station.py`.
|
||||
- Current Peptide reset selects `scheduler_reset`, `reset_order_status`, and `reset_location`, and passes ids to order/location resets.
|
||||
- `BioyondV1RPC.reset_devices()` already calls `/api/lims/device/reset-devices` with only `apiKey` and `requestTime`.
|
||||
- `BioyondV1RPC.scheduler_reset()` already calls `/api/lims/scheduler/reset` with only `apiKey` and `requestTime`.
|
||||
- `BioyondV1RPC.reset_order_status(order_id)` and `reset_location(location_id)` currently send `data`, but live probes showed that omitted `data` succeeds.
|
||||
|
||||
Live Peptide no-data reset probes using `temp_benyao/peptide/peptide_station_config.example.json`:
|
||||
|
||||
- `POST /api/lims/order/reset-order-status` with request keys `["apiKey", "requestTime"]` returned HTTP 200 and `code=1`.
|
||||
- `POST /api/lims/scheduler/reset` with request keys `["apiKey", "requestTime"]` returned HTTP 200 and `code=1`.
|
||||
- `POST /api/lims/storage/reset-location` with request keys `["apiKey", "requestTime"]` returned HTTP 200 and `code=1`.
|
||||
- `reset-devices` was not live-probed in this session, but the current RPC wrapper already sends no `data`.
|
||||
|
||||
Raw findings:
|
||||
|
||||
- `temp_benyao/peptide/_findings/2026-05-21_1613_reset_order_status_no_data_live.md`
|
||||
- `temp_benyao/peptide/_findings/2026-05-21_1615_remaining_resets_no_data_live.md`
|
||||
|
||||
## Proposed Public Actions
|
||||
|
||||
### `reset_auto`
|
||||
|
||||
Normal action node. This is the auto/no-manual-confirm path. It replaces the current public `reset` action; do not leave a second public `reset` action unless a later compatibility request explicitly asks for an alias.
|
||||
|
||||
Checkbox schema rule:
|
||||
|
||||
- Use plain `bool` annotations in the action signature.
|
||||
- Do not use `Annotated[bool, Field(...)]` for these checkbox params in this implementation plan.
|
||||
- The current AST registry schema path does not unwrap `Annotated[...]`; plain `bool` is required so generated JSON Schema marks the fields as boolean and the renderer can show checkboxes.
|
||||
- Put human-facing labels/descriptions in the method docstring or action description. If field-level `Field(description=...)` metadata is required later, add registry `Annotated` support and a schema test as a separate change.
|
||||
|
||||
Decorator shape:
|
||||
|
||||
```python
|
||||
@action(
|
||||
always_free=True,
|
||||
goal_default={
|
||||
"reset_scheduler": True,
|
||||
"reset_order_status": True,
|
||||
"reset_location": True,
|
||||
"reset_devices": False,
|
||||
},
|
||||
description="自动复位调度器/订单状态/库位，可选仪器复位",
|
||||
)
|
||||
def reset_auto(
|
||||
self,
|
||||
reset_scheduler: bool = True,
|
||||
reset_order_status: bool = True,
|
||||
reset_location: bool = True,
|
||||
reset_devices: bool = False,
|
||||
**kwargs: Any,
|
||||
) -> Dict[str, Any]:
|
||||
"""自动复位调度器/订单状态/库位，可选仪器复位。
|
||||
|
||||
Args:
|
||||
reset_scheduler[调度器复位]: 调用 /api/lims/scheduler/reset，默认勾选。
|
||||
reset_order_status[订单状态复位]: 调用 /api/lims/order/reset-order-status，默认勾选。
|
||||
reset_location[库位复位]: 调用 /api/lims/storage/reset-location，默认勾选。
|
||||
reset_devices[仪器复位]: 调用 /api/lims/device/reset-devices，默认不勾选。
|
||||
"""
|
||||
...
|
||||
```
|
||||
|
||||
Implementation notes:
|
||||
|
||||
- Use real plain-`bool` parameters, not hidden `**kwargs` and not `Annotated`, so the action renderer can expose four checkboxes.
|
||||
- Rename/replace the existing `reset` action as `reset_auto`; the implementation should not keep the old id-shaped `reset` action as another public path by default.
|
||||
- Keep the three routine reset defaults checked.
|
||||
- Keep `reset_devices` unchecked because it can be broader and more disruptive.
|
||||
- Do not require or resolve order ids or location ids.
|
||||
- Do not call `take_out`.
|
||||
- Do not call `refresh_material_cache`.
|
||||
|
||||
### `reset_manual`
|
||||
|
||||
Manual-confirm node. It should show the operator a physical cleanup warning, then execute the same reset helper as `reset_auto` after the operator confirms.
|
||||
|
||||
Actual manual-confirm decorator pattern in this repo:
|
||||
|
||||
- Use `@action(node_type=NodeType.MANUAL_CONFIRM)`.
|
||||
- Set `always_free=True`.
|
||||
- Add `placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"}`.
|
||||
- Include `timeout_seconds: int` and `assignee_user_ids: list[str]`.
|
||||
- Add `goal_default` for `timeout_seconds` and `assignee_user_ids`.
|
||||
- Manual-confirm actions are normally side-effect-light, but existing Peptide `start_experiment` is already a `MANUAL_CONFIRM` action that performs scheduler start after the operator gate, so a reset-after-confirm pattern is compatible with current Peptide style.
|
||||
|
||||
Proposed confirmation text:
|
||||
|
||||
```text
|
||||
请确认G3、CEM、Tecan、撕膜机、封膜机、打标机、旋转堆栈上下料位、3个转台等位置的物料已清理完毕；
|
||||
请开门检查冰箱、IDOT、酶标仪、离心机、LCMS内部没有遗留物料。
|
||||
```
|
||||
|
||||
Decorator/function shape:
|
||||
|
||||
```python
|
||||
RESET_MANUAL_CONFIRM_MESSAGE = (
|
||||
"请确认G3、CEM、Tecan、撕膜机、封膜机、打标机、旋转堆栈上下料位、3个转台等位置的物料已清理完毕；\n"
|
||||
"请开门检查冰箱、IDOT、酶标仪、离心机、LCMS内部没有遗留物料。"
|
||||
)
|
||||
|
||||
@action(
|
||||
always_free=True,
|
||||
node_type=NodeType.MANUAL_CONFIRM,
|
||||
placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"},
|
||||
goal_default={
|
||||
"reset_scheduler": True,
|
||||
"reset_order_status": True,
|
||||
"reset_location": True,
|
||||
"reset_devices": False,
|
||||
"physical_cleanup_confirmed": False,
|
||||
"timeout_seconds": 3600,
|
||||
"assignee_user_ids": [],
|
||||
},
|
||||
feedback_interval=300,
|
||||
description=RESET_MANUAL_CONFIRM_MESSAGE,
|
||||
)
|
||||
def reset_manual(
|
||||
self,
|
||||
reset_scheduler: bool = True,
|
||||
reset_order_status: bool = True,
|
||||
reset_location: bool = True,
|
||||
reset_devices: bool = False,
|
||||
physical_cleanup_confirmed: bool = False,
|
||||
timeout_seconds: int = 3600,
|
||||
assignee_user_ids: Optional[List[str]] = None,
|
||||
**kwargs: Any,
|
||||
) -> Dict[str, Any]:
|
||||
"""人工确认物理清理后执行复位。
|
||||
|
||||
Args:
|
||||
reset_scheduler[调度器复位]: 调用 /api/lims/scheduler/reset，默认勾选。
|
||||
reset_order_status[订单状态复位]: 调用 /api/lims/order/reset-order-status，默认勾选。
|
||||
reset_location[库位复位]: 调用 /api/lims/storage/reset-location，默认勾选。
|
||||
reset_devices[仪器复位]: 调用 /api/lims/device/reset-devices，默认不勾选。
|
||||
physical_cleanup_confirmed[物理清理确认]: 确认清理提示中的物料检查已经完成，默认不勾选。
|
||||
"""
|
||||
...
|
||||
```
|
||||
|
||||
Execution rule:
|
||||
|
||||
- If `physical_cleanup_confirmed` is false, return a blocked result and do not call any reset API.
|
||||
- If it is true, call the same internal helper as `reset_auto`.
|
||||
- Return `confirmation_message` in the result payload so call logs preserve the exact operator instruction text.
|
||||
|
||||
Renderer caveat:
|
||||
|
||||
- `description` should carry the warning in generated action metadata.
|
||||
- `physical_cleanup_confirmed` must remain a plain `bool` so it renders as a checkbox.
|
||||
- The cleanup warning should be carried by the action `description` and the docstring param description. Do not rely on `Field(description=...)` unless registry `Annotated` support has been implemented and tested.
|
||||
- If the current frontend does not show action descriptions or docstring field descriptions reliably, add a read-only string parameter such as `confirmation_message: str = RESET_MANUAL_CONFIRM_MESSAGE` with `goal_default`, or use a handle-based display only after renderer behavior is verified.
|
||||
|
||||
## Shared Internal Helper
|
||||
|
||||
Both public actions should delegate to one helper, for example:
|
||||
|
||||
```python
|
||||
def _execute_reset_operations(
|
||||
self,
|
||||
*,
|
||||
reset_scheduler: bool,
|
||||
reset_order_status: bool,
|
||||
reset_location: bool,
|
||||
reset_devices: bool,
|
||||
) -> Dict[str, Any]:
|
||||
...
|
||||
```
|
||||
|
||||
Call order:
|
||||
|
||||
1. `scheduler_reset`
|
||||
2. `reset_order_status`
|
||||
3. `reset_location`
|
||||
4. `reset_devices`
|
||||
|
||||
Result shape:
|
||||
|
||||
```python
|
||||
{
|
||||
"selected_operations": [
|
||||
{"key": "reset_scheduler", "label": "调度器复位", "selected": True},
|
||||
{"key": "reset_order_status", "label": "订单状态复位", "selected": True},
|
||||
{"key": "reset_location", "label": "库位复位", "selected": True},
|
||||
{"key": "reset_devices", "label": "仪器复位", "selected": False},
|
||||
],
|
||||
"executed_calls": [
|
||||
{"operation": "scheduler_reset", "endpoint": "/api/lims/scheduler/reset", "result": {"code": 1}},
|
||||
],
|
||||
"skipped_operations": [
|
||||
{"operation": "reset_devices", "reason": "checkbox_disabled"},
|
||||
],
|
||||
"warnings": [],
|
||||
}
|
||||
```
|
||||
|
||||
Failure handling:
|
||||
|
||||
- Execute selected operations sequentially and record each result.
