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31 Commits

Author SHA1 Message Date
Xuwznln
dd5a7cab75 支持Biomek创建 2025-06-05 16:04:44 +08:00
Xuwznln
39de3ac58e 更新transfer_biomek的msg 2025-06-05 15:41:16 +08:00
Xuwznln
b99969278c 更新transfer_biomek的msg 2025-06-05 15:30:51 +08:00
Guangxin Zhang
b957ad2f71 Merge branch '37-biomek-i5i7' of https://github.com/dptech-corp/Uni-Lab-OS into 37-biomek-i5i7 2025-06-04 21:49:27 +08:00
Guangxin Zhang
e1a7c3a103 Updated transfer_biomek 2025-06-04 21:49:22 +08:00
Guangxin Zhang
e63c15997c New transfer_biomek 2025-06-04 21:29:54 +08:00
Xuwznln
c5a495f409 新增transfer_biomek的msg 2025-06-04 19:03:00 +08:00
Guangxin Zhang
5b240cb0ea Update biomek.py 2025-06-04 17:30:53 +08:00
Guangxin Zhang
147b8f47c0 Biomek test 2025-06-04 16:38:18 +08:00
Guangxin Zhang
6d2489af5f Merge branch '37-biomek-i5i7' of https://github.com/dptech-corp/Uni-Lab-OS into 37-biomek-i5i7 2025-06-04 13:27:11 +08:00
Guangxin Zhang
807dcdd226 Update biomek.py 2025-06-04 13:27:05 +08:00
Guangxin Zhang
8a29bc5597 Remove warnings 2025-06-04 13:20:12 +08:00
Guangxin Zhang
6f6c70ee57 delete 's' 2025-06-04 13:11:45 +08:00
Xuwznln
478a85951c 修复biomek缺少的字段 2025-05-31 00:00:55 +08:00
Xuwznln
0f2555c90c 注册表上报handle和schema (param input) 2025-05-31 00:00:39 +08:00
Guangxin Zhang
d2dda6ee03 Merge branch '37-biomek-i5i7' of https://github.com/dptech-corp/Uni-Lab-OS into 37-biomek-i5i7 2025-05-30 17:11:23 +08:00
Guangxin Zhang
208540b307 Update biomek.py 2025-05-30 17:08:19 +08:00
Guangxin Zhang
cb7c56a1d9 Convert LH action to biomek. 2025-05-30 17:00:06 +08:00
Xuwznln
ea2e9c3e3a fix biomek success type 2025-05-30 16:50:13 +08:00
Guangxin Zhang
0452a68180 Test 2025-05-30 16:03:49 +08:00
Xuwznln
90a0f3db9b merge 2025-05-30 15:40:14 +08:00
Junhan Chang
055d120ba8 更新LiquidHandlerBiomek类,添加资源创建功能,优化协议创建方法,修复部分代码格式问题,更新YAML配置以支持新功能。 2025-05-30 15:38:23 +08:00
Junhan Chang
a948f09f60 add biomek.py demo implementation 2025-05-30 13:33:10 +08:00
Xuwznln
6f69df440c 修复linux 64构建问题 2025-05-30 01:27:34 +08:00
Xuwznln
b420d1fa8e bump version to 0.9.1 2025-05-29 22:17:50 +08:00
Xuwznln
767e0fcdee bump version to 0.9.1 2025-05-29 20:44:30 +08:00
Xuwznln
84944396e9 34 icon support online (#35)
* unify liquid_handler definition

* remove default values

* Dev Sync (#25)

* Update README and MQTTClient for installation instructions and code improvements

* feat: 支持local_config启动
add: 增加对crt path的说明,为传入config.py的相对路径
move: web component

* add: registry description

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* feat: node_info_update srv
fix: OTDeck cant create

* close #12
feat: slave node registry

* feat: show machine name
fix: host node registry not uploaded

* feat: add hplc registry

* feat: add hplc registry

* fix: hplc status typo

* fix: devices/

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* fix: device.class possible null

* fix: HPLC additions with online service

* fix: slave mode spin not working

* fix: slave mode spin not working

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* feat: 多ProtocolNode 允许子设备ID相同
feat: 上报发现的ActionClient
feat: Host重启动,通过discover机制要求slaveNode重新注册,实现信息及时上报

* feat: 支持env设置config

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* Device visualization (#14)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: missing hostname in devices_names
fix: upload_file for model file

* fix: missing paho-mqtt package
bump version to 0.9.0

* fix startup
add ResourceCreateFromOuter.action

* fix type hint

* update actions

* update actions

* host node add_resource_from_outer
fix cmake list

* pass device config to device class

* add: bind_parent_ids to resource create action
fix: message convert string

* fix: host node should not be re_discovered

* feat: resource tracker support dict

* feat: add more necessary params

* feat: fix boolean null in registry action data

* feat: add outer resource

* 编写mesh添加action

* feat: append resource

* add action

* feat: vis 2d for plr

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

* Device visualization (#22)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* 编写mesh添加action

* add action

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: multi channel

* fix: aspirate

* fix: aspirate

* fix: aspirate

* fix: aspirate

* 提交

* fix: jobadd

* fix: jobadd

* fix: msg converter

* tijiao

* add resource creat easy action

* identify debug msg

* mq client id

---------

Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>

* remove default behavior for visualization

* change liquidhandler name

* resource create from outer easy

* add easy resource creation

* easy resource creation logic

* remove wrongly debug msg from others

* remove wrongly debug msg from others

* add missing action clients

* fix device_id

* fix slot_on_deck

* fix registry typo

* complete require packages
msg converter support array string
implements create resource logic

* 修复port输入

* 修复必须两次启动edge后端才有节点生成的bug
新增resources报送

* 新增延迟统计

---------

Co-authored-by: Junhan Chang <changjh@pku.edu.cn>
Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>
2025-05-29 20:43:01 +08:00
Xuwznln
bfcb214b53 24 high level liquidhandler (#28)
* unify liquid_handler definition

* remove default values

* Dev Sync (#25)

* Update README and MQTTClient for installation instructions and code improvements

* feat: 支持local_config启动
add: 增加对crt path的说明,为传入config.py的相对路径
move: web component

* add: registry description

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* feat: node_info_update srv
fix: OTDeck cant create

* close #12
feat: slave node registry

* feat: show machine name
fix: host node registry not uploaded

* feat: add hplc registry

* feat: add hplc registry

* fix: hplc status typo

* fix: devices/

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* fix: device.class possible null

* fix: HPLC additions with online service

* fix: slave mode spin not working

* fix: slave mode spin not working

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* feat: 多ProtocolNode 允许子设备ID相同
feat: 上报发现的ActionClient
feat: Host重启动,通过discover机制要求slaveNode重新注册,实现信息及时上报

* feat: 支持env设置config

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* Device visualization (#14)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: missing hostname in devices_names
fix: upload_file for model file

* fix: missing paho-mqtt package
bump version to 0.9.0

* fix startup
add ResourceCreateFromOuter.action

* fix type hint

* update actions

* update actions

* host node add_resource_from_outer
fix cmake list

* pass device config to device class

* add: bind_parent_ids to resource create action
fix: message convert string

* fix: host node should not be re_discovered

* feat: resource tracker support dict

* feat: add more necessary params

* feat: fix boolean null in registry action data

* feat: add outer resource

* 编写mesh添加action

* feat: append resource

* add action

* feat: vis 2d for plr

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

* Device visualization (#22)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化,并输出物料ID:mesh的对应关系resource_model

添加物料模型管理类,遍历物料与resource_model,完成TF数据收集

* 完成TF发布

* 修改模型方向,在yaml中添加变换属性

* 添加物料tf变化时,发送topic到前端

另外修改了物料初始化的方法,防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* 编写mesh添加action

* add action

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: multi channel

* fix: aspirate

* fix: aspirate

* fix: aspirate

* fix: aspirate

* 提交

* fix: jobadd

* fix: jobadd

* fix: msg converter

* tijiao

* add resource creat easy action

* identify debug msg

* mq client id

---------

Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>

* remove default behavior for visualization

* change liquidhandler name

* resource create from outer easy

* add easy resource creation

* easy resource creation logic

* remove wrongly debug msg from others

* remove wrongly debug msg from others

* add missing action clients

* fix device_id

* fix slot_on_deck

* fix registry typo

* complete require packages
msg converter support array string
implements create resource logic

* 修复port输入

* fix: remove dirty actions

---------

Co-authored-by: Junhan Chang <changjh@pku.edu.cn>
Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>
2025-05-29 20:40:16 +08:00
Xuwznln
ec4e6c6cfd 增加英文readme描述 (#33) 2025-05-23 10:06:30 +08:00
Xuwznln
53b6457a88 修复property类型的Action执行失败 (#30) 2025-05-17 17:57:49 +08:00
Xuwznln
133dbf77bb 嵌套节点上报云端出现ID错误 (#27)
* 修复嵌套节点,mq发送任务id出错的问题
修正一处注册表命名错误

* 修复本地看板Action显示不全
修复本地子设备没有机器名称的bug

* 补全vacuum_pump.mock注册信息
2025-05-16 19:12:59 +08:00
50 changed files with 6853 additions and 378 deletions

1
.gitignore vendored
View File

@@ -6,6 +6,7 @@ __pycache__/
.vscode
*.py[cod]
*$py.class
service
# C extensions
*.so

View File

@@ -4,83 +4,86 @@
# Uni-Lab-OS
<!-- Language switcher -->
**English** | [中文](README_zh.md)
[![GitHub Stars](https://img.shields.io/github/stars/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/stargazers)
[![GitHub Forks](https://img.shields.io/github/forks/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/network/members)
[![GitHub Issues](https://img.shields.io/github/issues/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/issues)
[![GitHub License](https://img.shields.io/github/license/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/blob/main/LICENSE)
Uni-Lab 操作系统是一个用于实验室自动化的综合平台,旨在连接和控制各种实验设备,实现实验流程的自动化和标准化。
Uni-Lab Operating System is a platform for laboratory automation, designed to connect and control various experimental equipment, enabling automation and standardization of experimental workflows.
## 核心特点
## Key Features
- 多设备集成管理
- 自动化实验流程
- 云端连接能力
- 灵活的配置系统
- 支持多种实验协议
- Multi-device integration management
- Automated experimental workflows
- Cloud connectivity capabilities
- Flexible configuration system
- Support for multiple experimental protocols
## 文档
## Documentation
详细文档可在以下位置找到:
Detailed documentation can be found at:
- [在线文档](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/)
- [Online Documentation](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/)
## 快速开始
## Quick Start
1. 配置Conda环境
1. Configure Conda Environment
Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的操作系统选择适当的环境文件:
Uni-Lab-OS recommends using `mamba` for environment management. Choose the appropriate environment file for your operating system:
```bash
# 创建新环境
# Create new environment
mamba env create -f unilabos-[YOUR_OS].yaml
mamba activate unilab
# 或更新现有环境
# 其中 `[YOUR_OS]` 可以是 `win64`, `linux-64`, `osx-64`, `osx-arm64`
conda env update --file unilabos-[YOUR_OS].yml -n 环境名
# Or update existing environment
# Where `[YOUR_OS]` can be `win64`, `linux-64`, `osx-64`, or `osx-arm64`.
conda env update --file unilabos-[YOUR_OS].yml -n environment_name
# 现阶段,需要安装 `unilabos_msgs`
# 可以前往 Release 页面下载系统对应的包进行安装
conda install ros-humble-unilabos-msgs-0.9.0-xxxxx.tar.bz2
# Currently, you need to install the `unilabos_msgs` package
# You can download the system-specific package from the Release page
conda install ros-humble-unilabos-msgs-0.9.1-xxxxx.tar.bz2
# 安装PyLabRobot等前置
# Install PyLabRobot and other prerequisites
git clone https://github.com/PyLabRobot/pylabrobot plr_repo
cd plr_repo
pip install .[opentrons]
```
2. 安装 Uni-Lab-OS:
2. Install Uni-Lab-OS:
```bash
# 克隆仓库
# Clone the repository
git clone https://github.com/dptech-corp/Uni-Lab-OS.git
cd Uni-Lab-OS
# 安装 Uni-Lab-OS
# Install Uni-Lab-OS
pip install .
```
3. 启动 Uni-Lab 系统:
3. Start Uni-Lab System:
请见[文档-启动样例](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/boot_examples/index.html)
Please refer to [Documentation - Boot Examples](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/boot_examples/index.html)
## 消息格式
## Message Format
Uni-Lab-OS 使用预构建的 `unilabos_msgs` 进行系统通信。您可以在 [GitHub Releases](https://github.com/dptech-corp/Uni-Lab-OS/releases) 页面找到已构建的版本。
Uni-Lab-OS uses pre-built `unilabos_msgs` for system communication. You can find the built versions on the [GitHub Releases](https://github.com/dptech-corp/Uni-Lab-OS/releases) page.
## 许可证
## License
此项目采用 GPL-3.0 许可 - 详情请参阅 [LICENSE](LICENSE) 文件。
This project is licensed under GPL-3.0 - see the [LICENSE](LICENSE) file for details.
## 项目统计
## Project Statistics
### Stars 趋势
### Stars Trend
<a href="https://star-history.com/#dptech-corp/Uni-Lab-OS&Date">
<img src="https://api.star-history.com/svg?repos=dptech-corp/Uni-Lab-OS&type=Date" alt="Star History Chart" width="600">
</a>
## 联系我们
## Contact Us
- GitHub Issues: [https://github.com/dptech-corp/Uni-Lab-OS/issues](https://github.com/dptech-corp/Uni-Lab-OS/issues)