|
||||
- If an operation returns non-`1` code, add a warning and continue unless the caller later requests fail-fast.
|
||||
- If an RPC method raises, catch it, record an error entry, and continue to the next selected operation unless fail-fast is introduced.
|
||||
|
||||
## RPC Wrapper Adjustment
|
||||
|
||||
Adjust the two id-shaped wrappers to no-data calls:
|
||||
|
||||
- `BioyondV1RPC.reset_order_status()` should no longer require `order_id`.
|
||||
- `BioyondV1RPC.reset_location()` should no longer require `location_id`.
|
||||
|
||||
Current no-data wrappers already exist:
|
||||
|
||||
- `scheduler_reset()`
|
||||
- `reset_devices()`
|
||||
|
||||
Suggested RPC signatures:
|
||||
|
||||
```python
|
||||
def scheduler_reset(self) -> int: ...
|
||||
def reset_order_status(self) -> int: ...
|
||||
def reset_location(self) -> int: ...
|
||||
def reset_devices(self) -> int: ...
|
||||
```
|
||||
|
||||
Compatibility option:
|
||||
|
||||
```python
|
||||
def reset_order_status(self, order_id: Optional[str] = None) -> int:
|
||||
del order_id
|
||||
...
|
||||
|
||||
def reset_location(self, location_id: Optional[str] = None) -> int:
|
||||
del location_id
|
||||
...
|
||||
```
|
||||
|
||||
This keeps older code from crashing while making the actual wire request no-data.
|
||||
|
||||
## Adjusted Runtime API Schemas
|
||||
|
||||
These are the schemas Peptide reset code should target at runtime after the live no-data probes. They intentionally omit `data`, even though OpenAPI models nullable `data` for these endpoints.
|
||||
|
||||
All four requests use:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "string",
|
||||
"requestTime": "date-time"
|
||||
}
|
||||
```
|
||||
|
||||
No `data` field should be sent by default.
|
||||
|
||||
All four responses use:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 0
|
||||
}
|
||||
```
|
||||
|
||||
### 调度器复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/scheduler/reset
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-21T08:15:16.494Z"
|
||||
}
|
||||
```
|
||||
|
||||
Live response:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 1779351316072
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable int32.
|
||||
- Live Peptide accepted omitted `data`.
|
||||
|
||||
### 订单状态复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/order/reset-order-status
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-21T08:13:34.750Z"
|
||||
}
|
||||
```
|
||||
|
||||
Live response:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 1779351214422
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable string.
|
||||
- Live Peptide accepted omitted `data`.
|
||||
- Do not model this as order-id scoped unless Bioyond confirms backend behavior.
|
||||
|
||||
### 库位复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/storage/reset-location
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-21T08:15:18.924Z"
|
||||
}
|
||||
```
|
||||
|
||||
Live response:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 1779351318565
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable string.
|
||||
- Live Peptide accepted omitted `data`.
|
||||
- Do not model this as location-id scoped unless Bioyond confirms backend behavior.
|
||||
|
||||
### 仪器复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/device/reset-devices
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "date-time"
|
||||
}
|
||||
```
|
||||
|
||||
Expected response shape:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 0
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable string.
|
||||
- Current `BioyondV1RPC.reset_devices()` already sends no `data`.
|
||||
- This endpoint was not live-probed in the no-data reset session.
|
||||
- Keep checkbox default unchecked.
|
||||
|
||||
## Tests To Add Before Implementation
|
||||
|
||||
1. `reset_auto` is not `NodeType.MANUAL_CONFIRM`.
|
||||
2. `reset_manual` has `node_type=NodeType.MANUAL_CONFIRM`.
|
||||
3. `reset_manual` metadata includes:
|
||||
- `always_free=True`
|
||||
- `placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"}`
|
||||
- `timeout_seconds=3600`
|
||||
- `assignee_user_ids=[]`
|
||||
- `physical_cleanup_confirmed=False`
|
||||
4. Both reset actions expose four real boolean params:
|
||||
- `reset_scheduler`
|
||||
- `reset_order_status`
|
||||
- `reset_location`
|
||||
- `reset_devices`
|
||||
5. The generated registry schema marks those reset params as JSON Schema `type: boolean`, not `object` or `string`, so the frontend can render checkboxes.
|
||||
6. `reset_auto` replaces the current public `reset` action. Unless a later compatibility request adds an alias, no old id-shaped public `reset` action remains.
|
||||
7. Goal defaults are:
|
||||
- first three reset checkboxes `True`
|
||||
- `reset_devices=False`
|
||||
8. `reset_manual(..., physical_cleanup_confirmed=False)` does not call any RPC reset method.
|
||||
9. `reset_auto()` with defaults calls:
|
||||
- `scheduler_reset()`
|
||||
- `reset_order_status()`
|
||||
- `reset_location()`
|
||||
- not `reset_devices()`
|
||||
10. `reset_auto(reset_devices=True)` also calls `reset_devices()`.
|
||||
11. `reset_order_status()` and `reset_location()` RPC wrappers send no `data` key.
|
||||
12. No reset path calls `take_out`.
|
||||
13. No reset path calls `refresh_material_cache`.
|
||||
|
||||
## Non-Goals
|
||||
|
||||
- Do not implement `take_out` in reset.
|
||||
- Do not refresh `material_cache` from reset.
|
||||
- Do not resolve order ids or location ids for reset.
|
||||
- Do not add Project/cache/browser cleanup routes.
|
||||
- Do not make `reset_devices` default-on.
|
||||
- Do not execute this plan during planning.
|
||||
@@ -415,21 +415,25 @@ class BioyondV1RPC(BaseRequest):
|
||||
return {}
|
||||
return response.get("data", {})
|
||||
|
||||
def reset_location(self, location_id: str) -> int:
|
||||
def reset_location(self, location_id: Optional[str] = None) -> int:
|
||||
"""复位库位
|
||||
|
||||
现场实测 ``POST /api/lims/storage/reset-location`` 不传 ``data`` 即可成功
|
||||
（见 ``temp_benyao/peptide/_findings/2026-05-21_1615_remaining_resets_no_data_live.md``），
|
||||
因此默认无 ``data`` 字段；保留 ``location_id`` 仅为兼容旧调用，传入会被忽略。
|
||||
|
||||
参数:
|
||||
location_id: 库位ID
|
||||
location_id: 兼容入参，已被忽略；新逻辑不再以 location 为粒度复位。
|
||||
|
||||
返回值:
|
||||
int: 成功返回1，失败返回0
|
||||
"""
|
||||
del location_id
|
||||
response = self.post(
|
||||
url=f'{self.host}/api/lims/storage/reset-location',
|
||||
params={
|
||||
"apiKey": self.api_key,
|
||||
"requestTime": self.get_current_time_iso8601(),
|
||||
"data": location_id,
|
||||
})
|
||||
if not response or response['code'] != 1:
|
||||
return 0
|
||||
@@ -779,6 +783,49 @@ class BioyondV1RPC(BaseRequest):
|
||||
|
||||
return response.get("data", {})
|
||||
|
||||
def take_out(
|
||||
self,
|
||||
order_id: str,
|
||||
preintake_ids: list[str] | None = None,
|
||||
material_ids: list[str] | None = None,
|
||||
) -> dict:
|
||||
"""取出订单关联通量/物料
|
||||
|
||||
参数:
|
||||
order_id: 订单ID
|
||||
preintake_ids: 通量ID列表，可为空
|
||||
material_ids: 物料ID列表，可为空
|
||||
|
||||
返回值:
|
||||
dict: 服务端响应包，失败返回空字典
|
||||
"""
|
||||
if not order_id:
|
||||
self._logger.error("取出订单关联通量/物料错误: 缺少订单ID")
|
||||
return {}
|
||||
|
||||
params = {
|
||||
"orderId": order_id,
|
||||
"preintakeIds": list(preintake_ids or []),
|
||||
"materialIds": list(material_ids or []),
|
||||
}
|
||||
|
||||
response = self.post(
|
||||
url=f'{self.host}/api/lims/order/take-out',
|
||||
params={
|
||||
"apiKey": self.api_key,
|
||||
"requestTime": self.get_current_time_iso8601(),
|
||||
"data": params,
|
||||
})
|
||||
|
||||
if not response:
|
||||
return {}
|
||||
|
||||
if response['code'] != 1:
|
||||
self._logger.error(f"取出订单关联通量/物料错误: {response.get('message', '')}")
|
||||
return response
|
||||
|
||||
return response
|
||||
|
||||
def cancel_order(self, json_str: str) -> bool:
|
||||
"""取消指定任务
|
||||
|
||||
@@ -886,21 +933,25 @@ class BioyondV1RPC(BaseRequest):
|
||||
return {}
|
||||
return response.get("data", {})
|
||||
|
||||
def reset_order_status(self, order_id: str) -> int:
|
||||
def reset_order_status(self, order_id: Optional[str] = None) -> int:
|
||||
"""复位订单状态
|
||||
|
||||
现场实测 ``POST /api/lims/order/reset-order-status`` 不传 ``data`` 即可成功
|
||||
（见 ``temp_benyao/peptide/_findings/2026-05-21_1613_reset_order_status_no_data_live.md``），
|
||||
因此默认无 ``data`` 字段；保留 ``order_id`` 仅为兼容旧调用，传入会被忽略。
|
||||
|
||||
参数:
|
||||
order_id: 订单ID
|
||||
order_id: 兼容入参，已被忽略；新逻辑不再以单订单为粒度复位。
|
||||
|
||||
返回值:
|
||||
int: 成功返回1，失败返回0
|
||||
"""
|
||||
del order_id
|
||||
response = self.post(
|
||||
url=f'{self.host}/api/lims/order/reset-order-status',
|
||||
params={
|
||||
"apiKey": self.api_key,
|
||||
"requestTime": self.get_current_time_iso8601(),
|
||||
"data": order_id,
|
||||
})
|
||||
if not response or response['code'] != 1:
|
||||
return 0
|
||||
|
||||
459
unilabos/devices/workstation/bioyond_studio/debug_call_log.py
Normal file
459
unilabos/devices/workstation/bioyond_studio/debug_call_log.py
Normal file
@@ -0,0 +1,459 @@
|
||||
"""Per-action raw call/response log for Bioyond stations.
|
||||
|
||||
When a debug session is active, ``wrap_rpc_http`` replaces a ``BioyondV1RPC``
|
||||
instance's ``post`` / ``get`` methods with closures that perform the HTTP
|
||||
transport themselves, capture the request/response details, and append a record
|
||||
to the active session before returning exactly what ``BaseRequest`` would have
|
||||
returned. Outside of an active session the wrapped method delegates to the
|
||||
original (unwrapped) implementation, leaving non-debug behavior intact.
|
||||
|
||||
The session writes a Markdown file under ``out_dir`` mirroring the format of
|
||||
``bioyond_debug_records/2026-04-30_160316_day3_samplefile_only_raw_calls.md``
|
||||
minus the "Raw Payload Argument" section.
|
||||
|
||||
This module has no dependency on ``BioyondV1RPC`` itself; the only contract is
|
||||
that the wrapped instance descends from ``BaseRequest`` (i.e. has a logger
|
||||
returned by ``self.get_logger()``).
|
||||
"""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import contextvars
|
||||
import copy
|
||||
import inspect
|
||||
import json
|
||||
import re
|
||||
from contextlib import contextmanager
|
||||
from dataclasses import dataclass, field
|
||||
from datetime import datetime
|
||||
from pathlib import Path
|
||||
from typing import Any, Iterator, List, Optional
|
||||
|
||||
import requests
|
||||
|
||||
__all__ = [
|
||||
"CallRecord",
|
||||
"CallLogContext",
|
||||
"session",
|
||||
"wrap_rpc_http",
|
||||
"active_session",
|
||||
]
|
||||
|
||||
|
||||
_DEFAULT_TIMEOUT_GET = 30
|
||||
_DEFAULT_TIMEOUT_POST = 120
|
||||
|
||||
|
||||
@dataclass
|
||||
class CallRecord:
|
||||
"""One captured HTTP call inside a debug session."""
|
||||
|
||||
index: int
|
||||
method: str
|
||||
url: str
|
||||
path: str
|
||||
source: str
|
||||
transport: str
|
||||
http_status: Optional[int]
|
||||
request_body: Any
|
||||
response_body: Any
|
||||
error: Optional[str] = None
|
||||
|
||||
|
||||
@dataclass
|
||||
class CallLogContext:
|
||||
"""State for a single ``session()`` block.
|
||||
|
||||
A session lazily creates its file on the first appended record. Actions
|
||||
that abort before any RPC produce no file.
|
||||
"""
|
||||
|
||||
action: str
|
||||
out_dir: Path
|
||||
started_at: datetime
|
||||
calls: List[CallRecord] = field(default_factory=list)
|
||||
file_path: Optional[Path] = None
|
||||
|
||||
def append(self, record: CallRecord) -> None:
|
||||
record.index = len(self.calls) + 1
|
||||
self.calls.append(record)
|
||||
self._write_file()
|
||||
|
||||
# -- file I/O -------------------------------------------------------------
|
||||
|
||||
def _resolve_file_path(self) -> Path:
|
||||
if self.file_path is not None:
|
||||
return self.file_path
|
||||
timestamp = self.started_at.strftime("%Y-%m-%d_%H%M%S")
|
||||
slug = _slugify_action(self.action)
|
||||
candidate = self.out_dir / f"{timestamp}_{slug}_raw_calls.md"
|
||||
suffix = 2
|
||||
while candidate.exists():
|
||||
candidate = (
|
||||
self.out_dir
|
||||
/ f"{timestamp}_{slug}_raw_calls_{suffix:02d}.md"
|
||||
)
|
||||
suffix += 1
|
||||
self.file_path = candidate
|
||||
return self.file_path
|
||||
|
||||
def _write_file(self) -> None:
|
||||
path = self._resolve_file_path()
|
||||
path.parent.mkdir(parents=True, exist_ok=True)
|
||||
path.write_text(_render_markdown(self), encoding="utf-8")
|
||||
|
||||
|
||||
_active_session: contextvars.ContextVar[Optional[CallLogContext]] = (
|
||||
contextvars.ContextVar("_active_session", default=None)
|
||||
)
|
||||
|
||||
|
||||
def active_session() -> Optional[CallLogContext]:
|
||||
"""Return the currently active :class:`CallLogContext`, if any."""
|
||||
return _active_session.get()
|
||||
|
||||
|
||||
@contextmanager
|
||||
def session(action: str, out_dir: Path) -> Iterator[CallLogContext]:
|
||||
"""Open a per-action debug session.
|
||||
|
||||
On entry, sets the module-level ``_active_session`` ContextVar so any
|
||||
``wrap_rpc_http``'d clients on the same thread/task record their calls.
|
||||
On exit, the previous active session (if any) is restored.
|
||||
"""
|
||||
ctx = CallLogContext(
|
||||
action=str(action),
|
||||
out_dir=Path(out_dir),
|
||||
started_at=datetime.now(),
|
||||
)
|
||||
token = _active_session.set(ctx)
|
||||
try:
|
||||
yield ctx
|
||||
finally:
|
||||
_active_session.reset(token)
|
||||
|
||||
|
||||
def wrap_rpc_http(rpc: Any) -> None:
|
||||
"""Idempotently wrap ``rpc.post`` / ``rpc.get``.
|
||||
|
||||
When a session is active (``_active_session.get() is not None``), the
|
||||
wrapped methods perform the HTTP call themselves with ``requests`` and
|
||||
record the call before returning the same value ``BaseRequest`` would have
|
||||
returned. When no session is active, the wrapped methods delegate to the
|
||||
original implementation, preserving stock ``BaseRequest`` behavior.
|
||||
|
||||
Calling this twice on the same instance is a no-op. The wrapper does not
|
||||
alter ``rpc.form_post`` (no Sirna action calls it as of plan 3).
|
||||
"""
|
||||
if rpc is None:
|
||||
return
|
||||
if getattr(rpc, "_debug_call_log_wrapped", False):
|
||||
return
|
||||
|
||||
rpc._orig_post = rpc.post
|
||||
rpc._orig_get = rpc.get
|
||||
|
||||
def _wrapped_post(
|
||||
url: str,
|
||||
params: Any = None,
|
||||
files: Any = None,
|
||||
headers: Optional[dict] = None,
|
||||
) -> Any:
|
||||
ctx = _active_session.get()
|
||||
if ctx is None:
|
||||
kwargs = {}
|
||||
if params is not None:
|
||||
kwargs["params"] = params
|
||||
if files is not None:
|
||||
kwargs["files"] = files
|
||||
if headers is not None:
|
||||
kwargs["headers"] = headers
|
||||
return rpc._orig_post(url, **kwargs)
|
||||
effective_params = params if params is not None else {}
|
||||
effective_headers = (
|
||||
headers
|
||||
if headers is not None
|
||||
else {"Content-Type": "application/json"}
|
||||
)
|
||||
source = _detect_source(rpc)
|
||||
request_body = _redact(effective_params)
|
||||
record = CallRecord(
|
||||
index=0,
|
||||
method="POST",
|
||||
url=str(url),
|
||||
path=_url_path(url),
|
||||
source=source,
|
||||
transport=_pick_transport(effective_params),
|
||||
http_status=None,
|
||||
request_body=request_body,
|
||||
response_body=None,
|
||||
error=None,
|
||||
)
|
||||
return_value: Any = None
|
||||
try:
|
||||
response = requests.post(
|
||||
url,
|
||||
data=json.dumps(effective_params) if effective_params else None,
|
||||
headers=effective_headers,
|
||||
timeout=_DEFAULT_TIMEOUT_POST,
|
||||
files=files,
|
||||
)
|
||||
except Exception as exc: # pragma: no cover - delegated to logger
|
||||
record.error = f"transport error: {exc}"
|
||||
try:
|
||||
rpc.get_logger().error(f"Request ERROR: {exc}")
|
||||
except Exception:
|
||||
pass
|
||||
ctx.append(record)
|
||||
return None
|
||||
|
||||
record.http_status = response.status_code
|
||||
record.response_body, parse_error = _decode_response_body(response)
|
||||
try:
|
||||
rpc.get_logger().debug(
|
||||
f"Request >>> : {response.request.body} "
|
||||
f"{response.status_code} {response.text}"
|
||||
)
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
if response.status_code == 200:
|
||||
if parse_error is not None:
|
||||
record.error = f"json parse error: {parse_error}"
|
||||
return_value = None
|
||||
else:
|
||||
return_value = record.response_body
|
||||
else:
|
||||
record.error = f"HTTP {response.status_code}: {response.text}"
|
||||
try:
|
||||
rpc.get_logger().error(
|
||||
f"Request ERROR: ('Request ERROR:', {response.text!r})"
|
||||
)
|
||||
except Exception:
|
||||
pass
|
||||
return_value = None
|
||||
|
||||
ctx.append(record)
|
||||
return return_value
|
||||
|
||||
def _wrapped_get(
|
||||
url: str,
|
||||
params: Any = None,
|
||||
headers: Optional[dict] = None,
|
||||
) -> Any:
|
||||
ctx = _active_session.get()
|
||||
if ctx is None:
|
||||
kwargs = {}
|
||||
if params is not None:
|
||||
kwargs["params"] = params
|
||||
if headers is not None:
|
||||
kwargs["headers"] = headers
|
||||
return rpc._orig_get(url, **kwargs)
|
||||
effective_params = params if params is not None else {}
|
||||
effective_headers = (
|
||||
headers
|
||||
if headers is not None
|
||||
else {"Content-Type": "application/json"}
|
||||
)
|
||||
source = _detect_source(rpc)
|
||||
request_body = _redact(effective_params)
|
||||
record = CallRecord(
|
||||
index=0,
|
||||
method="GET",
|
||||
url=str(url),
|
||||
path=_url_path(url),
|
||||
source=source,
|
||||
transport="params",
|
||||
http_status=None,
|
||||
request_body=request_body,
|
||||
response_body=None,
|
||||
error=None,
|
||||
)
|
||||
return_value: Any = None
|
||||
try:
|
||||
response = requests.get(
|
||||
url,
|
||||
params=effective_params,
|
||||
headers=effective_headers,
|
||||
timeout=_DEFAULT_TIMEOUT_GET,
|
||||
)
|
||||
except Exception as exc: # pragma: no cover - delegated to logger
|
||||
record.error = f"transport error: {exc}"
|
||||
try:
|
||||
rpc.get_logger().error(f"Request ERROR: {exc}")
|
||||
except Exception:
|
||||
pass
|
||||
ctx.append(record)
|
||||
return None
|
||||
|
||||
record.http_status = response.status_code
|
||||
record.response_body, parse_error = _decode_response_body(response)
|
||||
try:
|
||||
rpc.get_logger().debug(
|
||||
f"Request >>> : {effective_params} "
|
||||
f"{response.status_code} {response.text}"
|
||||
)
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
if response.status_code == 200:
|
||||
if parse_error is not None:
|
||||
record.error = f"json parse error: {parse_error}"
|
||||
return_value = None
|
||||
else:
|
||||
return_value = record.response_body
|
||||
|
||||
ctx.append(record)
|
||||
return return_value
|
||||
|
||||
rpc.post = _wrapped_post
|
||||
rpc.get = _wrapped_get
|
||||
rpc._debug_call_log_wrapped = True
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Helpers
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
_URL_PATH_RE = re.compile(r"https?://[^/]+(/.*)?$")
|
||||
_SLUG_RE = re.compile(r"[^A-Za-z0-9._-]+")
|
||||
|
||||
|
||||
def _slugify_action(action: str) -> str:
|
||||
slug = _SLUG_RE.sub("_", str(action)).strip("_")
|
||||
return slug or "action"
|
||||
|
||||
|
||||
def _url_path(url: Any) -> str:
|
||||
text = str(url or "")
|
||||
match = _URL_PATH_RE.match(text)
|
||||
if match and match.group(1):
|
||||
return match.group(1)
|
||||
if text.startswith("/"):
|
||||
return text
|
||||
return text
|
||||
|
||||
|
||||
def _pick_transport(params: Any) -> str:
|
||||
if isinstance(params, dict) and "data" in params:
|
||||
return "data"
|
||||
return "params"
|
||||
|
||||
|
||||
def _detect_source(rpc: Any) -> str:
|
||||
"""Walk the call stack to find the outermost frame whose ``self`` is rpc."""