89
README_zh.md Normal file
View File

@@ -0,0 +1,89 @@
<div align="center">
<img src="docs/logo.png" alt="Uni-Lab Logo" width="200"/>
</div>
# Uni-Lab-OS
<!-- Language switcher -->
[English](README.md) | **中文**
[![GitHub Stars](https://img.shields.io/github/stars/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/stargazers)
[![GitHub Forks](https://img.shields.io/github/forks/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/network/members)
[![GitHub Issues](https://img.shields.io/github/issues/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/issues)
[![GitHub License](https://img.shields.io/github/license/dptech-corp/Uni-Lab-OS.svg)](https://github.com/dptech-corp/Uni-Lab-OS/blob/main/LICENSE)
Uni-Lab 操作系统是一个用于实验室自动化的综合平台,旨在连接和控制各种实验设备,实现实验流程的自动化和标准化。
## 核心特点
- 多设备集成管理
- 自动化实验流程
- 云端连接能力
- 灵活的配置系统
- 支持多种实验协议
## 文档
详细文档可在以下位置找到:
- [在线文档](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/)
## 快速开始
1. 配置Conda环境
Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的操作系统选择适当的环境文件:
```bash
# 创建新环境
mamba env create -f unilabos-[YOUR_OS].yaml
mamba activate unilab
# 或更新现有环境
# 其中 `[YOUR_OS]` 可以是 `win64`, `linux-64`, `osx-64`, 或 `osx-arm64`。
conda env update --file unilabos-[YOUR_OS].yml -n 环境名
# 现阶段,需要安装 `unilabos_msgs` 包
# 可以前往 Release 页面下载系统对应的包进行安装
conda install ros-humble-unilabos-msgs-0.9.1-xxxxx.tar.bz2
# 安装PyLabRobot等前置
git clone https://github.com/PyLabRobot/pylabrobot plr_repo
cd plr_repo
pip install .[opentrons]
```
2. 安装 Uni-Lab-OS:
```bash
# 克隆仓库
git clone https://github.com/dptech-corp/Uni-Lab-OS.git
cd Uni-Lab-OS
# 安装 Uni-Lab-OS
pip install .
```
3. 启动 Uni-Lab 系统:
请见[文档-启动样例](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/boot_examples/index.html)
## 消息格式
Uni-Lab-OS 使用预构建的 `unilabos_msgs` 进行系统通信。您可以在 [GitHub Releases](https://github.com/dptech-corp/Uni-Lab-OS/releases) 页面找到已构建的版本。
## 许可证
此项目采用 GPL-3.0 许可 - 详情请参阅 [LICENSE](LICENSE) 文件。
## 项目统计
### Stars 趋势
<a href="https://star-history.com/#dptech-corp/Uni-Lab-OS&Date">
<img src="https://api.star-history.com/svg?repos=dptech-corp/Uni-Lab-OS&type=Date" alt="Star History Chart" width="600">
</a>
## 联系我们
- GitHub Issues: [https://github.com/dptech-corp/Uni-Lab-OS/issues](https://github.com/dptech-corp/Uni-Lab-OS/issues)

View File

@@ -1,6 +1,6 @@
package:
name: ros-humble-unilabos-msgs
version: 0.9.0
version: 0.9.1
source:
path: ../../unilabos_msgs
folder: ros-humble-unilabos-msgs/src/work

View File

@@ -1,6 +1,6 @@
package:
name: unilabos
version: "0.9.0"
version: "0.9.1"
source:
path: ../..

View File

@@ -4,7 +4,7 @@ package_name = 'unilabos'
setup(
name=package_name,
version='0.9.0',
version='0.9.1',
packages=find_packages(),
include_package_data=True,
install_requires=['setuptools'],

View File

@@ -1,5 +1,5 @@
使用plr_test.json启动将Well加入Plate中
```bash
ros2 action send_goal /devices/host_node/add_resource_from_outer unilabos_msgs/action/_resource_create_from_outer/ResourceCreateFromOuter "{ resources: [ { 'category': '', 'children': [], 'config': { 'type': 'Well', 'size_x': 6.86, 'size_y': 6.86, 'size_z': 10.67, 'rotation': { 'x': 0, 'y': 0, 'z': 0, 'type': 'Rotation' }, 'category': 'well', 'model': null, 'max_volume': 360, 'material_z_thickness': 0.5, 'compute_volume_from_height': null, 'compute_height_from_volume': null, 'bottom_type': 'flat', 'cross_section_type': 'circle' }, 'data': { 'liquids': [], 'pending_liquids': [], 'liquid_history': [] }, 'id': 'plate_well_11_7', 'name': 'plate_well_11_7', 'pose': { 'orientation': { 'w': 1.0, 'x': 0.0, 'y': 0.0, 'z': 0.0 }, 'position': { 'x': 0.0, 'y': 0.0, 'z': 0.0 } }, 'sample_id': '', 'parent': 'plate', 'type': 'device' } ], device_ids: [ 'PLR_STATION' ], bind_parent_ids: [ 'plate' ], bind_locations: [ { 'x': 0.0, 'y': 0.0, 'z': 0.0 } ], other_calling_params: [ '{}' ] }"
ros2 action send_goal /devices/host_node/create_resource_detailed unilabos_msgs/action/_resource_create_from_outer/ResourceCreateFromOuter "{ resources: [ { 'category': '', 'children': [], 'config': { 'type': 'Well', 'size_x': 6.86, 'size_y': 6.86, 'size_z': 10.67, 'rotation': { 'x': 0, 'y': 0, 'z': 0, 'type': 'Rotation' }, 'category': 'well', 'model': null, 'max_volume': 360, 'material_z_thickness': 0.5, 'compute_volume_from_height': null, 'compute_height_from_volume': null, 'bottom_type': 'flat', 'cross_section_type': 'circle' }, 'data': { 'liquids': [], 'pending_liquids': [], 'liquid_history': [] }, 'id': 'plate_well_11_7', 'name': 'plate_well_11_7', 'pose': { 'orientation': { 'w': 1.0, 'x': 0.0, 'y': 0.0, 'z': 0.0 }, 'position': { 'x': 0.0, 'y': 0.0, 'z': 0.0 } }, 'sample_id': '', 'parent': 'plate', 'type': 'device' } ], device_ids: [ 'PLR_STATION' ], bind_parent_ids: [ 'plate' ], bind_locations: [ { 'x': 0.0, 'y': 0.0, 'z': 0.0 } ], other_calling_params: [ '{}' ] }"
```

View File

@@ -56,6 +56,8 @@ dependencies:
- ros-humble-moveit-servo
# simulation
- ros-humble-simulation
- ros-humble-tf-transformations
- transforms3d
# ros-humble-gazebo-ros // ignored because of the conflict with ign-gazebo
# ilab equipments
# - ros-humble-unilabos-msgs

View File

@@ -56,6 +56,8 @@ dependencies:
# - ros-humble-moveit-servo
# simulation
- ros-humble-simulation
- ros-humble-tf-transformations
- transforms3d
# ros-humble-gazebo-ros // ignored because of the conflict with ign-gazebo
# ilab equipments
# - ros-humble-unilabos-msgs

View File

@@ -58,6 +58,8 @@ dependencies:
- ros-humble-moveit-servo
# simulation
- ros-humble-simulation
- ros-humble-tf-transformations
- transforms3d
# ros-humble-gazebo-ros // ignored because of the conflict with ign-gazebo
# ilab equipments
# - ros-humble-unilabos-msgs

View File

@@ -56,6 +56,8 @@ dependencies:
- ros-humble-moveit-servo
# simulation
- ros-humble-simulation # ignored because of NO python3.11 package in WIN64
- ros-humble-tf-transformations
- transforms3d
# ros-humble-gazebo-ros // ignored because of the conflict with ign-gazebo
# ilab equipments
# ros-humble-unilabos-msgs

View File

@@ -31,6 +31,6 @@ def job_add(req: JobAddReq) -> JobData:
action_kwargs = {"command": json.dumps(action_kwargs)}
elif "command" in action_kwargs:
action_kwargs = action_kwargs["command"]
print(f"job_add:{req.device_id} {action_name} {action_kwargs}")
HostNode.get_instance().send_goal(req.device_id, action_name=action_name, action_kwargs=action_kwargs, goal_uuid=req.job_id)
# print(f"job_add:{req.device_id} {action_name} {action_kwargs}")
HostNode.get_instance().send_goal(req.device_id, action_name=action_name, action_kwargs=action_kwargs, goal_uuid=req.job_id, server_info=req.server_info)
return JobData(jobId=req.job_id)

View File

@@ -18,7 +18,6 @@ if unilabos_dir not in sys.path:
from unilabos.config.config import load_config, BasicConfig, _update_config_from_env
from unilabos.utils.banner_print import print_status, print_unilab_banner
from unilabos.device_mesh.resource_visalization import ResourceVisualization
def parse_args():
@@ -188,11 +187,12 @@ def main():
if args_dict["visual"] != "disable":
enable_rviz = args_dict["visual"] == "rviz"
if devices_and_resources is not None:
from unilabos.device_mesh.resource_visalization import ResourceVisualization # 此处开启后logger会变更为INFO有需要请调整
resource_visualization = ResourceVisualization(devices_and_resources, args_dict["resources_config"] ,enable_rviz=enable_rviz)
args_dict["resources_mesh_config"] = resource_visualization.resource_model
start_backend(**args_dict)
server_thread = threading.Thread(target=start_server, kwargs=dict(
open_browser=not args_dict["disable_browser"]
open_browser=not args_dict["disable_browser"], port=args_dict["port"],
))
server_thread.start()
asyncio.set_event_loop(asyncio.new_event_loop())
@@ -201,10 +201,10 @@ def main():
time.sleep(1)
else:
start_backend(**args_dict)
start_server(open_browser=not args_dict["disable_browser"])
start_server(open_browser=not args_dict["disable_browser"], port=args_dict["port"],)
else:
start_backend(**args_dict)
start_server(open_browser=not args_dict["disable_browser"])
start_server(open_browser=not args_dict["disable_browser"], port=args_dict["port"],)
if __name__ == "__main__":

View File

@@ -51,8 +51,9 @@ class Resp(BaseModel):
class JobAddReq(BaseModel):
device_id: str = Field(examples=["Gripper"], description="device id")
data: dict = Field(examples=[{"position": 30, "torque": 5, "action": "push_to"}])
job_id: str = Field(examples=["sfsfsfeq"], description="goal uuid")
node_id: str = Field(examples=["sfsfsfeq"], description="node uuid")
job_id: str = Field(examples=["job_id"], description="goal uuid")
node_id: str = Field(examples=["node_id"], description="node uuid")
server_info: dict = Field(examples=[{"send_timestamp": 1717000000.0}], description="server info")
class JobStepFinishReq(BaseModel):

View File

@@ -12,7 +12,7 @@ import tempfile
import os
from unilabos.config.config import MQConfig
from unilabos.app.controler import devices, job_add
from unilabos.app.controler import job_add
from unilabos.app.model import JobAddReq
from unilabos.utils import logger
from unilabos.utils.type_check import TypeEncoder
@@ -26,6 +26,7 @@ class MQTTClient:
def __init__(self):
self.mqtt_disable = not MQConfig.lab_id
self.client_id = f"{MQConfig.group_id}@@@{MQConfig.lab_id}{uuid.uuid4()}"
logger.info("[MQTT] Client_id: " + self.client_id)
self.client = mqtt.Client(CallbackAPIVersion.VERSION2, client_id=self.client_id, protocol=mqtt.MQTTv5)
self._setup_callbacks()
@@ -42,20 +43,14 @@ class MQTTClient:
def _on_connect(self, client, userdata, flags, rc, properties=None):
logger.info("[MQTT] Connected with result code " + str(rc))
client.subscribe(f"labs/{MQConfig.lab_id}/job/start/", 0)
isok, data = devices()
if not isok:
logger.error("[MQTT] on_connect ErrorHostNotInit")
return
client.subscribe(f"labs/{MQConfig.lab_id}/pong/", 0)
def _on_message(self, client, userdata, msg) -> None:
logger.info("[MQTT] on_message<<<< " + msg.topic + " " + str(msg.payload))
# logger.info("[MQTT] on_message<<<< " + msg.topic + " " + str(msg.payload))
try:
payload_str = msg.payload.decode("utf-8")
payload_json = json.loads(payload_str)
logger.debug(f"Topic: {msg.topic}")
logger.debug("Payload:", json.dumps(payload_json, indent=2, ensure_ascii=False))
if msg.topic == f"labs/{MQConfig.lab_id}/job/start/":
logger.debug("job_add", type(payload_json), payload_json)
if "data" not in payload_json:
payload_json["data"] = {}
if "action" in payload_json:
@@ -65,6 +60,14 @@ class MQTTClient:
job_req = JobAddReq.model_validate(payload_json)
data = job_add(job_req)
return
elif msg.topic == f"labs/{MQConfig.lab_id}/pong/":
# 处理pong响应通知HostNode
from unilabos.ros.nodes.presets.host_node import HostNode
host_instance = HostNode.get_instance(0)
if host_instance:
host_instance.handle_pong_response(payload_json)
return
except json.JSONDecodeError as e:
logger.error(f"[MQTT] JSON 解析错误: {e}")
@@ -181,6 +184,28 @@ class MQTTClient:
self.client.publish(address, json.dumps(action_info), qos=2)
logger.debug(f"Action data published: address: {address}, {action_id}, {action_info}")
def send_ping(self, ping_id: str, timestamp: float):
"""发送ping消息到服务端"""
if self.mqtt_disable:
return
address = f"labs/{MQConfig.lab_id}/ping/"
ping_data = {"ping_id": ping_id, "client_timestamp": timestamp, "type": "ping"}
self.client.publish(address, json.dumps(ping_data), qos=2)
def setup_pong_subscription(self):
"""设置pong消息订阅"""
if self.mqtt_disable:
return
pong_topic = f"labs/{MQConfig.lab_id}/pong/"
self.client.subscribe(pong_topic, 0)
logger.debug(f"Subscribed to pong topic: {pong_topic}")
def handle_pong(self, pong_data: dict):
"""处理pong响应这个方法会在收到pong消息时被调用"""
logger.debug(f"Pong received: {pong_data}")
# 这里会被HostNode的ping-pong处理逻辑调用
pass
mqtt_client = MQTTClient()