|
||||
try:
|
||||
stack = inspect.stack()
|
||||
except Exception:
|
||||
return ""
|
||||
candidate = ""
|
||||
try:
|
||||
for frame_info in stack:
|
||||
frame = frame_info.frame
|
||||
if frame.f_locals.get("self", None) is rpc:
|
||||
candidate = frame_info.function
|
||||
return candidate
|
||||
finally:
|
||||
del stack
|
||||
|
||||
|
||||
def _redact(params: Any) -> Any:
|
||||
"""Return a copy of ``params`` with ``apiKey`` redacted."""
|
||||
try:
|
||||
cloned = copy.deepcopy(params)
|
||||
except Exception:
|
||||
return params
|
||||
_redact_in_place(cloned)
|
||||
return cloned
|
||||
|
||||
|
||||
def _redact_in_place(value: Any) -> None:
|
||||
if isinstance(value, dict):
|
||||
for key in list(value.keys()):
|
||||
if isinstance(key, str) and key.lower() == "apikey":
|
||||
value[key] = "<redacted>"
|
||||
else:
|
||||
_redact_in_place(value[key])
|
||||
elif isinstance(value, list):
|
||||
for item in value:
|
||||
_redact_in_place(item)
|
||||
|
||||
|
||||
def _decode_response_body(response: Any) -> tuple[Any, Optional[str]]:
|
||||
"""Best-effort response decoding used for both record + return value."""
|
||||
text = getattr(response, "text", "")
|
||||
try:
|
||||
return response.json(), None
|
||||
except Exception as exc:
|
||||
if text:
|
||||
return {"raw_text": text}, str(exc)
|
||||
return None, str(exc)
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Markdown rendering
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def _render_markdown(ctx: CallLogContext) -> str:
|
||||
title = f"# {ctx.action} Raw Call/Response Log"
|
||||
parts: List[str] = [title, ""]
|
||||
parts.append("## LIMS Calls")
|
||||
parts.append("")
|
||||
parts.append("| # | Method | Path | Source | HTTP |")
|
||||
parts.append("|---|---|---|---|---|")
|
||||
for record in ctx.calls:
|
||||
anchor = _row_anchor(record)
|
||||
http = (
|
||||
f"`{record.http_status}`"
|
||||
if record.http_status is not None
|
||||
else "`-`"
|
||||
)
|
||||
parts.append(
|
||||
f"| [{record.index}](#{anchor}) | `{record.method}` | "
|
||||
f"`{record.path}` | `{record.source}` | {http} |"
|
||||
)
|
||||
parts.append("")
|
||||
|
||||
for record in ctx.calls:
|
||||
parts.append(f"## {record.index} {record.method} {record.path}")
|
||||
parts.append("")
|
||||
parts.append(f"- Source: `{record.source}`")
|
||||
parts.append(f"- Transport: `{record.transport}`")
|
||||
if record.http_status is not None:
|
||||
parts.append(f"- HTTP status: `{record.http_status}`")
|
||||
else:
|
||||
parts.append("- HTTP status: `-`")
|
||||
if record.error:
|
||||
parts.append(f"- Error: {record.error}")
|
||||
parts.append("")
|
||||
parts.append("### Request Body")
|
||||
parts.append("")
|
||||
parts.append("```json")
|
||||
parts.append(_to_json_block(record.request_body))
|
||||
parts.append("```")
|
||||
parts.append("")
|
||||
parts.append("### Response Body")
|
||||
parts.append("")
|
||||
parts.append("```json")
|
||||
parts.append(_to_json_block(record.response_body))
|
||||
parts.append("```")
|
||||
parts.append("")
|
||||
|
||||
return "\n".join(parts).rstrip() + "\n"
|
||||
|
||||
|
||||
def _row_anchor(record: CallRecord) -> str:
|
||||
"""Build a GitHub-style anchor matching ``## N METHOD /path``."""
|
||||
raw = f"{record.index}-{record.method}-{record.path}"
|
||||
raw = raw.lower()
|
||||
raw = re.sub(r"[^a-z0-9]+", "-", raw)
|
||||
return raw.strip("-")
|
||||
|
||||
|
||||
def _to_json_block(value: Any) -> str:
|
||||
try:
|
||||
return json.dumps(value, ensure_ascii=False, indent=2, sort_keys=True)
|
||||
except TypeError:
|
||||
return json.dumps(str(value), ensure_ascii=False, indent=2)
|
||||
@@ -0,0 +1,3 @@
|
||||
from .peptide_station import BioyondPeptideStation, fetch_workflow_list, load_peptide_config
|
||||
|
||||
__all__ = ["BioyondPeptideStation", "fetch_workflow_list", "load_peptide_config"]
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -7,6 +7,7 @@ Bioyond Workstation Implementation
|
||||
import time
|
||||
import traceback
|
||||
import threading
|
||||
from contextlib import contextmanager
|
||||
from datetime import datetime
|
||||
from typing import Dict, Any, List, Optional, Union
|
||||
import json
|
||||
@@ -14,6 +15,7 @@ from pathlib import Path
|
||||
|
||||
from unilabos.devices.workstation.workstation_base import WorkstationBase, ResourceSynchronizer
|
||||
from unilabos.devices.workstation.bioyond_studio.bioyond_rpc import BioyondV1RPC
|
||||
from unilabos.devices.workstation.bioyond_studio import debug_call_log
|
||||
from unilabos.registry.placeholder_type import ResourceSlot, DeviceSlot
|
||||
from unilabos.resources.warehouse import WareHouse
|
||||
from unilabos.utils.log import logger
|
||||
@@ -54,13 +56,17 @@ class ConnectionMonitor:
|
||||
def _monitor_loop(self):
|
||||
while self._running:
|
||||
try:
|
||||
# 使用 lightweight API 检查连接
|
||||
# query_matial_type_list 是比较快的查询
|
||||
start_time = time.time()
|
||||
result = self.workstation.hardware_interface.material_type_list()
|
||||
# 使用轻量级调度状态接口检查连接，避免启动时打印完整物料类型列表。
|
||||
result = self.workstation.hardware_interface.scheduler_status()
|
||||
|
||||
status = "online" if result else "offline"
|
||||
msg = "Connection established" if status == "online" else "Failed to get material type list"
|
||||
if status == "online":
|
||||
msg = (
|
||||
f"Scheduler status={result.get('status')}, "
|
||||
f"hasTask={result.get('hasTask')}"
|
||||
)
|
||||
else:
|
||||
msg = "Failed to get scheduler status"
|
||||
|
||||
if status != self._last_status:
|
||||
logger.info(f"Bioyond连接状态变更: {self._last_status} -> {status}")
|
||||
@@ -174,6 +180,8 @@ class BioyondResourceSynchronizer(ResourceSynchronizer):
|
||||
logger.warning("从Bioyond获取的物料数据为空")
|
||||
return False
|
||||
|
||||
self._update_material_cache_from_stock(all_bioyond_data)
|
||||
|
||||
# 转换为UniLab格式
|
||||
unilab_resources = resource_bioyond_to_plr(
|
||||
all_bioyond_data,
|
||||
@@ -187,6 +195,29 @@ class BioyondResourceSynchronizer(ResourceSynchronizer):
|
||||
logger.error(f"从Bioyond同步物料数据失败: {e}")
|
||||
return False
|
||||
|
||||
def _update_material_cache_from_stock(self, materials: List[Dict[str, Any]]) -> None:
|
||||
"""用本次库存查询结果同步 RPC 的 name -> material id 缓存。"""
|
||||
material_cache = getattr(self.bioyond_api_client, "material_cache", None)
|
||||
if not isinstance(material_cache, dict):
|
||||
return
|
||||
|
||||
before_count = len(material_cache)
|
||||
for material in materials:
|
||||
material_name = material.get("name")
|
||||
material_id = material.get("id")
|
||||
if material_name and material_id:
|
||||
material_cache[material_name] = material_id
|
||||
|
||||
for detail_material in material.get("detail", []) or []:
|
||||
detail_name = detail_material.get("name")
|
||||
detail_id = detail_material.get("detailMaterialId") or detail_material.get("id")
|
||||
if detail_name and detail_id:
|
||||
material_cache[detail_name] = detail_id
|
||||
|
||||
logger.debug(
|
||||
f"已用Bioyond库存同步物料缓存: {before_count} -> {len(material_cache)}"
|
||||
)
|
||||
|
||||
def sync_to_external(self, resource: Any) -> bool:
|
||||
"""将本地物料数据变更同步到Bioyond系统"""
|
||||
try:
|
||||
@@ -678,6 +709,70 @@ class BioyondWorkstation(WorkstationBase):
|
||||
集成Bioyond物料管理的工作站实现
|
||||
"""
|
||||
|
||||
# 子类（如 sirna / peptide）覆写以指定默认 raw-call 日志目录。
|
||||
# 路径相对仓库根；为 None 时若 debug_log=True 仍会写入临时位置。
|
||||
_DEBUG_LOG_DEFAULT_DIR: Optional[str] = None
|
||||
|
||||
def _create_bioyond_rpc(self, config: Dict[str, Any]) -> BioyondV1RPC:
|
||||
"""创建 Bioyond RPC 客户端并应用调试包装。
|
||||
|
||||
所有创建 ``BioyondV1RPC`` 的路径（饿汉初始化、Sirna 延迟初始化、
|
||||
以及未来的前端重新配置路径）都应通过该 helper，
|
||||
以确保 debug_log 包装与命名/日志策略保持一致。
|
||||
"""
|
||||
rpc = BioyondV1RPC(config)
|
||||
debug_call_log.wrap_rpc_http(rpc)
|
||||
return rpc
|
||||
|
||||
def _set_hardware_interface(self, rpc: BioyondV1RPC) -> BioyondV1RPC:
|
||||
"""将已构造的 RPC 客户端设置到 ``self.hardware_interface``，并应用调试包装。"""
|
||||
debug_call_log.wrap_rpc_http(rpc)
|
||||
self.hardware_interface = rpc
|
||||
return rpc
|
||||
|
||||
def _debug_log_resolved_dir(self) -> Path:
|
||||
"""解析 ``debug_log_dir`` 为绝对路径。"""
|
||||
configured = (getattr(self, "bioyond_config", {}) or {}).get("debug_log_dir")
|
||||
default_dir = getattr(self, "_DEBUG_LOG_DEFAULT_DIR", None)
|
||||
candidate = configured or default_dir or "bioyond_debug_records"
|
||||
path = Path(candidate)
|
||||
if not path.is_absolute():
|
||||
repo_root = Path(__file__).resolve().parents[4]
|
||||
path = repo_root / path
|
||||
return path
|
||||
|
||||
def _ensure_debug_log_state(self) -> None:
|
||||
"""从 ``self.bioyond_config`` 派生 ``_debug_log_enabled`` / ``_debug_log_dir``。
|
||||
|
||||
每次进入 ``_debug_call_session`` 时都重新解析，以兼容前端在运行时
|
||||
修改 ``bioyond_config['debug_log']`` 或目录的场景；同时也容忍
|
||||
子类（如 Sirna 延迟初始化）在 ``__init__`` 早期未触发本方法。
|
||||
"""
|
||||
cfg = getattr(self, "bioyond_config", {}) or {}
|
||||
self._debug_log_enabled = bool(cfg.get("debug_log"))
|
||||
self._debug_log_dir = self._debug_log_resolved_dir()
|
||||
|
||||
@contextmanager
|
||||
def _debug_call_session(self, action_name: str):
|
||||
"""在 action 体外加一层 debug 会话上下文。
|
||||
|
||||
- ``debug_log`` 关闭时是空上下文，开销为 0。
|
||||
- ``debug_log`` 开启时进入 :func:`debug_call_log.session`，所有
|
||||
已被 ``wrap_rpc_http`` 包装过的 RPC 客户端都会捕获本次 action
|
||||
产生的 HTTP 调用并写入 Markdown 文件。
|
||||
|
||||
子类（如 ``end_experiment``、``manual_unload`` 等）可以直接在
|
||||
action 体里以 ``with self._debug_call_session("action_name"):`` 包裹。
|
||||
"""
|
||||
cfg = getattr(self, "bioyond_config", {}) or {}
|
||||
enabled = bool(cfg.get("debug_log"))
|
||||
if not enabled:
|
||||
yield None
|
||||
return
|
||||
out_dir = BioyondWorkstation._debug_log_resolved_dir(self)
|
||||
with debug_call_log.session(action_name, out_dir) as ctx:
|
||||
yield ctx
|
||||
|
||||
def _publish_task_status(
|
||||
self,
|
||||
task_id: str,
|
||||
@@ -862,7 +957,7 @@ class BioyondWorkstation(WorkstationBase):
|
||||
self.bioyond_config = {}
|
||||
print("警告: 未提供 bioyond_config，请确保在 JSON 配置文件中提供完整配置")
|
||||
|
||||
self.hardware_interface = BioyondV1RPC(self.bioyond_config)
|
||||
self.hardware_interface = self._create_bioyond_rpc(self.bioyond_config)
|
||||
|
||||
def resource_tree_add(self, resources: List[ResourcePLR]) -> None:
|
||||
"""添加资源到资源树并更新ROS节点
|
||||
@@ -1338,11 +1433,7 @@ class BioyondWorkstation(WorkstationBase):
|
||||
if self.hardware_interface:
|
||||
self.hardware_interface.scheduler_reset()
|
||||
|
||||
# 刷新物料缓存
|
||||
if self.hardware_interface:
|
||||
self.hardware_interface.refresh_material_cache()
|
||||
|
||||
# 重新同步资源
|
||||
# 重新同步资源，并用同一次库存查询结果更新物料缓存
|
||||
if self.resource_synchronizer:
|
||||
self.resource_synchronizer.sync_from_external()
|
||||
|
||||
|
||||
@@ -0,0 +1,9 @@
|
||||
try:
|
||||
from . import peptide_materials # noqa: F401 ensure @resource classes are importable for PLR deserialize
|
||||
except Exception: # pragma: no cover - 允许轻量环境导入非资源辅助函数
|
||||
peptide_materials = None # type: ignore[assignment]
|
||||
|
||||
try:
|
||||
from . import sirna_materials # noqa: F401 ensure @resource classes are importable for PLR deserialize
|
||||
except Exception: # pragma: no cover - 允许轻量环境导入非资源辅助函数
|
||||
sirna_materials = None # type: ignore[assignment]
|
||||
|
||||
@@ -1,6 +1,8 @@
|
||||
from os import name
|
||||
|
||||
from pylabrobot.resources import Deck, Coordinate, Rotation
|
||||
|
||||
from unilabos.registry.decorators import resource
|
||||
from unilabos.resources.bioyond.YB_warehouses import (
|
||||
bioyond_warehouse_1x4x4,
|
||||
bioyond_warehouse_1x4x4_right, # 新增：右侧仓库 (A05～D08)
|
||||
@@ -23,6 +25,11 @@ from unilabos.resources.bioyond.YB_warehouses import (
|
||||
from unilabos.resources.bioyond.warehouses import (
|
||||
bioyond_warehouse_tipbox_storage_left, # 新增：Tip盒堆栈(左)
|
||||
bioyond_warehouse_tipbox_storage_right, # 新增：Tip盒堆栈(右)
|
||||
bioyond_warehouse_sirna_automation_stack,
|
||||
bioyond_warehouse_sirna_centrifuge_balance_plate_stack,
|
||||
bioyond_warehouse_sirna_g3_liquid_handler,
|
||||
bioyond_warehouse_numeric_stack, # 新增：数字编码堆栈 (用于多肽站)
|
||||
bioyond_warehouse_live_grid,
|
||||
)
|
||||
|
||||
|
||||
@@ -101,6 +108,83 @@ class BIOYOND_PolymerPreparationStation_Deck(Deck):
|
||||
for warehouse_name, warehouse in self.warehouses.items():
|
||||
self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
|
||||
|
||||
@resource(
|
||||
id="BIOYOND_SirnaStation_Deck",
|
||||
category=["deck"],
|
||||
description="BIOYOND 小核酸工作站 Deck",
|
||||
icon="配液站.webp",
|
||||
)
|
||||
class BIOYOND_SirnaStation_Deck(Deck):
|
||||
WAREHOUSE_BIOYOND_AXIS = {
|
||||
"G3移液站": "xy_col_row",
|
||||
"自动化堆栈": "xy_col_row",
|
||||
"离心机配平板堆栈": "xy_col_row",
|
||||
}
|
||||
WAREHOUSE_BIOYOND_KEY_AXIS = {
|
||||
"G3移液站": "col_row",
|
||||
"自动化堆栈": "col_row",
|
||||
"离心机配平板堆栈": "col_row",
|
||||
}
|
||||
# Bioyond warehouse UUID -> 本地仓库名称 映射。
|
||||
# 留空时由配置（station config 的 ``warehouse_bioyond_ids``）注入。
|
||||
# graph 节点也可在 deck.config.warehouse_bioyond_ids 覆盖。
|
||||
WAREHOUSE_BIOYOND_IDS: dict = {}
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
name: str = "SirnaStation_Deck",
|
||||
size_x: float = 2700.0,
|
||||
size_y: float = 1080.0,
|
||||
size_z: float = 1500.0,
|
||||
category: str = "deck",
|
||||
setup: bool = False,
|
||||
warehouse_bioyond_ids: dict | None = None,
|
||||
**kwargs,
|
||||
) -> None:
|
||||
super().__init__(name=name, size_x=size_x, size_y=size_y, size_z=size_z)
|
||||
# 按需写入实例级覆盖；保留默认空 mapping，避免改动模型常量。
|
||||
self.warehouse_bioyond_ids: dict = dict(self.WAREHOUSE_BIOYOND_IDS)
|
||||
if warehouse_bioyond_ids:
|
||||
self.warehouse_bioyond_ids.update(warehouse_bioyond_ids)
|
||||
if setup:
|
||||
self.setup()
|
||||
|
||||
@classmethod
|
||||
def deserialize(cls, data: dict, allow_marshal: bool = False):
|
||||
if data.get("children") and data.get("setup") is True:
|
||||
data = data.copy()
|
||||
data["setup"] = False
|
||||
result = super().deserialize(data, allow_marshal=allow_marshal)
|
||||
result._ensure_sirna_warehouse_metadata()
|
||||
return result
|
||||
|
||||
def _ensure_sirna_warehouse_metadata(self) -> None:
|
||||
for child in getattr(self, "children", []):
|
||||
name = getattr(child, "name", "")
|
||||
axis = self.WAREHOUSE_BIOYOND_AXIS.get(name)
|
||||
if axis and not hasattr(child, "bioyond_axis"):
|
||||
child.bioyond_axis = axis
|
||||
key_axis = self.WAREHOUSE_BIOYOND_KEY_AXIS.get(name)
|
||||
if key_axis and not hasattr(child, "bioyond_key_axis"):
|
||||
child.bioyond_key_axis = key_axis
|
||||
|
||||
def setup(self) -> None:
|
||||
# Sirna 读接口 /api/storage/location/locations-by-type 返回完整固定堆栈清单。
|
||||
# LIMS 在库物料接口仍使用相同的 自动化堆栈 名称和数字库位编码。
|
||||
self.warehouses = {
|
||||
"G3移液站": bioyond_warehouse_sirna_g3_liquid_handler(),
|
||||
"自动化堆栈": bioyond_warehouse_sirna_automation_stack(),
|
||||
"离心机配平板堆栈": bioyond_warehouse_sirna_centrifuge_balance_plate_stack(),
|
||||
}
|
||||
self.warehouse_locations = {
|
||||
"G3移液站": Coordinate(0.0, 0.0, 0.0),
|
||||
"自动化堆栈": Coordinate(220.0, 0.0, 0.0),
|
||||
"离心机配平板堆栈": Coordinate(1740.0, 0.0, 0.0),
|
||||
}
|
||||
|
||||
for warehouse_name, warehouse in self.warehouses.items():
|
||||
self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
|
||||
|
||||
class BIOYOND_YB_Deck(Deck):
|
||||
def __init__(
|
||||
self,
|
||||