View File

@@ -42,7 +42,7 @@ def get_host_node_info() -> Dict[str, Any]:
host_info["subscribed_topics"] = sorted(list(host_node._subscribed_topics))
# 获取动作客户端信息
for action_id, client in host_node._action_clients.items():
host_info["action_clients"] = {action_id: get_action_info(client, full_name=action_id)}
host_info["action_clients"][action_id] = get_action_info(client, full_name=action_id)
# 获取设备状态
host_info["device_status"] = host_node.device_status

View File

@@ -0,0 +1,842 @@
import requests
from typing import List, Sequence, Optional, Union, Literal
from geometry_msgs.msg import Point
from pylabrobot.liquid_handling import LiquidHandler
from unilabos_msgs.msg import Resource
from pylabrobot.resources import (
TipRack,
Container,
Coordinate,
)
from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker # type: ignore
from .liquid_handler_abstract import LiquidHandlerAbstract
import json
from typing import Sequence, Optional, List, Union, Literal
class LiquidHandlerBiomek(LiquidHandlerAbstract):
"""
Biomek液体处理器的实现类继承自LiquidHandlerAbstract。
该类用于处理Biomek液体处理器的特定操作。
"""
def __init__(self, backend=None, deck=None, *args, **kwargs):
super().__init__(backend, deck, *args, **kwargs)
self._status = "Idle" # 初始状态为 Idle
self._success = False # 初始成功状态为 False
self._status_queue = kwargs.get("status_queue", None) # 状态队列
self.temp_protocol = {}
self.py32_path = "/opt/py32" # Biomek的Python 3.2路径
self.aspirate_techniques = {
'MC P300 high':{
"Solvent": "Water",
}
}
self.dispense_techniques = {
'MC P300 high':{
"Span8": False,
"Pod": "Pod1",
"Wash": False,
"Dynamic?": True,
"AutoSelectActiveWashTechnique": False,
"ActiveWashTechnique": "",
"ChangeTipsBetweenDests": True,
"ChangeTipsBetweenSources": False,
"DefaultCaption": "",
"UseExpression": False,
"LeaveTipsOn": False,
"MandrelExpression": "",
"Repeats": "1",
"RepeatsByVolume": False,
"Replicates": "1",
"ShowTipHandlingDetails": False,
"ShowTransferDetails": True,
"Span8Wash": False,
"Span8WashVolume": "2",
"Span8WasteVolume": "1",
"SplitVolume": False,
"SplitVolumeCleaning": False,
"Stop": "Destinations",
"UseCurrentTips": False,
"UseDisposableTips": False,
"UseFixedTips": False,
"UseJIT": True,
"UseMandrelSelection": True,
"UseProbes": [True, True, True, True, True, True, True, True],
"WashCycles": "3",
"WashVolume": "110%",
"Wizard": False
}
}
@classmethod
def deserialize(cls, data: dict, allow_marshal: bool = False) -> LiquidHandler:
return LiquidHandler.deserialize(data, allow_marshal)
def create_protocol(
self,
protocol_name: str,
protocol_description: str,
protocol_version: str,
protocol_author: str,
protocol_date: str,
protocol_type: str,
none_keys: List[str] = [],
):
"""
创建一个新的协议。
Args:
protocol_name (str): 协议名称
protocol_description (str): 协议描述
protocol_version (str): 协议版本
protocol_author (str): 协议作者
protocol_date (str): 协议日期
protocol_type (str): 协议类型
none_keys (List[str]): 需要设置为None的键列表
Returns:
dict: 创建的协议字典
"""
self.temp_protocol = {
"meta": {
"name": protocol_name,
"description": protocol_description,
"version": protocol_version,
"author": protocol_author,
"date": protocol_date,
"type": protocol_type,
},
"labwares": [],
"steps": [],
}
return self.temp_protocol
def run_protocol(self):
"""
执行创建的实验流程。
工作站的完整执行流程是,
从 create_protocol 开始,创建新的 method
随后执行 transfer_liquid 等操作向实验流程添加步骤,
最后 run_protocol 执行整个方法。
Returns:
dict: 执行结果
"""
#use popen or subprocess to create py32 process and communicate send the temp protocol to it
if not self.temp_protocol:
raise ValueError("No protocol created. Please create a protocol first.")
# 模拟执行协议
self._status = "Running"
self._success = True
# 在这里可以添加实际执行协议的逻辑
response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
def create_resource(
self,
resource_tracker: DeviceNodeResourceTracker,
resources: list[Resource],
bind_parent_id: str,
bind_location: dict[str, float],
liquid_input_slot: list[int],
liquid_type: list[str],
liquid_volume: list[int],
slot_on_deck: int,
):
"""
创建一个新的资源。
Args:
device_id (str): 设备ID
res_id (str): 资源ID
class_name (str): 资源类名
parent (str): 父级ID
bind_locations (Point): 绑定位置
liquid_input_slot (list[int]): 液体输入槽列表
liquid_type (list[str]): 液体类型列表
liquid_volume (list[int]): 液体体积列表
slot_on_deck (int): 甲板上的槽位
Returns:
dict: 创建的资源字典
"""
# TODO需要对好接口下面这个是临时的
for resource in resources:
res_id = resource.id
class_name = resource.class_name
parent = bind_parent_id
bind_locations = Coordinate.from_point(resource.bind_location)
liquid_input_slot = liquid_input_slot
liquid_type = liquid_type
liquid_volume = liquid_volume
slot_on_deck = slot_on_deck
resource = {
"id": res_id,
"class": class_name,
"parent": parent,
"bind_locations": bind_locations.to_dict(),
"liquid_input_slot": liquid_input_slot,
"liquid_type": liquid_type,
"liquid_volume": liquid_volume,
"slot_on_deck": slot_on_deck,
}
self.temp_protocol["labwares"].append(resource)
return resource
def transfer_liquid(
self,
sources: Sequence[Container],
targets: Sequence[Container],
tip_racks: Sequence[TipRack],
*,
use_channels: Optional[List[int]] = None,
asp_vols: Union[List[float], float],
dis_vols: Union[List[float], float],
asp_flow_rates: Optional[List[Optional[float]]] = None,
dis_flow_rates: Optional[List[Optional[float]]] = None,
offsets: Optional[List[Coordinate]] = None,
touch_tip: bool = False,
liquid_height: Optional[List[Optional[float]]] = None,
blow_out_air_volume: Optional[List[Optional[float]]] = None,
spread: Literal["wide", "tight", "custom"] = "wide",
is_96_well: bool = False,
mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
mix_times: Optional[int] = None,
mix_vol: Optional[int] = None,
mix_rate: Optional[int] = None,
mix_liquid_height: Optional[float] = None,
delays: Optional[List[int]] = None,
none_keys: List[str] = []
):
transfer_params = {
"Span8": False,
"Pod": "Pod1",
"items": {},
"Wash": False,
"Dynamic?": True,
"AutoSelectActiveWashTechnique": False,
"ActiveWashTechnique": "",
"ChangeTipsBetweenDests": False,
"ChangeTipsBetweenSources": False,
"DefaultCaption": "",
"UseExpression": False,
"LeaveTipsOn": False,
"MandrelExpression": "",
"Repeats": "1",
"RepeatsByVolume": False,
"Replicates": "1",
"ShowTipHandlingDetails": False,
"ShowTransferDetails": True,
"Solvent": "Well Content",
"Span8Wash": False,
"Span8WashVolume": "2",
"Span8WasteVolume": "1",
"SplitVolume": False,
"SplitVolumeCleaning": False,
"Stop": "Destinations",
"TipLocation": "BC1025F",
"UseCurrentTips": False,
"UseDisposableTips": True,
"UseFixedTips": False,
"UseJIT": True,
"UseMandrelSelection": True,
"UseProbes": [True, True, True, True, True, True, True, True],
"WashCycles": "1",
"WashVolume": "110%",
"Wizard": False
}
items: dict = {}
for idx, (src, dst) in enumerate(zip(sources, targets)):
items[str(idx)] = {
"Source": str(src),
"Destination": str(dst),
"Volume": dis_vols[idx]
}
transfer_params["items"] = items
transfer_params["Solvent"] = "Water"
TipLocation = tip_racks[0].name
transfer_params["TipLocation"] = TipLocation
if len(tip_racks) == 1:
transfer_params['UseCurrentTips'] = True
elif len(tip_racks) > 1:
transfer_params["ChangeTipsBetweenDests"] = True
self.temp_protocol["steps"].append(transfer_params)
return
def transfer_biomek(
self,
source: str,
target: str,
tip_rack: str,
volume: float,
aspirate_techniques: str,
dispense_techniques: str,
):
"""
处理Biomek的液体转移操作。
"""
asp_params = self.aspirate_techniques.get(aspirate_techniques, {})
dis_params = self.dispense_techniques.get(dispense_techniques, {})
transfer_params = {
"Span8": False,
"Pod": "Pod1",
"items": {},
"Wash": False,
"Dynamic?": True,
"AutoSelectActiveWashTechnique": False,
"ActiveWashTechnique": "",
"ChangeTipsBetweenDests": False,
"ChangeTipsBetweenSources": True,
"DefaultCaption": "",
"UseExpression": False,
"LeaveTipsOn": False,
"MandrelExpression": "",
"Repeats": "1",
"RepeatsByVolume": False,
"Replicates": "1",
"ShowTipHandlingDetails": False,
"ShowTransferDetails": True,
"Solvent": "Water",
"Span8Wash": False,
"Span8WashVolume": "2",
"Span8WasteVolume": "1",
"SplitVolume": False,
"SplitVolumeCleaning": False,
"Stop": "Destinations",
"TipLocation": "BC1025F",
"UseCurrentTips": False,
"UseDisposableTips": True,
"UseFixedTips": False,
"UseJIT": True,
"UseMandrelSelection": True,
"UseProbes": [True, True, True, True, True, True, True, True],
"WashCycles": "1",
"WashVolume": "110%",
"Wizard": False
}
items: dict = {}
items["Source"] = source
items["Destination"] = target
items["Volume"] = volume
transfer_params["items"] = items
transfer_params["Solvent"] = asp_params['Solvent']
transfer_params["TipLocation"] = tip_rack
transfer_params.update(asp_params)
transfer_params.update(dis_params)
self.temp_protocol["steps"].append(transfer_params)
return
if __name__ == "__main__":
steps_info = '''
{
"steps": [
{
"step_number": 1,
"operation": "transfer",
"description": "转移PCR产物或酶促反应液至0.05ml 96孔板中",
"parameters": {
"source": "P1",
"target": "P11",
"tip_rack": "BC230",
"volume": 50
}
},
{
"step_number": 2,
"operation": "transfer",
"description": "加入2倍体积Bind Beads BC至产物中",
"parameters": {
"source": "P2",
"target": "P11",
"tip_rack": "BC230",
"volume": 100
}
},
{
"step_number": 3,
"operation": "move_labware",
"description": "移动P11至Orbital1用于振荡混匀",
"parameters": {
"source": "P11",
"target": "Orbital1"
}
},
{
"step_number": 4,
"operation": "oscillation",
"description": "在Orbital1上振荡混匀Bind Beads BC与PCR产物700-900rpm300秒",
"parameters": {
"rpm": 800,
"time": 300
}
},
{
"step_number": 5,
"operation": "move_labware",
"description": "移动混匀后的板回P11",
"parameters": {
"source": "Orbital1",
"target": "P11"
}
},
{
"step_number": 6,
"operation": "move_labware",
"description": "将P11移动到磁力架P12吸附3分钟",
"parameters": {
"source": "P11",
"target": "P12"
}
},
{
"step_number": 7,
"operation": "incubation",
"description": "磁力架上室温静置3分钟完成吸附",
"parameters": {
"time": 180
}
},
{
"step_number": 8,
"operation": "transfer",
"description": "去除上清液至废液槽",
"parameters": {
"source": "P12",
"target": "P22",
"tip_rack": "BC230",
"volume": 150
}
},
{
"step_number": 9,
"operation": "transfer",
"description": "加入300-500μl 75%乙醇清洗",
"parameters": {
"source": "P3",
"target": "P12",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 10,
"operation": "move_labware",
"description": "移动清洗板到Orbital1进行振荡",
"parameters": {
"source": "P12",
"target": "Orbital1"
}
},
{
"step_number": 11,
"operation": "oscillation",
"description": "乙醇清洗液振荡混匀700-900rpm, 45秒",
"parameters": {
"rpm": 800,
"time": 45
}
},
{
"step_number": 12,
"operation": "move_labware",
"description": "振荡后将板移回磁力架P12吸附",
"parameters": {
"source": "Orbital1",
"target": "P12"
}
},
{
"step_number": 13,
"operation": "incubation",
"description": "吸附3分钟",
"parameters": {
"time": 180
}
},
{
"step_number": 14,
"operation": "transfer",
"description": "去除乙醇上清液至废液槽",
"parameters": {
"source": "P12",
"target": "P22",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 15,
"operation": "transfer",
"description": "第二次加入300-500μl 75%乙醇清洗",
"parameters": {
"source": "P3",
"target": "P12",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 16,
"operation": "move_labware",
"description": "再次移动清洗板到Orbital1振荡",
"parameters": {
"source": "P12",
"target": "Orbital1"
}
},
{
"step_number": 17,
"operation": "oscillation",
"description": "再次乙醇清洗液振荡混匀700-900rpm, 45秒",
"parameters": {
"rpm": 800,
"time": 45
}
},
{
"step_number": 18,
"operation": "move_labware",
"description": "振荡后板送回磁力架P12吸附",
"parameters": {
"source": "Orbital1",
"target": "P12"
}
},
{
"step_number": 19,
"operation": "incubation",
"description": "再次吸附3分钟",
"parameters": {
"time": 180
}
},
{
"step_number": 20,
"operation": "transfer",
"description": "去除乙醇上清液至废液槽",
"parameters": {
"source": "P12",
"target": "P22",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 21,
"operation": "incubation",
"description": "空气干燥15分钟",
"parameters": {
"time": 900
}
},
{
"step_number": 22,
"operation": "transfer",
"description": "加30-50μl Elution Buffer洗脱",
"parameters": {
"source": "P4",
"target": "P12",
"tip_rack": "BC230",
"volume": 40
}
},
{
"step_number": 23,
"operation": "move_labware",
"description": "移动到Orbital1振荡混匀60秒",
"parameters": {
"source": "P12",
"target": "Orbital1"
}
},
{
"step_number": 24,
"operation": "oscillation",
"description": "Elution Buffer振荡混匀700-900rpm, 60秒",
"parameters": {
"rpm": 800,
"time": 60
}
},
{
"step_number": 25,
"operation": "move_labware",
"description": "振荡后送回磁力架P12",
"parameters": {
"source": "Orbital1",
"target": "P12"
}
},
{
"step_number": 26,
"operation": "incubation",
"description": "室温静置3分钟洗脱反应",
"parameters": {
"time": 180
}
},
{
"step_number": 27,
"operation": "transfer",
"description": "将上清液DNA转移到新板P13",
"parameters": {
"source": "P12",
"target": "P13",
"tip_rack": "BC230",
"volume": 40
}
}
]
}
'''
labware_with_liquid = '''
[ {
"id": "stock plate on P1",
"parent": "deck",
"slot_on_deck": "P1",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"master_mix"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "Tip Rack BC230 TL2",
"parent": "deck",
"slot_on_deck": "TL2",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on TL3",
"parent": "deck",
"slot_on_deck": "TL3",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on TL4",
"parent": "deck",
"slot_on_deck": "TL4",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on TL5",
"parent": "deck",
"slot_on_deck": "TL5",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P5",
"parent": "deck",
"slot_on_deck": "P5",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P6",
"parent": "deck",
"slot_on_deck": "P6",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P7",
"parent": "deck",
"slot_on_deck": "P7",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P8",
"parent": "deck",
"slot_on_deck": "P8",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 P16",
"parent": "deck",
"slot_on_deck": "P16",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "stock plate on 4",
"parent": "deck",
"slot_on_deck": "P2",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"bind beads"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "stock plate on P2",
"parent": "deck",
"slot_on_deck": "P2",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"bind beads"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "stock plate on P3",
"parent": "deck",
"slot_on_deck": "P3",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"ethyl alcohol"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "oscillation",
"parent": "deck",
"slot_on_deck": "Orbital1",
"class_name": "Orbital",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "working plate on P11",
"parent": "deck",
"slot_on_deck": "P11",
"class_name": "NEST 2ml Deep Well Plate",
"liquid_type": [
],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "magnetics module on P12",
"parent": "deck",
"slot_on_deck": "P12",
"class_name": "magnetics module",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "working plate on P13",
"parent": "deck",
"slot_on_deck": "P13",
"class_name": "NEST 2ml Deep Well Plate",
"liquid_type": [
],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "waste on P22",
"parent": "deck",
"slot_on_deck": "P22",
"class_name": "nest_1_reservoir_195ml",
"liquid_type": [
],
"liquid_volume": [],
"liquid_input_wells": [
]
}
]
'''
handler = LiquidHandlerBiomek()
handler.temp_protocol = {
"meta": {},
"labwares": [],
"steps": []
}
input_steps = json.loads(steps_info)
labwares = json.loads(labware_with_liquid)
for step in input_steps['steps']:
if step['operation'] != 'transfer':
continue
parameters = step['parameters']
tip_rack=parameters['tip_rack']
# 找到labwares中与tip_rack匹配的项的id
tip_rack_id = [lw['id'] for lw in labwares if lw['class_name'] == tip_rack][0]
handler.transfer_biomek(source=parameters['source'],
target=parameters['target'],
volume=parameters['volume'],
tip_rack=tip_rack_id,
aspirate_techniques='MC P300 high',
dispense_techniques='MC P300 high'
)
print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))