@@ -150,12 +234,207 @@ class BIOYOND_YB_Deck(Deck):
|
||||
for warehouse_name, warehouse in self.warehouses.items():
|
||||
self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
|
||||
|
||||
@resource(
|
||||
id="BIOYOND_PeptideStation_Deck",
|
||||
category=["deck"],
|
||||
description="BIOYOND 多肽工作站 Deck",
|
||||
icon="preparation_station.webp",
|
||||
)
|
||||
class BIOYOND_PeptideStation_Deck(Deck):
|
||||
WAREHOUSE_BIOYOND_AXIS = dict.fromkeys(
|
||||
[
|
||||
"自动化堆栈",
|
||||
"低温冰箱仓库",
|
||||
"Tecan移液站库",
|
||||
"G3移液站库",
|
||||
"IDOT移液站库",
|
||||
"G3缓冲库",
|
||||
"盖板缓冲库",
|
||||
"配平板缓冲库",
|
||||
"IDOT缓冲库",
|
||||
"固相合成板底座缓冲位",
|
||||
"离心机库位",
|
||||
"热封膜机位",
|
||||
],
|
||||
"xy_col_row",
|
||||
)
|
||||
WAREHOUSE_BIOYOND_KEY_AXIS = dict.fromkeys(WAREHOUSE_BIOYOND_AXIS, "col_row")
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
name: str = "PeptideStation_Deck",
|
||||
size_x: float = 2700.0,
|
||||
size_y: float = 2000.0,
|
||||
size_z: float = 1500.0,
|
||||
category: str = "deck",
|
||||
setup: bool = False
|
||||
) -> None:
|
||||
super().__init__(name=name, size_x=size_x, size_y=size_y, size_z=size_z)
|
||||
if setup:
|
||||
self.setup()
|
||||
|
||||
@classmethod
|
||||
def deserialize(cls, data: dict, allow_marshal: bool = False):
|
||||
if data.get("children") and data.get("setup") is True:
|
||||
data = data.copy()
|
||||
data["setup"] = False
|
||||
# 已有序列化子资源，跳过 setup 避免重复创建
|
||||
result = super(BIOYOND_PeptideStation_Deck, cls).deserialize(data, allow_marshal=allow_marshal)
|
||||
else:
|
||||
result = super(BIOYOND_PeptideStation_Deck, cls).deserialize(data, allow_marshal=allow_marshal)
|
||||
result._ensure_peptide_warehouse_metadata()
|
||||
return result
|
||||
|
||||
def _ensure_peptide_warehouse_metadata(self) -> None:
|
||||
for child in getattr(self, "children", []):
|
||||
name = getattr(child, "name", "")
|
||||
axis = self.WAREHOUSE_BIOYOND_AXIS.get(name)
|
||||
if axis and not hasattr(child, "bioyond_axis"):
|
||||
child.bioyond_axis = axis
|
||||
key_axis = self.WAREHOUSE_BIOYOND_KEY_AXIS.get(name)
|
||||
if key_axis and not hasattr(child, "bioyond_key_axis"):
|
||||
child.bioyond_key_axis = key_axis
|
||||
|
||||
def _frontend_y_flipped_coordinate(self, display_x: float, display_y: float, child) -> Coordinate:
|
||||
"""把期望显示坐标转换为兼容前端 y 轴翻转的存储坐标。"""
|
||||
return Coordinate(display_x, self.get_size_y() - display_y - child.get_size_y(), 0.0)
|
||||
|
||||
def setup(self) -> None:
|
||||
# 多肽工作站仓库配置
|
||||
# 基于 2026-05-09 live API probe 发现的实际仓库拓扑 (12个仓库)
|
||||
# 数据来源: Bioyond 现场仓库发现结果。
|
||||
self.warehouses = {
|
||||
# 主自动化堆栈 - live API: code 10-17 -> x=17, y=10，显示为 17 行×10 列
|
||||
"自动化堆栈": bioyond_warehouse_numeric_stack(
|
||||
"自动化堆栈",
|
||||
rows=17,
|
||||
columns=10,
|
||||
bioyond_axis="xy_col_row",
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 低温存储
|
||||
"低温冰箱仓库": bioyond_warehouse_live_grid(
|
||||
"低温冰箱仓库",
|
||||
rows=3,
|
||||
columns=2,
|
||||
slot_keys=["1", "2", "3", "4", "5", "6"],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 移液站库位
|
||||
"Tecan移液站库": bioyond_warehouse_live_grid(
|
||||
"Tecan移液站库",
|
||||
rows=18,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 19)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"G3移液站库": bioyond_warehouse_live_grid(
|
||||
"G3移液站库",
|
||||
rows=18,
|
||||
columns=1,
|
||||
slot_keys=["1", "2", "3", "4", "垃圾桶", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18"],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"IDOT移液站库": bioyond_warehouse_live_grid(
|
||||
"IDOT移液站库",
|
||||
rows=12,
|
||||
columns=1,
|
||||
slot_keys=[f"0009-{index:04d}" for index in range(1, 13)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 缓冲库位
|
||||
"G3缓冲库": bioyond_warehouse_live_grid(
|
||||
"G3缓冲库",
|
||||
rows=5,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 6)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"盖板缓冲库": bioyond_warehouse_live_grid(
|
||||
"盖板缓冲库",
|
||||
rows=7,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 8)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"配平板缓冲库": bioyond_warehouse_live_grid(
|
||||
"配平板缓冲库",
|
||||
rows=3,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 4)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"IDOT缓冲库": bioyond_warehouse_live_grid(
|
||||
"IDOT缓冲库",
|
||||
rows=2,
|
||||
columns=1,
|
||||
slot_keys=["1", "1"],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"固相合成板底座缓冲位": bioyond_warehouse_live_grid(
|
||||
"固相合成板底座缓冲位",
|
||||
rows=4,
|
||||
columns=1,
|
||||
slot_keys=[f"0015-{index:04d}" for index in range(1, 5)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 设备库位
|
||||
"离心机库位": bioyond_warehouse_live_grid(
|
||||
"离心机库位",
|
||||
rows=4,
|
||||
columns=1,
|
||||
slot_keys=[f"0017-{index:04d}" for index in range(1, 5)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"热封膜机位": bioyond_warehouse_live_grid(
|
||||
"热封膜机位",
|
||||
rows=2,
|
||||
columns=1,
|
||||
slot_keys=[f"0016-{index:04d}" for index in range(1, 3)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
}
|
||||
|
||||
# 仓库显示布局：紧凑排列；存储 y 坐标按前端兼容翻转预先反向。
|
||||
display_layout = {
|
||||
"自动化堆栈": (0.0, 0.0),
|
||||
"Tecan移液站库": (1520.0, 0.0),
|
||||
"G3移液站库": (1710.0, 0.0),
|
||||
"IDOT移液站库": (1900.0, 0.0),
|
||||
"G3缓冲库": (2090.0, 0.0),
|
||||
"盖板缓冲库": (2090.0, 580.0),
|
||||
"低温冰箱仓库": (2280.0, 0.0),
|
||||
"配平板缓冲库": (2280.0, 370.0),
|
||||
"IDOT缓冲库": (2470.0, 370.0),
|
||||
"固相合成板底座缓冲位": (2280.0, 740.0),
|
||||
"离心机库位": (2470.0, 740.0),
|
||||
"热封膜机位": (2280.0, 1210.0),
|
||||
}
|
||||
self.warehouse_locations = {
|
||||
name: self._frontend_y_flipped_coordinate(x, y, self.warehouses[name])
|
||||
for name, (x, y) in display_layout.items()
|
||||
}
|
||||
|
||||
for warehouse_name, warehouse in self.warehouses.items():
|
||||
self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
|
||||
|
||||
def YB_Deck(name: str) -> Deck:
|
||||
by=BIOYOND_YB_Deck(name=name)
|
||||
by.setup()
|
||||
return by
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
247
unilabos/resources/bioyond/peptide_materials.py
Normal file
247
unilabos/resources/bioyond/peptide_materials.py
Normal file
@@ -0,0 +1,247 @@
|
||||
"""Peptide Station Material Resource Definitions."""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
from collections import OrderedDict
|
||||
|
||||
try:
|
||||
from pylabrobot.resources import Container, Plate, TipRack
|
||||
except Exception: # pragma: no cover - 允许无 pylabrobot 的轻量动作测试导入
|
||||
class _FallbackResource:
|
||||
def __init__(self, *args, **kwargs):
|
||||
self.args = args
|
||||
self.kwargs = kwargs
|
||||
|
||||
class Container(_FallbackResource): # type: ignore[no-redef]
|
||||
pass
|
||||
|
||||
class Plate(_FallbackResource): # type: ignore[no-redef]
|
||||
pass
|
||||
|
||||
class TipRack(_FallbackResource): # type: ignore[no-redef]
|
||||
pass
|
||||
|
||||
try:
|
||||
from unilabos.registry.decorators import resource
|
||||
except Exception: # pragma: no cover - 允许无完整 registry 依赖时导入常量
|
||||
def resource(*args, **kwargs):
|
||||
def decorator(cls):
|
||||
return cls
|
||||
|
||||
return decorator
|
||||
|
||||
|
||||
def _ensure_itemized_ordering(kwargs: dict) -> None:
|
||||
if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
|
||||
kwargs["ordering"] = OrderedDict()
|
||||
|
||||
|
||||
class _PeptideTipRack(TipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 64.0)
|
||||
kwargs.setdefault("with_tips", True)
|
||||
_ensure_itemized_ordering(kwargs)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
class _PeptidePlate(Plate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 14.35)
|
||||
kwargs.setdefault("plate_type", "skirted")
|
||||
_ensure_itemized_ordering(kwargs)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_1000ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="1000uL tip rack for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_1000ul_TipRack(_PeptideTipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_1000ul_tip_rack")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_200ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="200uL tip rack for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_200ul_TipRack(_PeptideTipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_200ul_tip_rack")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_50ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="50uL tip rack for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_50ul_TipRack(_PeptideTipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_50ul_tip_rack")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_deep_well_plate",
|
||||
category=["labware", "plate"],
|
||||
description="96 well deep well plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellDeepWellPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_deep_well_plate")
|
||||
kwargs.setdefault("size_z", 44.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_synthesis_plate",
|
||||
category=["labware", "plate"],
|
||||
description="96 well solid-phase synthesis plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellSynthesisPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_synthesis_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_synthesis_plate_base",
|
||||
category=["labware", "adapter"],
|
||||
description="96 well solid-phase synthesis plate base for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellSynthesisPlateBase(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_synthesis_plate_base")
|
||||
kwargs.setdefault("size_z", 20.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_balance_plate",
|
||||
category=["labware", "plate"],
|
||||
description="96 well balance plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellBalancePlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_balance_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_384_well_plate",
|
||||
category=["labware", "plate"],
|
||||
description="384 well plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_384WellPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_384_well_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_384_lcms_plate",
|
||||
category=["labware", "plate"],
|
||||
description="384 well LCMS plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_384LCMSPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_384_lcms_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_384_balance_plate",
|
||||
category=["labware", "plate"],
|
||||
description="384 well balance plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_384BalancePlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_384_balance_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_cover_plate",
|
||||
category=["labware", "cover"],
|
||||
description="Cover plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_CoverPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_cover_plate")
|
||||
kwargs.setdefault("size_z", 8.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_sealing_base",
|
||||
category=["labware", "adapter"],
|
||||
description="Sealing base for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_SealingBase(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_sealing_base")
|
||||
kwargs.setdefault("size_z", 20.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_reagent_trough",
|
||||
category=["labware", "trough"],
|
||||
description="Reagent trough for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_ReagentTrough(Container):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 44.0)
|
||||
kwargs.setdefault("max_volume", 300000.0)
|
||||
kwargs.setdefault("model", "bioyond_peptide_reagent_trough")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
DEFAULT_PEPTIDE_MATERIAL_TYPE_MAPPINGS = {
|
||||
"bioyond_peptide_1000ul_tip_rack": ["1000μL枪头盒", "3a1890bb-736e-cfdd-3213-eb314e8a60f9"],
|
||||
"bioyond_peptide_200ul_tip_rack": ["200μL枪头盒", "3a1890bb-36d1-964a-18bd-0bf0f2877a7b"],
|
||||
"bioyond_peptide_50ul_tip_rack": ["50μL枪头盒", "3a1890bc-5fae-361c-cc09-e6f2f6dcd71d"],
|
||||
"bioyond_peptide_96_well_deep_well_plate": ["96孔深孔板", "3a1890bc-1fa8-fe39-9faa-12279ed4569b"],
|
||||
"bioyond_peptide_96_well_synthesis_plate": ["96孔固相合成板", "3a1871cb-99f3-f01d-23e2-08dbbd0045b5"],
|
||||
"bioyond_peptide_96_well_synthesis_plate_base": ["96孔固相合成板底座", "3a1b997e-241b-64f0-80d1-47bca08799d1"],
|
||||
"bioyond_peptide_96_well_balance_plate": ["96孔配平板", "3a187661-2378-1e20-fa5c-a27d49fdc15d"],
|
||||
"bioyond_peptide_384_well_plate": ["384孔酶标板", "3a1890bf-2148-ed20-92bd-d85869947d9a"],
|
||||
"bioyond_peptide_384_lcms_plate": ["384孔LCMS板", "3a1e6a8b-cb61-74da-a089-8e6f197f80f0"],
|
||||
"bioyond_peptide_384_balance_plate": ["384孔配平板", "3a18be7e-47cc-888c-fc68-055753286826"],
|
||||
"bioyond_peptide_cover_plate": ["防挥发盖板", "3a19d5a6-b0e2-b486-e5eb-bcabc632f4de"],
|
||||
"bioyond_peptide_sealing_base": ["封膜底座", "3a1d1d7b-e33b-6975-165d-c56cba5ed345"],
|
||||
"bioyond_peptide_reagent_trough": ["12道试剂槽", "3a18b431-ac58-ca2e-9680-2a4f5880ea45"],
|
||||
}
|
||||
|
||||
|
||||
MATERIAL_TYPE_CODE_TO_CLASS = {
|
||||
"0001": BioyondPeptide_96WellSynthesisPlate,
|
||||
"0002": BioyondPeptide_96WellBalancePlate,
|
||||
"0008": BioyondPeptide_200ul_TipRack,
|
||||
"0009": BioyondPeptide_1000ul_TipRack,
|
||||
"0011": BioyondPeptide_96WellDeepWellPlate,
|
||||
"0012": BioyondPeptide_50ul_TipRack,
|
||||
"0016": BioyondPeptide_384WellPlate,
|
||||
"0018": BioyondPeptide_384WellPlate,
|
||||
"0024": BioyondPeptide_ReagentTrough,
|
||||
"0026": BioyondPeptide_384BalancePlate,
|
||||
"0035": BioyondPeptide_CoverPlate,
|
||||
"0039": BioyondPeptide_96WellSynthesisPlateBase,
|
||||
"0041": BioyondPeptide_SealingBase,
|
||||
"0049": BioyondPeptide_384LCMSPlate,
|
||||
}
|
||||
|
||||
|
||||
def get_material_class_by_type_code(type_code: str):
|
||||
"""Return a peptide material class by Bioyond material type code."""
|
||||
return MATERIAL_TYPE_CODE_TO_CLASS.get(type_code)
|
||||
@@ -1,5 +1,192 @@
|
||||
from pylabrobot.resources import Coordinate
|
||||
from pylabrobot.resources.carrier import ResourceHolder, create_homogeneous_resources
|
||||
|
||||
from unilabos.resources.warehouse import WareHouse, warehouse_factory
|
||||
|
||||
|
||||
class BioyondWareHouse(WareHouse):
|
||||
"""Bioyond 仓库，额外保存服务端 x/y 坐标和库位标签语义。"""
|
||||
|
||||
def __init__(self, *args, bioyond_axis: str = "xy_row_col", bioyond_key_axis: str = "row_col", **kwargs):
|
||||
super().__init__(*args, **kwargs)
|
||||
self.bioyond_axis = bioyond_axis
|
||||
self.bioyond_key_axis = bioyond_key_axis
|
||||
|
||||
def serialize(self) -> dict:
|
||||
data = super().serialize()
|
||||
data["bioyond_axis"] = self.bioyond_axis
|
||||
data["bioyond_key_axis"] = self.bioyond_key_axis
|
||||
return data
|
||||
|
||||
|
||||
def bioyond_warehouse_numeric_stack(
|
||||
name: str,
|
||||
rows: int = 10,
|
||||
columns: int = 17,
|
||||
bioyond_axis: str = "xy_row_col",
|
||||
bioyond_key_axis: str = "row_col",
|
||||
frontend_y_flip: bool = False,
|
||||
) -> WareHouse:
|
||||
"""创建 Bioyond 数字库位堆栈，库位名使用服务端返回的 行-列 格式。
|
||||
|
||||
bioyond_axis: 仓库级别的 Bioyond 坐标轴约定，供 graphio 的坐标映射使用。
|
||||
- "xy_row_col" (default): Bioyond x→row, y→col (reaction/peptide 历史约定).
|
||||
- "xy_col_row": Bioyond x→col, y→row (Sirna live API 实测约定).