View File

@@ -0,0 +1,747 @@
import requests
from typing import List, Sequence, Optional, Union, Literal
# from geometry_msgs.msg import Point
# from unilabos_msgs.msg import Resource
from pylabrobot.resources import (
Resource,
TipRack,
Container,
Coordinate,
Well
)
# from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker # type: ignore
# from .liquid_handler_abstract import LiquidHandlerAbstract
import json
from typing import Sequence, Optional, List, Union, Literal
steps_info = '''
{
"steps": [
{
"step_number": 1,
"operation": "transfer",
"description": "转移PCR产物或酶促反应液至0.05ml 96孔板中",
"parameters": {
"source": "P1",
"target": "P11",
"tip_rack": "BC230",
"volume": 50
}
},
{
"step_number": 2,
"operation": "transfer",
"description": "加入2倍体积Bind Beads BC至产物中",
"parameters": {
"source": "P2",
"target": "P11",
"tip_rack": "BC230",
"volume": 100
}
},
{
"step_number": 3,
"operation": "move_labware",
"description": "移动P11至Orbital1用于振荡混匀",
"parameters": {
"source": "P11",
"target": "Orbital1"
}
},
{
"step_number": 4,
"operation": "oscillation",
"description": "在Orbital1上振荡混匀Bind Beads BC与PCR产物700-900rpm300秒",
"parameters": {
"rpm": 800,
"time": 300
}
},
{
"step_number": 5,
"operation": "move_labware",
"description": "移动混匀后的板回P11",
"parameters": {
"source": "Orbital1",
"target": "P11"
}
},
{
"step_number": 6,
"operation": "move_labware",
"description": "将P11移动到磁力架P12吸附3分钟",
"parameters": {
"source": "P11",
"target": "P12"
}
},
{
"step_number": 7,
"operation": "incubation",
"description": "磁力架上室温静置3分钟完成吸附",
"parameters": {
"time": 180
}
},
{
"step_number": 8,
"operation": "transfer",
"description": "去除上清液至废液槽",
"parameters": {
"source": "P12",
"target": "P22",
"tip_rack": "BC230",
"volume": 150
}
},
{
"step_number": 9,
"operation": "transfer",
"description": "加入300-500μl 75%乙醇清洗",
"parameters": {
"source": "P3",
"target": "P12",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 10,
"operation": "move_labware",
"description": "移动清洗板到Orbital1进行振荡",
"parameters": {
"source": "P12",
"target": "Orbital1"
}
},
{
"step_number": 11,
"operation": "oscillation",
"description": "乙醇清洗液振荡混匀700-900rpm, 45秒",
"parameters": {
"rpm": 800,
"time": 45
}
},
{
"step_number": 12,
"operation": "move_labware",
"description": "振荡后将板移回磁力架P12吸附",
"parameters": {
"source": "Orbital1",
"target": "P12"
}
},
{
"step_number": 13,
"operation": "incubation",
"description": "吸附3分钟",
"parameters": {
"time": 180
}
},
{
"step_number": 14,
"operation": "transfer",
"description": "去除乙醇上清液至废液槽",
"parameters": {
"source": "P12",
"target": "P22",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 15,
"operation": "transfer",
"description": "第二次加入300-500μl 75%乙醇清洗",
"parameters": {
"source": "P3",
"target": "P12",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 16,
"operation": "move_labware",
"description": "再次移动清洗板到Orbital1振荡",
"parameters": {
"source": "P12",
"target": "Orbital1"
}
},
{
"step_number": 17,
"operation": "oscillation",
"description": "再次乙醇清洗液振荡混匀700-900rpm, 45秒",
"parameters": {
"rpm": 800,
"time": 45
}
},
{
"step_number": 18,
"operation": "move_labware",
"description": "振荡后板送回磁力架P12吸附",
"parameters": {
"source": "Orbital1",
"target": "P12"
}
},
{
"step_number": 19,
"operation": "incubation",
"description": "再次吸附3分钟",
"parameters": {
"time": 180
}
},
{
"step_number": 20,
"operation": "transfer",
"description": "去除乙醇上清液至废液槽",
"parameters": {
"source": "P12",
"target": "P22",
"tip_rack": "BC230",
"volume": 400
}
},
{
"step_number": 21,
"operation": "incubation",
"description": "空气干燥15分钟",
"parameters": {
"time": 900
}
},
{
"step_number": 22,
"operation": "transfer",
"description": "加30-50μl Elution Buffer洗脱",
"parameters": {
"source": "P4",
"target": "P12",
"tip_rack": "BC230",
"volume": 40
}
},
{
"step_number": 23,
"operation": "move_labware",
"description": "移动到Orbital1振荡混匀60秒",
"parameters": {
"source": "P12",
"target": "Orbital1"
}
},
{
"step_number": 24,
"operation": "oscillation",
"description": "Elution Buffer振荡混匀700-900rpm, 60秒",
"parameters": {
"rpm": 800,
"time": 60
}
},
{
"step_number": 25,
"operation": "move_labware",
"description": "振荡后送回磁力架P12",
"parameters": {
"source": "Orbital1",
"target": "P12"
}
},
{
"step_number": 26,
"operation": "incubation",
"description": "室温静置3分钟洗脱反应",
"parameters": {
"time": 180
}
},
{
"step_number": 27,
"operation": "transfer",
"description": "将上清液DNA转移到新板P13",
"parameters": {
"source": "P12",
"target": "P13",
"tip_rack": "BC230",
"volume": 40
}
}
]
}
'''
#class LiquidHandlerBiomek(LiquidHandlerAbstract):
class LiquidHandlerBiomek:
"""
Biomek液体处理器的实现类继承自LiquidHandlerAbstract。
该类用于处理Biomek液体处理器的特定操作。
"""
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._status = "Idle" # 初始状态为 Idle
self._success = False # 初始成功状态为 False
self._status_queue = kwargs.get("status_queue", None) # 状态队列
self.temp_protocol = {}
self.py32_path = "/opt/py32" # Biomek的Python 3.2路径
self.aspirate_techniques = {
'MC P300 high':{
"Solvent": "Water",
}
}
self.dispense_techniques = {
'MC P300 high':{
"Span8": False,
"Pod": "Pod1",
"Wash": False,
"Dynamic?": True,
"AutoSelectActiveWashTechnique": False,
"ActiveWashTechnique": "",
"ChangeTipsBetweenDests": True,
"ChangeTipsBetweenSources": False,
"DefaultCaption": "",
"UseExpression": False,
"LeaveTipsOn": False,
"MandrelExpression": "",
"Repeats": "1",
"RepeatsByVolume": False,
"Replicates": "1",
"ShowTipHandlingDetails": False,
"ShowTransferDetails": True,
"Span8Wash": False,
"Span8WashVolume": "2",
"Span8WasteVolume": "1",
"SplitVolume": False,
"SplitVolumeCleaning": False,
"Stop": "Destinations",
"UseCurrentTips": False,
"UseDisposableTips": False,
"UseFixedTips": False,
"UseJIT": True,
"UseMandrelSelection": True,
"UseProbes": [True, True, True, True, True, True, True, True],
"WashCycles": "3",
"WashVolume": "110%",
"Wizard": False
}
}
def create_protocol(
self,
protocol_name: str,
protocol_description: str,
protocol_version: str,
protocol_author: str,
protocol_date: str,
protocol_type: str,
none_keys: List[str] = [],
):
"""
创建一个新的协议。
Args:
protocol_name (str): 协议名称
protocol_description (str): 协议描述
protocol_version (str): 协议版本
protocol_author (str): 协议作者
protocol_date (str): 协议日期
protocol_type (str): 协议类型
none_keys (List[str]): 需要设置为None的键列表
Returns:
dict: 创建的协议字典
"""
self.temp_protocol = {
"meta": {
"name": protocol_name,
"description": protocol_description,
"version": protocol_version,
"author": protocol_author,
"date": protocol_date,
"type": protocol_type,
},
"labwares": [],
"steps": [],
}
return self.temp_protocol
# def run_protocol(self):
# """
# 执行创建的实验流程。
# 工作站的完整执行流程是,
# 从 create_protocol 开始,创建新的 method
# 随后执行 transfer_liquid 等操作向实验流程添加步骤,
# 最后 run_protocol 执行整个方法。
# Returns:
# dict: 执行结果
# """
# #use popen or subprocess to create py32 process and communicate send the temp protocol to it
# if not self.temp_protocol:
# raise ValueError("No protocol created. Please create a protocol first.")
# # 模拟执行协议
# self._status = "Running"
# self._success = True
# # 在这里可以添加实际执行协议的逻辑
# response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
# def create_resource(
# self,
# resource_tracker: DeviceNodeResourceTracker,
# resources: list[Resource],
# bind_parent_id: str,
# bind_location: dict[str, float],
# liquid_input_slot: list[int],
# liquid_type: list[str],
# liquid_volume: list[int],
# slot_on_deck: int,
# res_id,
# class_name,
# bind_locations,
# parent
# ):
# """
# 创建一个新的资源。
# Args:
# device_id (str): 设备ID
# res_id (str): 资源ID
# class_name (str): 资源类名
# parent (str): 父级ID
# bind_locations (Point): 绑定位置
# liquid_input_slot (list[int]): 液体输入槽列表
# liquid_type (list[str]): 液体类型列表
# liquid_volume (list[int]): 液体体积列表
# slot_on_deck (int): 甲板上的槽位
# Returns:
# dict: 创建的资源字典
# """
# # TODO需要对好接口下面这个是临时的
# resource = {
# "id": res_id,
# "class": class_name,
# "parent": parent,
# "bind_locations": bind_locations.to_dict(),
# "liquid_input_slot": liquid_input_slot,
# "liquid_type": liquid_type,
# "liquid_volume": liquid_volume,
# "slot_on_deck": slot_on_deck,
# }
# self.temp_protocol["labwares"].append(resource)
# return resource
def transfer_biomek(
self,
source: str,
target: str,
tip_rack: str,
volume: float,
aspirate_techniques: str,
dispense_techniques: str,
):
"""
处理Biomek的液体转移操作。
"""
asp_params = self.aspirate_techniques.get(aspirate_techniques, {})
dis_params = self.dispense_techniques.get(dispense_techniques, {})
transfer_params = {
"Span8": False,
"Pod": "Pod1",
"items": {},
"Wash": False,
"Dynamic?": True,
"AutoSelectActiveWashTechnique": False,
"ActiveWashTechnique": "",
"ChangeTipsBetweenDests": False,
"ChangeTipsBetweenSources": True,
"DefaultCaption": "",
"UseExpression": False,
"LeaveTipsOn": False,
"MandrelExpression": "",
"Repeats": "1",
"RepeatsByVolume": False,
"Replicates": "1",
"ShowTipHandlingDetails": False,
"ShowTransferDetails": True,
"Solvent": "Water",
"Span8Wash": False,
"Span8WashVolume": "2",
"Span8WasteVolume": "1",
"SplitVolume": False,
"SplitVolumeCleaning": False,
"Stop": "Destinations",
"TipLocation": "BC1025F",
"UseCurrentTips": False,
"UseDisposableTips": True,
"UseFixedTips": False,
"UseJIT": True,
"UseMandrelSelection": True,
"UseProbes": [True, True, True, True, True, True, True, True],
"WashCycles": "1",
"WashVolume": "110%",
"Wizard": False
}
items: dict = {}
items["Source"] = source
items["Destination"] = target
items["Volume"] = volume
transfer_params["items"] = items
transfer_params["Solvent"] = asp_params['Solvent']
transfer_params["TipLocation"] = tip_rack
transfer_params.update(asp_params)
transfer_params.update(dis_params)
self.temp_protocol["steps"].append(transfer_params)
return
labware_with_liquid = '''
[ {
"id": "stock plate on P1",
"parent": "deck",
"slot_on_deck": "P1",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"master_mix"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "Tip Rack BC230 TL2",
"parent": "deck",
"slot_on_deck": "TL2",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on TL3",
"parent": "deck",
"slot_on_deck": "TL3",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on TL4",
"parent": "deck",
"slot_on_deck": "TL4",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on TL5",
"parent": "deck",
"slot_on_deck": "TL5",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P5",
"parent": "deck",
"slot_on_deck": "P5",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P6",
"parent": "deck",
"slot_on_deck": "P6",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P7",
"parent": "deck",
"slot_on_deck": "P7",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 on P8",
"parent": "deck",
"slot_on_deck": "P8",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "Tip Rack BC230 P16",
"parent": "deck",
"slot_on_deck": "P16",
"class_name": "BC230",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "stock plate on 4",
"parent": "deck",
"slot_on_deck": "P2",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"bind beads"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "stock plate on P2",
"parent": "deck",
"slot_on_deck": "P2",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"bind beads"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "stock plate on P3",
"parent": "deck",
"slot_on_deck": "P3",
"class_name": "nest_12_reservoir_15ml",
"liquid_type": [
"ethyl alcohol"
],
"liquid_volume": [10000],
"liquid_input_wells": [
"A1"
]
},
{
"id": "oscillation",
"parent": "deck",
"slot_on_deck": "Orbital1",
"class_name": "Orbital",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "working plate on P11",
"parent": "deck",
"slot_on_deck": "P11",
"class_name": "NEST 2ml Deep Well Plate",
"liquid_type": [
],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "magnetics module on P12",
"parent": "deck",
"slot_on_deck": "P12",
"class_name": "magnetics module",
"liquid_type": [],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "working plate on P13",
"parent": "deck",
"slot_on_deck": "P13",
"class_name": "NEST 2ml Deep Well Plate",
"liquid_type": [
],
"liquid_volume": [],
"liquid_input_wells": [
]
},
{
"id": "waste on P22",
"parent": "deck",
"slot_on_deck": "P22",
"class_name": "nest_1_reservoir_195ml",
"liquid_type": [
],
"liquid_volume": [],
"liquid_input_wells": [
]
}
]
'''
handler = LiquidHandlerBiomek()
handler.temp_protocol = {
"meta": {},
"labwares": [],
"steps": []
}
input_steps = json.loads(steps_info)
labwares = json.loads(labware_with_liquid)
for step in input_steps['steps']:
if step['operation'] != 'transfer':
continue
parameters = step['parameters']
handler.transfer_biomek(source=parameters['source'],
target=parameters['target'],
volume=parameters['volume'],
tip_rack=parameters['tip_rack'],
aspirate_techniques='MC P300 high',
dispense_techniques='MC P300 high'
)
print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))

View File

@@ -6,21 +6,29 @@ import asyncio
import time
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.resources import (
Resource,
TipRack,
Container,
Coordinate,
Well
)
from pylabrobot.resources import Resource, TipRack, Container, Coordinate, Well
class DPLiquidHandler(LiquidHandler):
class LiquidHandlerAbstract(LiquidHandler):
"""Extended LiquidHandler with additional operations."""
# ---------------------------------------------------------------
# REMOVE LIQUID --------------------------------------------------
# ---------------------------------------------------------------
async def create_protocol(
self,
protocol_name: str,
protocol_description: str,
protocol_version: str,
protocol_author: str,
protocol_date: str,
protocol_type: str,
none_keys: List[str] = [],
):
"""Create a new protocol with the given metadata."""
pass
async def remove_liquid(
self,
vols: List[float],
@@ -35,26 +43,26 @@ class DPLiquidHandler(LiquidHandler):
spread: Optional[Literal["wide", "tight", "custom"]] = "wide",
delays: Optional[List[int]] = None,
is_96_well: Optional[bool] = False,
top: Optional[List(float)] = None,
none_keys: List[str] = []
top: Optional[List[float]] = None,
none_keys: List[str] = [],
):
"""A complete *remove* (aspirate → waste) operation."""
trash = self.deck.get_trash_area()
try:
if is_96_well:
pass # This mode is not verified
pass # This mode is not verified
else:
if len(vols) != len(sources):
raise ValueError("Length of `vols` must match `sources`.")
for src, vol in zip(sources, vols):
self.move_to(src, dis_to_top=top[0] if top else 0)
await self.move_to(src, dis_to_top=top[0] if top else 0)
tip = next(self.current_tip)
await self.pick_up_tips(tip)
await self.aspirate(
resources=[src],
vols=[vol],
use_channels=use_channels, # only aspirate96 used, default to None
use_channels=use_channels, # only aspirate96 used, default to None
flow_rates=[flow_rates[0]] if flow_rates else None,
offsets=[offsets[0]] if offsets else None,
liquid_height=[liquid_height[0]] if liquid_height else None,
@@ -64,15 +72,15 @@ class DPLiquidHandler(LiquidHandler):
await self.custom_delay(seconds=delays[0] if delays else 0)
await self.dispense(
resources=waste_liquid,
vols=[vol],
use_channels=use_channels,
flow_rates=[flow_rates[1]] if flow_rates else None,
offsets=[offsets[1]] if offsets else None,
liquid_height=[liquid_height[1]] if liquid_height else None,
blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
spread=spread,
)
await self.discard_tips() # For now, each of tips is discarded after use
vols=[vol],
use_channels=use_channels,
flow_rates=[flow_rates[1]] if flow_rates else None,
offsets=[offsets[1]] if offsets else None,
liquid_height=[liquid_height[1]] if liquid_height else None,
blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
spread=spread,
)
await self.discard_tips() # For now, each of tips is discarded after use
except Exception as e:
raise RuntimeError(f"Liquid removal failed: {e}") from e
@@ -100,13 +108,13 @@ class DPLiquidHandler(LiquidHandler):
mix_vol: Optional[int] = None,
mix_rate: Optional[int] = None,
mix_liquid_height: Optional[float] = None,
none_keys: List[str] = []
none_keys: List[str] = [],
):
"""A complete *add* (aspirate reagent → dispense into targets) operation."""
try:
if is_96_well:
pass # This mode is not verified.
pass # This mode is not verified.
else:
if len(asp_vols) != len(targets):
raise ValueError("Length of `vols` must match `targets`.")
@@ -122,7 +130,7 @@ class DPLiquidHandler(LiquidHandler):
offsets=[offsets[0]] if offsets else None,
liquid_height=[liquid_height[0]] if liquid_height else None,
blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
spread=spread
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
@@ -144,7 +152,8 @@ class DPLiquidHandler(LiquidHandler):
mix_vol=mix_vol,
offsets=offsets if offsets else None,
height_to_bottom=mix_liquid_height if mix_liquid_height else None,
mix_rate=mix_rate if mix_rate else None)
mix_rate=mix_rate if mix_rate else None,
)
if delays is not None:
await self.custom_delay(seconds=delays[1])
await self.touch_tip(targets[_])
@@ -158,13 +167,13 @@ class DPLiquidHandler(LiquidHandler):
# ---------------------------------------------------------------
async def transfer_liquid(
self,
asp_vols: Union[List[float], float],
dis_vols: Union[List[float], float],
sources: Sequence[Container],
targets: Sequence[Container],
tip_racks: Sequence[TipRack],
*,
use_channels: Optional[List[int]] = None,
asp_vols: Union[List[float], float],
dis_vols: Union[List[float], float],
asp_flow_rates: Optional[List[Optional[float]]] = None,
dis_flow_rates: Optional[List[Optional[float]]] = None,
offsets: Optional[List[Coordinate]] = None,
@@ -179,7 +188,7 @@ class DPLiquidHandler(LiquidHandler):
mix_rate: Optional[int] = None,
mix_liquid_height: Optional[float] = None,
delays: Optional[List[int]] = None,
none_keys: List[str] = []
none_keys: List[str] = [],
):
"""Transfer liquid from each *source* well/plate to the corresponding *target*.
@@ -201,14 +210,15 @@ class DPLiquidHandler(LiquidHandler):
# 96channel head mode
# ------------------------------------------------------------------
if is_96_well:
pass # This mode is not verified
pass # This mode is not verified
else:
if not (len(asp_vols) == len(sources) and len(dis_vols) == len(targets)):
raise ValueError("`sources`, `targets`, and `vols` must have the same length.")
tip_iter = self.iter_tips(tip_racks)
for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in (
zip(sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates)):
for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in zip(
sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates
):
tip = next(tip_iter)
await self.pick_up_tips(tip)
# Aspirate from source
@@ -247,9 +257,9 @@ class DPLiquidHandler(LiquidHandler):
except Exception as exc:
raise RuntimeError(f"Liquid transfer failed: {exc}") from exc
# ---------------------------------------------------------------
# Helper utilities
# ---------------------------------------------------------------
# ---------------------------------------------------------------
# Helper utilities
# ---------------------------------------------------------------
async def custom_delay(self, seconds=0, msg=None):
"""
@@ -266,28 +276,26 @@ class DPLiquidHandler(LiquidHandler):
print(f"Done: {msg}")
print(f"Current time: {time.strftime('%H:%M:%S')}")
async def touch_tip(self,
targets: Sequence[Container],
):
async def touch_tip(self, targets: Sequence[Container]):
"""Touch the tip to the side of the well."""
await self.aspirate(
resources=[targets],
vols=[0],
use_channels=None,
flow_rates=None,
offsets=[Coordinate(x=-targets.get_size_x()/2,y=0,z=0)],
offsets=[Coordinate(x=-targets.get_size_x() / 2, y=0, z=0)],
liquid_height=None,
blow_out_air_volume=None
blow_out_air_volume=None,
)
#await self.custom_delay(seconds=1) # In the simulation, we do not need to wait
# await self.custom_delay(seconds=1) # In the simulation, we do not need to wait
await self.aspirate(
resources=[targets],
vols=[0],
use_channels=None,
flow_rates=None,
offsets=[Coordinate(x=targets.get_size_x()/2,y=0,z=0)],
offsets=[Coordinate(x=targets.get_size_x() / 2, y=0, z=0)],
liquid_height=None,
blow_out_air_volume=None
blow_out_air_volume=None,
)
async def mix(
@@ -298,9 +306,9 @@ class DPLiquidHandler(LiquidHandler):
height_to_bottom: Optional[float] = None,
offsets: Optional[Coordinate] = None,
mix_rate: Optional[float] = None,
none_keys: List[str] = []
none_keys: List[str] = [],
):
if mix_time is None: # No mixing required
if mix_time is None: # No mixing required
return
"""Mix the liquid in the target wells."""
for _ in range(mix_time):
@@ -333,7 +341,7 @@ class DPLiquidHandler(LiquidHandler):
tip_iter = self.iter_tips(tip_racks)
self.current_tip = tip_iter
async def move_to(self, well: Well, dis_to_top: float = 0 , channel: int = 0):
async def move_to(self, well: Well, dis_to_top: float = 0, channel: int = 0):
"""
Move a single channel to a specific well with a given z-height.
@@ -352,4 +360,3 @@ class DPLiquidHandler(LiquidHandler):
await self.move_channel_x(channel, abs_loc.x)
await self.move_channel_y(channel, abs_loc.y)
await self.move_channel_z(channel, abs_loc.z + well_height + dis_to_top)