|
||||
bioyond_key_axis: 库位标签生成约定。
|
||||
- "row_col" (default): 视觉行列和标签行列一致，例如 10 行 x 17 列 → 1-1..10-17。
|
||||
- "col_row": 视觉行列转置，但标签仍保持 Bioyond row-col，例如
|
||||
17 行 x 10 列 → 1-1..10-17。
|
||||
未设置时 graphio 回退到默认 "xy_row_col"，其他调用方保持原行为。
|
||||
"""
|
||||
num_items_x = columns
|
||||
num_items_y = rows
|
||||
num_items_z = 1
|
||||
dx = 10.0
|
||||
dy = 10.0
|
||||
dz = 10.0
|
||||
item_dx = 147.0
|
||||
item_dy = 106.0
|
||||
item_dz = 130.0
|
||||
resource_size_x = 127.0
|
||||
resource_size_y = 86.0
|
||||
resource_size_z = 25.0
|
||||
size_y = dy + item_dy * num_items_y
|
||||
locations = []
|
||||
for row in range(num_items_y):
|
||||
display_y = dy + row * item_dy
|
||||
y = size_y - display_y - resource_size_y if frontend_y_flip else display_y
|
||||
for col in range(num_items_x):
|
||||
locations.append(Coordinate(dx + col * item_dx, y, dz))
|
||||
holders = create_homogeneous_resources(
|
||||
klass=ResourceHolder,
|
||||
locations=locations,
|
||||
resource_size_x=resource_size_x,
|
||||
resource_size_y=resource_size_y,
|
||||
resource_size_z=resource_size_z,
|
||||
name_prefix=name,
|
||||
)
|
||||
if bioyond_key_axis == "row_col":
|
||||
keys = [
|
||||
f"{row + 1}-{col + 1}"
|
||||
for row in range(num_items_y)
|
||||
for col in range(num_items_x)
|
||||
]
|
||||
elif bioyond_key_axis == "col_row":
|
||||
keys = [
|
||||
f"{col + 1}-{row + 1}"
|
||||
for row in range(num_items_y)
|
||||
for col in range(num_items_x)
|
||||
]
|
||||
else:
|
||||
raise ValueError(f"未知 Bioyond 库位标签约定: {bioyond_key_axis!r}")
|
||||
warehouse = BioyondWareHouse(
|
||||
name=name,
|
||||
size_x=dx + item_dx * num_items_x,
|
||||
size_y=size_y,
|
||||
size_z=dz + item_dz * num_items_z,
|
||||
num_items_x=num_items_x,
|
||||
num_items_y=num_items_y,
|
||||
num_items_z=num_items_z,
|
||||
ordering_layout="row-major",
|
||||
sites={key: holder for key, holder in zip(keys, holders.values())},
|
||||
category="warehouse",
|
||||
bioyond_axis=bioyond_axis,
|
||||
bioyond_key_axis=bioyond_key_axis,
|
||||
)
|
||||
return warehouse
|
||||
|
||||
|
||||
def bioyond_warehouse_live_grid(
|
||||
name: str,
|
||||
rows: int,
|
||||
columns: int,
|
||||
slot_keys: list[str] | None = None,
|
||||
bioyond_axis: str = "xy_col_row",
|
||||
bioyond_key_axis: str = "row_col",
|
||||
frontend_y_flip: bool = False,
|
||||
) -> WareHouse:
|
||||
"""创建 Bioyond 实测库位网格，按服务端 code 保存位点标签。
|
||||
|
||||
默认用于 Peptide live API 返回的坐标：x 是视觉列，y 是视觉行。
|
||||
当服务端 code 重复时，为保持 PLR ordering 唯一性，会给后续重复项追加 ``#N``。
|
||||
"""
|
||||
num_items_x = columns
|
||||
num_items_y = rows
|
||||
num_items_z = 1
|
||||
dx = 10.0
|
||||
dy = 10.0
|
||||
dz = 10.0
|
||||
item_dx = 147.0
|
||||
item_dy = 106.0
|
||||
item_dz = 130.0
|
||||
resource_size_x = 127.0
|
||||
resource_size_y = 86.0
|
||||
resource_size_z = 25.0
|
||||
size_y = dy + item_dy * num_items_y
|
||||
locations = []
|
||||
for row in range(num_items_y):
|
||||
display_y = dy + row * item_dy
|
||||
y = size_y - display_y - resource_size_y if frontend_y_flip else display_y
|
||||
for col in range(num_items_x):
|
||||
locations.append(Coordinate(dx + col * item_dx, y, dz))
|
||||
holders = create_homogeneous_resources(
|
||||
klass=ResourceHolder,
|
||||
locations=locations,
|
||||
resource_size_x=resource_size_x,
|
||||
resource_size_y=resource_size_y,
|
||||
resource_size_z=resource_size_z,
|
||||
name_prefix=name,
|
||||
)
|
||||
keys = slot_keys or [str(index + 1) for index in range(num_items_x * num_items_y)]
|
||||
if len(keys) != len(holders):
|
||||
raise ValueError(f"{name} 库位数量不匹配: keys={len(keys)}, holders={len(holders)}")
|
||||
|
||||
seen: dict[str, int] = {}
|
||||
unique_keys: list[str] = []
|
||||
for key in keys:
|
||||
count = seen.get(key, 0) + 1
|
||||
seen[key] = count
|
||||
unique_keys.append(key if count == 1 else f"{key}#{count}")
|
||||
|
||||
return BioyondWareHouse(
|
||||
name=name,
|
||||
size_x=dx + item_dx * num_items_x,
|
||||
size_y=size_y,
|
||||
size_z=dz + item_dz * num_items_z,
|
||||
num_items_x=num_items_x,
|
||||
num_items_y=num_items_y,
|
||||
num_items_z=num_items_z,
|
||||
ordering_layout="row-major",
|
||||
sites={key: holder for key, holder in zip(unique_keys, holders.values())},
|
||||
category="warehouse",
|
||||
bioyond_axis=bioyond_axis,
|
||||
bioyond_key_axis=bioyond_key_axis,
|
||||
)
|
||||
|
||||
|
||||
# ================ 小核酸工作站相关堆栈 ================
|
||||
|
||||
def bioyond_warehouse_sirna_g3_liquid_handler(name: str = "G3移液站") -> WareHouse:
|
||||
"""创建小核酸 G3 移液站库位堆栈：显示为 14 行 x 1 列，标签保持 1-1..1-14。"""
|
||||
return bioyond_warehouse_numeric_stack(
|
||||
name, rows=14, columns=1, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
|
||||
)
|
||||
|
||||
|
||||
def bioyond_warehouse_sirna_automation_stack(name: str = "自动化堆栈") -> WareHouse:
|
||||
"""创建小核酸自动化堆栈：显示为 17 行 x 10 列，标签保持 1-1..10-17。"""
|
||||
return bioyond_warehouse_numeric_stack(
|
||||
name, rows=17, columns=10, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
|
||||
)
|
||||
|
||||
|
||||
def bioyond_warehouse_sirna_centrifuge_balance_plate_stack(name: str = "离心机配平板堆栈") -> WareHouse:
|
||||
"""创建小核酸离心机配平板堆栈：显示为 1 行 x 2 列，标签保持 1-1、2-1。"""
|
||||
return bioyond_warehouse_numeric_stack(
|
||||
name, rows=1, columns=2, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
|
||||
)
|
||||
|
||||
|
||||
# ================ 反应站相关堆栈 ================
|
||||
|
||||
def bioyond_warehouse_1x4x4(name: str) -> WareHouse:
|
||||
|
||||
@@ -736,7 +736,7 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
|
||||
logger.warning(f"物料 {unique_name} 不是有效的 ResourcePLR 实例，类型: {type(plr_material)}")
|
||||
continue
|
||||
|
||||
plr_material.code = material.get("code", "") and material.get("barCode", "") or ""
|
||||
plr_material.code = material.get("barCode") or material.get("code") or ""
|
||||
plr_material.unilabos_uuid = str(uuid.uuid4())
|
||||
|
||||
# ⭐ 保存 Bioyond 原始信息到 unilabos_extra（用于出库时查询）
|
||||
@@ -864,11 +864,22 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
|
||||
warehouse = deck.warehouses[wh_name]
|
||||
logger.debug(f"[Warehouse匹配] 找到warehouse: {wh_name} (容量: {warehouse.capacity}, 行×列: {warehouse.num_items_x}×{warehouse.num_items_y})")
|
||||
|
||||
# Bioyond坐标映射 (重要！): x→行(1=A,2=B...), y→列(1=01,2=02...), z→层(通常=1)
|
||||
x = loc.get("x", 1) # 行号 (1-based: 1=A, 2=B, 3=C, 4=D)
|
||||
y = loc.get("y", 1) # 列号 (1-based: 1=01, 2=02, 3=03...)
|
||||
# Bioyond坐标映射:
|
||||
# - 历史 row_col 仓库中 x/y 直接按行/列参与索引。
|
||||
# - Sirna 的库位标签为 col-row，stock-material 返回 x=标签第二段、y=标签第一段。
|
||||
# 因此 x=13,y=4 应落到 key=4-13，而不是交换后落到 3-5。
|
||||
x = loc.get("x", 1)
|
||||
y = loc.get("y", 1)
|
||||
z = loc.get("z", 1) # 层号 (1-based, 通常为1)
|
||||
|
||||
# 仓库级别的轴约定覆盖。
|
||||
# 对旧的 row-col 视觉标签，bioyond_axis="xy_col_row" 需要交换 x/y。
|
||||
# 对 Sirna 的 col-row 库位标签，原始 x/y 已能直接索引到 code 对应位置，不再交换。
|
||||
bioyond_axis = getattr(warehouse, "bioyond_axis", "xy_row_col")
|
||||
bioyond_key_axis = getattr(warehouse, "bioyond_key_axis", "row_col")
|
||||
if bioyond_axis == "xy_col_row" and bioyond_key_axis != "col_row":
|
||||
x, y = y, x
|
||||
|
||||
# 如果是右侧堆栈，需要调整列号 (5→1, 6→2, 7→3, 8→4)
|
||||
if wh_name == "堆栈1右":
|
||||
y = y - 4 # 将5-8映射到1-4
|
||||
@@ -912,10 +923,43 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
|
||||
logger.debug(f"列优先warehouse {wh_name}: x={x}(行),y={y}(列) → row={row_idx},col={col_idx} → idx={idx}")
|
||||
|
||||
if 0 <= idx < warehouse.capacity:
|
||||
if warehouse[idx] is None or isinstance(warehouse[idx], ResourceHolder):
|
||||
slot_key = None
|
||||
ordering = getattr(warehouse, "_ordering", {})
|
||||
sites = getattr(warehouse, "sites", [])
|
||||
if isinstance(ordering, dict) and idx < len(sites):
|
||||
site_at_idx = sites[idx]
|
||||
slot_key = next(
|
||||
(key for key, site in ordering.items() if site is site_at_idx),
|
||||
None,
|
||||
)
|
||||
|
||||
current_resource = warehouse[idx]
|
||||
if current_resource is None or isinstance(current_resource, (ResourceHolder, str)):
|
||||
if isinstance(current_resource, str):
|
||||
logger.warning(
|
||||
f"⚠️ 物料 {unique_name} 覆盖 {wh_name}[{idx}]"
|
||||
f"{f'({slot_key})' if slot_key else ''} 的旧占位 occupied_by={current_resource!r}"
|
||||
)
|
||||
# 物料尺寸已在放入warehouse前根据需要进行了交换
|
||||
warehouse[idx] = plr_material
|
||||
logger.debug(f"✅ 物料 {unique_name} 放置到 {wh_name}[{idx}] (Bioyond坐标: x={loc.get('x')}, y={loc.get('y')})")
|
||||
logger.debug(
|
||||
f"✅ 物料 {unique_name} 放置到 {wh_name}[{idx}]"
|
||||
f"{f'({slot_key})' if slot_key else ''} "
|
||||
f"(Bioyond坐标: x={loc.get('x')}, y={loc.get('y')})"
|
||||
)
|
||||
else:
|
||||
parent = getattr(current_resource, "parent", None)
|
||||
current_repr = repr(current_resource)
|
||||
current_len = len(current_resource) if isinstance(current_resource, str) else None
|
||||
logger.warning(
|
||||
f"⚠️ 物料 {unique_name} 跳过放置到 {wh_name}[{idx}]"
|
||||
f"{f'({slot_key})' if slot_key else ''}：目标库位已有 "
|
||||
f"{type(current_resource).__name__}"
|
||||
f"(value={current_repr}, len={current_len})"
|
||||
f"(name={getattr(current_resource, 'name', None)}, "
|
||||
f"parent={getattr(parent, 'name', None)}, "
|
||||
f"uuid={getattr(current_resource, 'unilabos_uuid', None)})"
|
||||
)
|
||||
else:
|
||||
logger.warning(f"❌ 物料 {unique_name} 的索引 {idx} 超出仓库 {wh_name} 容量 {warehouse.capacity}")
|
||||
else:
|
||||
|
||||
@@ -18,3 +18,7 @@ def register():
|
||||
from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
|
||||
from unilabos.devices.liquid_handling.laiyu.backend.laiyu_v_backend import UniLiquidHandlerLaiyuBackend
|
||||
|
||||
# noinspection PyUnresolvedReferences
|
||||
from unilabos.resources.bioyond.decks import BIOYOND_SirnaStation_Deck
|
||||
# noinspection PyUnresolvedReferences
|
||||
from unilabos.resources.bioyond.decks import BIOYOND_PeptideStation_Deck
|
||||
|
||||
Reference in New Issue
Block a user