View File

@@ -0,0 +1,154 @@
import json
from typing import Sequence, Optional, List, Union, Literal
json_path = "/Users/guangxinzhang/Documents/Deep Potential/opentrons/convert/protocols/enriched_steps/sci-lucif-assay4.json"
with open(json_path, "r") as f:
data = json.load(f)
transfer_example = data[0]
#print(transfer_example)
temp_protocol = []
TipLocation = "BC1025F" # Assuming this is a fixed tip location for the transfer
sources = transfer_example["sources"] # Assuming sources is a list of Container objects
targets = transfer_example["targets"] # Assuming targets is a list of Container objects
tip_racks = transfer_example["tip_racks"] # Assuming tip_racks is a list of TipRack objects
asp_vols = transfer_example["asp_vols"] # Assuming asp_vols is a list of volumes
solvent = "PBS"
def transfer_liquid(
#self,
sources,#: Sequence[Container],
targets,#: Sequence[Container],
tip_racks,#: Sequence[TipRack],
TipLocation,
# *,
# use_channels: Optional[List[int]] = None,
asp_vols: Union[List[float], float],
solvent: Optional[str] = None,
# dis_vols: Union[List[float], float],
# asp_flow_rates: Optional[List[Optional[float]]] = None,
# dis_flow_rates: Optional[List[Optional[float]]] = None,
# offsets,#: Optional[List[]] = None,
# touch_tip: bool = False,
# liquid_height: Optional[List[Optional[float]]] = None,
# blow_out_air_volume: Optional[List[Optional[float]]] = None,
# spread: Literal["wide", "tight", "custom"] = "wide",
# is_96_well: bool = False,
# mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
# mix_times,#: Optional[list() = None,
# mix_vol: Optional[int] = None,
# mix_rate: Optional[int] = None,
# mix_liquid_height: Optional[float] = None,
# delays: Optional[List[int]] = None,
# none_keys: List[str] = []
):
# -------- Build Biomek transfer step --------
# 1) Construct default parameter scaffold (values mirror Biomek “Transfer” block).
transfer_params = {
"Span8": False,
"Pod": "Pod1",
"items": {}, # to be filled below
"Wash": False,
"Dynamic?": True,
"AutoSelectActiveWashTechnique": False,
"ActiveWashTechnique": "",
"ChangeTipsBetweenDests": False,
"ChangeTipsBetweenSources": False,
"DefaultCaption": "", # filled after we know first pair/vol
"UseExpression": False,
"LeaveTipsOn": False,
"MandrelExpression": "",
"Repeats": "1",
"RepeatsByVolume": False,
"Replicates": "1",
"ShowTipHandlingDetails": False,
"ShowTransferDetails": True,
"Solvent": "Water",
"Span8Wash": False,
"Span8WashVolume": "2",
"Span8WasteVolume": "1",
"SplitVolume": False,
"SplitVolumeCleaning": False,
"Stop": "Destinations",
"TipLocation": "BC1025F",
"UseCurrentTips": False,
"UseDisposableTips": True,
"UseFixedTips": False,
"UseJIT": True,
"UseMandrelSelection": True,
"UseProbes": [True, True, True, True, True, True, True, True],
"WashCycles": "1",
"WashVolume": "110%",
"Wizard": False
}
items: dict = {}
for idx, (src, dst) in enumerate(zip(sources, targets)):
items[str(idx)] = {
"Source": str(src),
"Destination": str(dst),
"Volume": asp_vols[idx]
}
transfer_params["items"] = items
transfer_params["Solvent"] = solvent if solvent else "Water"
transfer_params["TipLocation"] = TipLocation
if len(tip_racks) == 1:
transfer_params['UseCurrentTips'] = True
elif len(tip_racks) > 1:
transfer_params["ChangeTipsBetweenDests"] = True
return transfer_params
action = transfer_liquid(sources=sources,targets=targets,tip_racks=tip_racks, asp_vols=asp_vols,solvent = solvent, TipLocation=TipLocation)
print(json.dumps(action,indent=2))
# print(action)
"""
"transfer": {
"items": {},
"Wash": false,
"Dynamic?": true,
"AutoSelectActiveWashTechnique": false,
"ActiveWashTechnique": "",
"ChangeTipsBetweenDests": true,
"ChangeTipsBetweenSources": false,
"DefaultCaption": "Transfer 100 µL from P13 to P3",
"UseExpression": false,
"LeaveTipsOn": false,
"MandrelExpression": "",
"Repeats": "1",
"RepeatsByVolume": false,
"Replicates": "1",
"ShowTipHandlingDetails": true,
"ShowTransferDetails": true,
"Span8Wash": false,
"Span8WashVolume": "2",
"Span8WasteVolume": "1",
"SplitVolume": false,
"SplitVolumeCleaning": false,
"Stop": "Destinations",
"TipLocation": "BC1025F",
"UseCurrentTips": false,
"UseDisposableTips": false,
"UseFixedTips": false,
"UseJIT": true,
"UseMandrelSelection": true,
"UseProbes": [true, true, true, true, true, true, true, true],
"WashCycles": "3",
"WashVolume": "110%",
"Wizard": false
"""

File diff suppressed because it is too large Load Diff

View File

@@ -5,22 +5,22 @@ class SolenoidValveMock:
def __init__(self, port: str = "COM6"):
self._status = "Idle"
self._valve_position = "OPEN"
@property
def status(self) -> str:
return self._status
@property
def valve_position(self) -> str:
return self._valve_position
def get_valve_position(self) -> str:
return self._valve_position
def set_valve_position(self, position):
self._status = "Busy"
time.sleep(5)
self._valve_position = position
time.sleep(5)
self._status = "Idle"

View File

@@ -4,17 +4,17 @@ import time
class VacuumPumpMock:
def __init__(self, port: str = "COM6"):
self._status = "OPEN"
@property
def status(self) -> str:
return self._status
def get_status(self) -> str:
return self._status
def set_status(self, position):
time.sleep(5)
self._status = position
time.sleep(5)

View File

@@ -1,11 +1,97 @@
liquid_handler:
description: Liquid handler device controlled by pylabrobot
icon: icon_yiyezhan.webp
class:
module: pylabrobot.liquid_handling:LiquidHandler
module: unilabos.devices.liquid_handling.liquid_handler_abstract:LiquidHandlerAbstract
type: python
status_types:
name: String
action_value_mappings:
remove:
type: LiquidHandlerRemove
goal:
vols: vols
sources: sources
waste_liquid: waste_liquid
use_channels: use_channels
flow_rates: flow_rates
offsets: offsets
liquid_height: liquid_height
blow_out_air_volume: blow_out_air_volume
spread: spread
delays: delays
is_96_well: is_96_well
top: top
none_keys: none_keys
feedback: {}
result: {}
add_liquid:
type: LiquidHandlerAdd
goal:
asp_vols: asp_vols
dis_vols: dis_vols
reagent_sources: reagent_sources
targets: targets
use_channels: use_channels
flow_rates: flow_rates
offsets: offsets
liquid_height: liquid_height
blow_out_air_volume: blow_out_air_volume
spread: spread
is_96_well: is_96_well
mix_time: mix_time
mix_vol: mix_vol
mix_rate: mix_rate
mix_liquid_height: mix_liquid_height
none_keys: none_keys
feedback: {}
result: {}
transfer_liquid:
type: LiquidHandlerTransfer
goal:
asp_vols: asp_vols
dis_vols: dis_vols
sources: sources
targets: targets
tip_racks: tip_racks
use_channels: use_channels
asp_flow_rates: asp_flow_rates
dis_flow_rates: dis_flow_rates
offsets: offsets
touch_tip: touch_tip
liquid_height: liquid_height
blow_out_air_volume: blow_out_air_volume
spread: spread
is_96_well: is_96_well
mix_stage: mix_stage
mix_times: mix_times
mix_vol: mix_vol
mix_rate: mix_rate
mix_liquid_height: mix_liquid_height
delays: delays
none_keys: none_keys
feedback: {}
result: {}
mix:
type: LiquidHandlerMix
goal:
targets: targets
mix_time: mix_time
mix_vol: mix_vol
height_to_bottom: height_to_bottom
offsets: offsets
mix_rate: mix_rate
none_keys: none_keys
feedback: {}
result: {}
move_to:
type: LiquidHandlerMoveTo
goal:
well: well
dis_to_top: dis_to_top
channel: channel
feedback: {}
result: {}
aspirate:
type: LiquidHandlerAspirate
goal:
@@ -160,6 +246,21 @@ liquid_handler:
target_vols: target_vols
aspiration_flow_rate: aspiration_flow_rate
dispense_flow_rates: dispense_flow_rates
handles:
input:
- handler_key: liquid-input
label: Liquid Input
data_type: resource
io_type: target
data_source: handle
data_key: liquid
output:
- handler_key: liquid-output
label: Liquid Output
data_type: resource
io_type: source
data_source: executor
data_key: liquid
schema:
type: object
properties:
@@ -170,55 +271,51 @@ liquid_handler:
- name
additionalProperties: false
dp_liquid_handler:
description: 通用液体处理
liquid_handler.revvity:
class:
module: unilabos.devices.liquid_handling.action_definition:DPLiquidHandler
module: unilabos.devices.liquid_handling.revvity:Revvity
type: python
status_types:
status: String
action_value_mappings:
remove_liquid:
type: DPLiquidHandlerRemoveLiquid
run:
type: WorkStationRun
goal:
vols: vols
sources: sources
waste_liquid: waste_liquid
use_channels: use_channels
flow_rates: flow_rates
offsets: offsets
liquid_height: liquid_height
blow_out_air_volume: blow_out_air_volume
spread: spread
delays: delays
is_96_well: is_96_well
top: top
wf_name: file_path
params: params
resource: resource
feedback:
status: status
result:
success: success
liquid_handler.biomek:
description: Biomek液体处理器设备基于pylabrobot控制
icon: icon_yiyezhan.webp
class:
module: unilabos.devices.liquid_handling.biomek:LiquidHandlerBiomek
type: python
status_types: {}
action_value_mappings:
create_protocol:
type: LiquidHandlerProtocolCreation
goal:
protocol_name: protocol_name
protocol_description: protocol_description
protocol_version: protocol_version
protocol_author: protocol_author
protocol_date: protocol_date
protocol_type: protocol_type
none_keys: none_keys
feedback: {}
result: {}
add_liquid:
type: DPLiquidHandlerAddLiquid
goal:
asp_vols: asp_vols
dis_vols: dis_vols
reagent_sources: reagent_sources
targets: targets
use_channels: use_channels
flow_rates: flow_rates
offsets: offsets
liquid_height: liquid_height
blow_out_air_volume: blow_out_air_volume
spread: spread
is_96_well: is_96_well
mix_time: mix_time
mix_vol: mix_vol
mix_rate: mix_rate
mix_liquid_height: mix_liquid_height
none_keys: none_keys
run_protocol:
type: EmptyIn
goal: {}
feedback: {}
result: {}
transfer_liquid:
type: DPLiquidHandlerTransferLiquid
type: LiquidHandlerTransfer
goal:
asp_vols: asp_vols
dis_vols: dis_vols
@@ -243,68 +340,19 @@ dp_liquid_handler:
none_keys: none_keys
feedback: {}
result: {}
custom_delay:
type: DPLiquidHandlerCustomDelay
transfer_biomek:
type: LiquidHandlerTransferBiomek
goal:
seconds: seconds
msg: msg
feedback: {}
result: {}
touch_tip:
type: DPLiquidHandlerTouchTip
goal:
targets: targets
feedback: {}
result: {}
mix:
type: DPLiquidHandlerMix
goal:
targets: targets
mix_time: mix_time
mix_vol: mix_vol
height_to_bottom: height_to_bottom
offsets: offsets
mix_rate: mix_rate
none_keys: none_keys
feedback: {}
result: {}
set_tiprack:
type: DPLiquidHandlerSetTiprack
goal:
tip_racks: tip_racks
feedback: {}
result: {}
move_to:
type: DPLiquidHandlerMoveTo
goal:
well: well
dis_to_top: dis_to_top
channel: channel
source: source,
target: target,
tip_rack: tip_rack,
volume: volume,
aspirate_techniques: aspirate_techniques,
dispense_techniques: dispense_techniques,
feedback: {}
result: {}
schema:
type: object
properties:
name:
type: string
description: 物料名
required:
- name
liquid_handler.revvity:
class:
module: unilabos.devices.liquid_handling.revvity:Revvity
type: python
status_types:
status: String
action_value_mappings:
run:
type: WorkStationRun
goal:
wf_name: file_path
params: params
resource: resource
feedback:
status: status
result:
success: success
properties: {}
required: []
additionalProperties: false

View File

@@ -12,7 +12,7 @@ separator.homemade:
goal:
stir_time: stir_time,
stir_speed: stir_speed
settling_time": settling_time
settling_time: settling_time
feedback:
status: status
result:

View File

@@ -23,20 +23,51 @@ syringe_pump_with_valve.runze:
type: string
description: The position of the valve
required:
- status
- position
- valve_position
- status
- position
- valve_position
additionalProperties: false
solenoid_valve.mock:
description: Mock solenoid valve
class:
module: unilabos.devices.pump_and_valve.solenoid_valve_mock:SolenoidValveMock
type: python
status_types:
status: String
valve_position: String
action_value_mappings:
open:
type: EmptyIn
goal: {}
feedback: {}
result: {}
close:
type: EmptyIn
goal: {}
feedback: {}
result: {}
handles:
input:
- handler_key: fluid-input
label: Fluid Input
data_type: fluid
output:
- handler_key: fluid-output
label: Fluid Output
data_type: fluid
init_param_schema:
type: object
properties:
port:
type: string
description: "通信端口"
default: "COM6"
required:
- port
solenoid_valve:
description: Solenoid valve
class:
module: unilabos.devices.pump_and_valve.solenoid_valve:SolenoidValve
type: python
type: python

View File

@@ -3,9 +3,95 @@ vacuum_pump.mock:
class:
module: unilabos.devices.pump_and_valve.vacuum_pump_mock:VacuumPumpMock
type: python
status_types:
status: String
action_value_mappings:
open:
type: EmptyIn
goal: {}
feedback: {}
result: {}
close:
type: EmptyIn
goal: {}
feedback: {}
result: {}
set_status:
type: StrSingleInput
goal:
string: string
feedback: {}
result: {}
handles:
input:
- handler_key: fluid-input
label: Fluid Input
data_type: fluid
io_type: target
data_source: handle
data_key: fluid_in
output:
- handler_key: fluid-output
label: Fluid Output
data_type: fluid
io_type: source
data_source: executor
data_key: fluid_out
init_param_schema:
type: object
properties:
port:
type: string
description: "通信端口"
default: "COM6"
required:
- port
gas_source.mock:
description: Mock gas source
class:
module: unilabos.devices.pump_and_valve.vacuum_pump_mock:VacuumPumpMock
type: python
status_types:
status: String
action_value_mappings:
open:
type: EmptyIn
goal: {}
feedback: {}
result: {}
close:
type: EmptyIn
goal: {}
feedback: {}
result: {}
set_status:
type: StrSingleInput
goal:
string: string
feedback: {}
result: {}
handles:
input:
- handler_key: fluid-input
label: Fluid Input
data_type: fluid
io_type: target
data_source: handle
data_key: fluid_in
output:
- handler_key: fluid-output
label: Fluid Output
data_type: fluid
io_type: source
data_source: executor
data_key: fluid_out
init_param_schema:
type: object
properties:
port:
type: string
description: "通信端口"
default: "COM6"
required:
- port

View File

@@ -4,4 +4,4 @@ workstation:
module: unilabos.ros.nodes.presets.protocol_node:ROS2ProtocolNode
type: ros2
schema:
properties: {}
properties: {}

View File

@@ -1,5 +1,4 @@
import io
import json
import os
import sys
from pathlib import Path
@@ -7,10 +6,9 @@ from typing import Any
import yaml
from unilabos.utils import logger
from unilabos.ros.msgs.message_converter import msg_converter_manager, ros_action_to_json_schema
from unilabos.utils import logger
from unilabos.utils.decorator import singleton
from unilabos.utils.type_check import TypeEncoder
DEFAULT_PATHS = [Path(__file__).absolute().parent]
@@ -21,43 +19,14 @@ class Registry:
self.registry_paths = DEFAULT_PATHS.copy() # 使用copy避免修改默认值
if registry_paths:
self.registry_paths.extend(registry_paths)
action_type = self._replace_type_with_class(
"ResourceCreateFromOuter", "host_node", f"动作 add_resource_from_outer"
self.ResourceCreateFromOuter = self._replace_type_with_class(
"ResourceCreateFromOuter", "host_node", f"动作 create_resource_detailed"
)
schema = ros_action_to_json_schema(action_type)
self.device_type_registry = {
"host_node": {
"description": "UniLabOS主机节点",
"class": {
"module": "unilabos.ros.nodes.presets.host_node",
"type": "python",
"status_types": {},
"action_value_mappings": {
"add_resource_from_outer": {
"type": msg_converter_manager.search_class("ResourceCreateFromOuter"),
"goal": {
"resources": "resources",
"device_ids": "device_ids",
"bind_parent_ids": "bind_parent_ids",
"bind_locations": "bind_locations",
"other_calling_params": "other_calling_params",
},
"feedback": {},
"result": {
"success": "success"
},
"schema": schema
}
}
},
"schema": {
"properties": {},
"additionalProperties": False,
"type": "object"
},
"file_path": "/"
}
}
self.ResourceCreateFromOuterEasy = self._replace_type_with_class(
"ResourceCreateFromOuterEasy", "host_node", f"动作 create_resource"
)
self.EmptyIn = self._replace_type_with_class("EmptyIn", "host_node", f"")
self.device_type_registry = {}
self.resource_type_registry = {}
self._setup_called = False # 跟踪setup是否已调用
# 其他状态变量
@@ -69,9 +38,72 @@ class Registry:
logger.critical("[UniLab Registry] setup方法已被调用过不允许多次调用")
return
# 标记setup已被调用
self._setup_called = True
from unilabos.app.web.utils.action_utils import get_yaml_from_goal_type
self.device_type_registry.update(
{
"host_node": {
"description": "UniLabOS主机节点",
"class": {
"module": "unilabos.ros.nodes.presets.host_node",
"type": "python",
"status_types": {},
"action_value_mappings": {
"create_resource_detailed": {
"type": self.ResourceCreateFromOuter,
"goal": {
"resources": "resources",
"device_ids": "device_ids",
"bind_parent_ids": "bind_parent_ids",
"bind_locations": "bind_locations",
"other_calling_params": "other_calling_params",
},
"feedback": {},
"result": {"success": "success"},
"schema": ros_action_to_json_schema(self.ResourceCreateFromOuter),
"goal_default": yaml.safe_load(
io.StringIO(get_yaml_from_goal_type(self.ResourceCreateFromOuter.Goal))
),
},
"create_resource": {
"type": self.ResourceCreateFromOuterEasy,
"goal": {
"res_id": "res_id",
"class_name": "class_name",
"parent": "parent",
"device_id": "device_id",
"bind_locations": "bind_locations",
"liquid_input_slot": "liquid_input_slot[]",
"liquid_type": "liquid_type[]",
"liquid_volume": "liquid_volume[]",
"slot_on_deck": "slot_on_deck",
},
"feedback": {},
"result": {"success": "success"},
"schema": ros_action_to_json_schema(self.ResourceCreateFromOuterEasy),
"goal_default": yaml.safe_load(
io.StringIO(get_yaml_from_goal_type(self.ResourceCreateFromOuterEasy.Goal))
),
},
"test_latency": {
"type": self.EmptyIn,
"goal": {},
"feedback": {},
"result": {"latency_ms": "latency_ms", "time_diff_ms": "time_diff_ms"},
"schema": ros_action_to_json_schema(self.EmptyIn),
"goal_default": {},
},
},
},
"icon": "icon_device.webp",
"registry_type": "device",
"handles": [],
"init_param_schema": {},
"schema": {"properties": {}, "additionalProperties": False, "type": "object"},
"file_path": "/",
}
}
)
logger.debug(f"[UniLab Registry] ----------Setup----------")
self.registry_paths = [Path(path).absolute() for path in self.registry_paths]
for i, path in enumerate(self.registry_paths):
@@ -81,6 +113,8 @@ class Registry:
self.load_device_types(path)
self.load_resource_types(path)
logger.info("[UniLab Registry] 注册表设置完成")
# 标记setup已被调用
self._setup_called = True
def load_resource_types(self, path: os.PathLike):
abs_path = Path(path).absolute()
@@ -96,6 +130,13 @@ class Registry:
resource_info["file_path"] = str(file.absolute()).replace("\\", "/")
if "description" not in resource_info:
resource_info["description"] = ""
if "icon" not in resource_info:
resource_info["icon"] = ""
if "handles" not in resource_info:
resource_info["handles"] = []
if "init_param_schema" not in resource_info:
resource_info["init_param_schema"] = {}
resource_info["registry_type"] = "resource"
self.resource_type_registry.update(data)
logger.debug(
f"[UniLab Registry] Resource-{current_resource_number} File-{i+1}/{len(files)} "
@@ -145,6 +186,7 @@ class Registry:
)
current_device_number = len(self.device_type_registry) + 1
from unilabos.app.web.utils.action_utils import get_yaml_from_goal_type
for i, file in enumerate(files):
data = yaml.safe_load(open(file, encoding="utf-8"))
if data:
@@ -154,6 +196,13 @@ class Registry:
device_config["file_path"] = str(file.absolute()).replace("\\", "/")
if "description" not in device_config:
device_config["description"] = ""
if "icon" not in device_config:
device_config["icon"] = ""
if "handles" not in device_config:
device_config["handles"] = []
if "init_param_schema" not in device_config:
device_config["init_param_schema"] = {}
device_config["registry_type"] = "device"
if "class" in device_config:
# 处理状态类型
if "status_types" in device_config["class"]:
@@ -169,8 +218,15 @@ class Registry:
action_config["type"] = self._replace_type_with_class(
action_config["type"], device_id, f"动作 {action_name}"
)
action_config["goal_default"] = yaml.safe_load(io.StringIO(get_yaml_from_goal_type(action_config["type"].Goal)))
action_config["schema"] = ros_action_to_json_schema(action_config["type"])
if action_config["type"] is not None:
action_config["goal_default"] = yaml.safe_load(
io.StringIO(get_yaml_from_goal_type(action_config["type"].Goal))
)
action_config["schema"] = ros_action_to_json_schema(action_config["type"])
else:
logger.warning(
f"[UniLab Registry] 设备 {device_id} 的动作 {action_name} 类型为空,跳过替换"
)
self.device_type_registry.update(data)
@@ -188,13 +244,17 @@ class Registry:
def obtain_registry_device_info(self):
devices = []
for device_id, device_info in self.device_type_registry.items():
msg = {
"id": device_id,
**device_info
}
msg = {"id": device_id, **device_info}
devices.append(msg)
return devices
def obtain_registry_resource_info(self):
resources = []
for resource_id, resource_info in self.resource_type_registry.items():
msg = {"id": resource_id, **resource_info}
resources.append(msg)
return resources
# 全局单例实例
lab_registry = Registry()

View File

@@ -1,35 +1,35 @@
agilent_1_reservoir_290ml:
description: Agilent 1 reservoir 290ml
class:
module: pylabrobot.resources.opentrons.reserviors:agilent_1_reservoir_290ml
module: pylabrobot.resources.opentrons.reservoirs:agilent_1_reservoir_290ml
type: pylabrobot
axygen_1_reservoir_90ml:
description: Axygen 1 reservoir 90ml
class:
module: pylabrobot.resources.opentrons.reserviors:axygen_1_reservoir_90ml
module: pylabrobot.resources.opentrons.reservoirs:axygen_1_reservoir_90ml
type: pylabrobot
nest_12_reservoir_15ml:
description: Nest 12 reservoir 15ml
class:
module: pylabrobot.resources.opentrons.reserviors:nest_12_reservoir_15ml
module: pylabrobot.resources.opentrons.reservoirs:nest_12_reservoir_15ml
type: pylabrobot
nest_1_reservoir_195ml:
description: Nest 1 reservoir 195ml
class:
module: pylabrobot.resources.opentrons.reserviors:nest_1_reservoir_195ml
module: pylabrobot.resources.opentrons.reservoirs:nest_1_reservoir_195ml
type: pylabrobot
nest_1_reservoir_290ml:
description: Nest 1 reservoir 290ml
class:
module: pylabrobot.resources.opentrons.reserviors:nest_1_reservoir_290ml
module: pylabrobot.resources.opentrons.reservoirs:nest_1_reservoir_290ml
type: pylabrobot
usascientific_12_reservoir_22ml:
description: USAScientific 12 reservoir 22ml
class:
module: pylabrobot.resources.opentrons.reserviors:usascientific_12_reservoir_22ml
module: pylabrobot.resources.opentrons.reservoirs:usascientific_12_reservoir_22ml
type: pylabrobot

View File

@@ -189,6 +189,7 @@ def dict_from_graph(graph: nx.Graph) -> dict:
def dict_to_tree(nodes: dict, devices_only: bool = False) -> list[dict]:
# 将节点转换为字典,以便通过 ID 快速查找
nodes_list = [node for node in nodes.values() if node.get("type") == "device" or not devices_only]
id_list = [node["id"] for node in nodes_list]
# 初始化每个节点的 children 为包含节点字典的列表
for node in nodes_list:
@@ -196,7 +197,7 @@ def dict_to_tree(nodes: dict, devices_only: bool = False) -> list[dict]:
# 找到根节点并返回
root_nodes = [
node for node in nodes_list if len(nodes_list) == 1 or node.get("parent", node.get("parent_name")) in [None, "", "None", np.nan]
node for node in nodes_list if len(nodes_list) == 1 or node.get("parent", node.get("parent_name")) in [None, "", "None", np.nan] or node.get("parent", node.get("parent_name")) not in id_list
]
# 如果存在多个根节点,返回所有根节点
@@ -421,7 +422,7 @@ def resource_plr_to_ulab(resource_plr: "ResourcePLR", parent_name: str = None):
return r
def initialize_resource(resource_config: dict, lab_registry: dict) -> list[dict]:
def initialize_resource(resource_config: dict) -> list[dict]:
"""Initializes a resource based on its configuration.
If the config is detailed, then do nothing;
@@ -433,6 +434,7 @@ def initialize_resource(resource_config: dict, lab_registry: dict) -> list[dict]
Returns:
None
"""
from unilabos.registry.registry import lab_registry
resource_class_config = resource_config.get("class", None)
if resource_class_config is None:
return [resource_config]
@@ -476,11 +478,8 @@ def initialize_resources(resources_config) -> list[dict]:
None
"""
from unilabos.registry.registry import lab_registry
resources = []
for resource_config in resources_config:
if resource_config["parent"] == "tip_rack" or resource_config["parent"] == "plate_well":
continue
resources.extend(initialize_resource(resource_config, lab_registry))
resources.extend(initialize_resource(resource_config))
return resources

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@@ -131,7 +131,7 @@ _msg_converter: Dict[Type, Any] = {
Bool: lambda x: Bool(data=bool(x)),
str: str,
String: lambda x: String(data=str(x)),
Point: lambda x: Point(x=x.x, y=x.y, z=x.z),
Point: lambda x: Point(x=x.x, y=x.y, z=x.z) if not isinstance(x, dict) else Point(x=x.get("x", 0), y=x.get("y", 0), z=x.get("z", 0)),
Resource: lambda x: Resource(
id=x.get("id", ""),
name=x.get("name", ""),
@@ -348,10 +348,16 @@ def convert_to_ros_msg(ros_msg_type: Union[Type, Any], obj: Any) -> Any:
if isinstance(td, NamespacedType):
target_class = msg_converter_manager.get_class(f"{'.'.join(td.namespaces)}.{td.name}")
setattr(ros_msg, key, [convert_to_ros_msg(target_class, v) for v in value])
elif isinstance(td, UnboundedString):
setattr(ros_msg, key, value)
else:
logger.warning(f"Not Supported type: {td}")
setattr(ros_msg, key, []) # FIXME
elif "array.array" in str(type(attr)):
setattr(ros_msg, key, value)
if attr.typecode == "f":
setattr(ros_msg, key, [float(i) for i in value])
else:
setattr(ros_msg, key, value)
else:
nested_ros_msg = convert_to_ros_msg(type(attr)(), value)
setattr(ros_msg, key, nested_ros_msg)
@@ -574,6 +580,7 @@ basic_type_map = {
'int64': {'type': 'integer'},
'uint64': {'type': 'integer', 'minimum': 0},
'double': {'type': 'number'},
'float': {'type': 'number'},
'float32': {'type': 'number'},
'float64': {'type': 'number'},
'string': {'type': 'string'},

View File

@@ -1,3 +1,5 @@
import copy
import functools
import json
import threading
import time
@@ -19,7 +21,7 @@ from unilabos_msgs.action import SendCmd
from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response
from unilabos.resources.graphio import convert_resources_to_type, convert_resources_from_type, resource_ulab_to_plr, \
initialize_resources
initialize_resources, list_to_nested_dict, dict_to_tree, resource_plr_to_ulab, tree_to_list
from unilabos.ros.msgs.message_converter import (
convert_to_ros_msg,
convert_from_ros_msg,
@@ -311,7 +313,10 @@ class BaseROS2DeviceNode(Node, Generic[T]):
# 物料传输到对应的node节点
rclient = self.create_client(ResourceAdd, "/resources/add")
rclient.wait_for_service()
rclient2 = self.create_client(ResourceAdd, "/resources/add")
rclient2.wait_for_service()
request = ResourceAdd.Request()
request2 = ResourceAdd.Request()
command_json = json.loads(req.command)
namespace = command_json["namespace"]
bind_parent_id = command_json["bind_parent_id"]
@@ -320,11 +325,23 @@ class BaseROS2DeviceNode(Node, Generic[T]):
other_calling_param = command_json["other_calling_param"]
resources = command_json["resource"]
initialize_full = other_calling_param.pop("initialize_full", False)
# 用来增加液体
ADD_LIQUID_TYPE = other_calling_param.pop("ADD_LIQUID_TYPE", [])
LIQUID_VOLUME = other_calling_param.pop("LIQUID_VOLUME", [])
LIQUID_INPUT_SLOT = other_calling_param.pop("LIQUID_INPUT_SLOT", [])
slot = other_calling_param.pop("slot", -1)
if slot >= 0: # slot为负数的时候采用assign方法
other_calling_param["slot"] = slot
# 本地拿到这个物料,可能需要先做初始化?
if isinstance(resources, list):
if initialize_full:
if len(resources) == 1 and isinstance(resources[0], list) and not initialize_full: # 取消,不存在的情况
# 预先initialize过以整组的形式传入
request.resources = [convert_to_ros_msg(Resource, resource_) for resource_ in resources[0]]
elif initialize_full:
resources = initialize_resources(resources)
request.resources = [convert_to_ros_msg(Resource, resource) for resource in resources]
request.resources = [convert_to_ros_msg(Resource, resource) for resource in resources]
else:
request.resources = [convert_to_ros_msg(Resource, resource) for resource in resources]
else:
if initialize_full:
resources = initialize_resources([resources])
@@ -332,22 +349,47 @@ class BaseROS2DeviceNode(Node, Generic[T]):
response = rclient.call(request)
# 应该先add_resource了
res.response = "OK"
# 如果driver自己就有assign的方法那就使用driver自己的assign方法
if hasattr(self.driver_instance, "create_resource"):
create_resource_func = getattr(self.driver_instance, "create_resource")
create_resource_func(
resource_tracker=self.resource_tracker,
resources=request.resources,
bind_parent_id=bind_parent_id,
bind_location=location,
liquid_input_slot=LIQUID_INPUT_SLOT,
liquid_type=ADD_LIQUID_TYPE,
liquid_volume=LIQUID_VOLUME,
slot_on_deck=slot,
)
return res
# 接下来该根据bind_parent_id进行assign了目前只有plr可以进行assign不然没有办法输入到物料系统中
resource = self.resource_tracker.figure_resource({"name": bind_parent_id})
request.resources = [convert_to_ros_msg(Resource, resources)]
# request.resources = [convert_to_ros_msg(Resource, resources)]
try:
from pylabrobot.resources.resource import Resource as ResourcePLR
from pylabrobot.resources.deck import Deck
from pylabrobot.resources import Coordinate
from pylabrobot.resources import OTDeck
from pylabrobot.resources import Plate
contain_model = not isinstance(resource, Deck)
if isinstance(resource, ResourcePLR):
# resources.list()
plr_instance = resource_ulab_to_plr(resources, contain_model)
resources_tree = dict_to_tree(copy.deepcopy({r["id"]: r for r in resources}))
plr_instance = resource_ulab_to_plr(resources_tree[0], contain_model)
if isinstance(plr_instance, Plate):
empty_liquid_info_in = [(None, 0)] * plr_instance.num_items
for liquid_type, liquid_volume, liquid_input_slot in zip(ADD_LIQUID_TYPE, LIQUID_VOLUME, LIQUID_INPUT_SLOT):
empty_liquid_info_in[liquid_input_slot] = (liquid_type, liquid_volume)
plr_instance.set_well_liquids(empty_liquid_info_in)
if isinstance(resource, OTDeck) and "slot" in other_calling_param:
resource.assign_child_at_slot(plr_instance, **other_calling_param)
resource.assign_child_resource(plr_instance, Coordinate(location["x"], location["y"], location["z"]), **other_calling_param)
else:
_discard_slot = other_calling_param.pop("slot", -1)
resource.assign_child_resource(plr_instance, Coordinate(location["x"], location["y"], location["z"]), **other_calling_param)
request2.resources = [convert_to_ros_msg(Resource, r) for r in tree_to_list([resource_plr_to_ulab(resource)])]
rclient2.call(request2)
# 发送给ResourceMeshManager
action_client = ActionClient(
self, SendCmd, "/devices/resource_mesh_manager/add_resource_mesh", callback_group=self.callback_group
@@ -404,6 +446,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
# 加入全局注册表
registered_devices[self.device_id] = device_info
from unilabos.config.config import BasicConfig
from unilabos.ros.nodes.presets.host_node import HostNode
if not BasicConfig.is_host_mode:
sclient = self.create_client(SerialCommand, "/node_info_update")
# 启动线程执行发送任务
@@ -413,6 +456,10 @@ class BaseROS2DeviceNode(Node, Generic[T]):
daemon=True,
name=f"ROSDevice{self.device_id}_send_slave_node_info"
).start()
else:
host_node = HostNode.get_instance(0)
if host_node is not None:
host_node.device_machine_names[self.device_id] = "本地"
def send_slave_node_info(self, sclient):
sclient.wait_for_service()
@@ -481,6 +528,17 @@ class BaseROS2DeviceNode(Node, Generic[T]):
self.lab_logger().debug(f"发布动作: {action_name}, 类型: {str_action_type}")
def get_real_function(self, instance, attr_name):
if hasattr(instance.__class__, attr_name):
obj = getattr(instance.__class__, attr_name)
if isinstance(obj, property):
return lambda *args, **kwargs: obj.fset(instance, *args, **kwargs), get_type_hints(obj.fset)
obj = getattr(instance, attr_name)
return obj, get_type_hints(obj)
else:
obj = getattr(instance, attr_name)
return obj, get_type_hints(obj)
def _create_execute_callback(self, action_name, action_value_mapping):
"""创建动作执行回调函数"""
@@ -495,22 +553,21 @@ class BaseROS2DeviceNode(Node, Generic[T]):
for i, action in enumerate(self._action_value_mappings["sequence"]):
if i == 0:
self.lab_logger().info(f"执行序列动作第一步: {action}")
getattr(self.driver_instance, action)(**kwargs)
self.get_real_function(self.driver_instance, action)[0](**kwargs)
else:
self.lab_logger().info(f"执行序列动作后续步骤: {action}")
getattr(self.driver_instance, action)()
self.get_real_function(self.driver_instance, action)[0]()
action_paramtypes = get_type_hints(
getattr(self.driver_instance, self._action_value_mappings["sequence"][0])
)
self.get_real_function(self.driver_instance, self._action_value_mappings["sequence"][0])
)[1]
else:
ACTION = getattr(self.driver_instance, action_name)
action_paramtypes = get_type_hints(ACTION)
ACTION, action_paramtypes = self.get_real_function(self.driver_instance, action_name)
action_kwargs = convert_from_ros_msg_with_mapping(goal, action_value_mapping["goal"])
self.lab_logger().debug(f"接收到原始目标: {action_kwargs}")
# 向Host查询物料当前状态如果是host本身的增加物料的请求则直接跳过
if action_name != "add_resource_from_outer":
if action_name not in ["create_resource_detailed", "create_resource"]:
for k, v in goal.get_fields_and_field_types().items():
if v in ["unilabos_msgs/Resource", "sequence<unilabos_msgs/Resource>"]:
self.lab_logger().info(f"查询资源状态: Key: {k} Type: {v}")
@@ -609,7 +666,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
del future
# 向Host更新物料当前状态
if action_name != "add_resource_from_outer":
if action_name not in ["create_resource_detailed", "create_resource"]:
for k, v in goal.get_fields_and_field_types().items():
if v not in ["unilabos_msgs/Resource", "sequence<unilabos_msgs/Resource>"]:
continue
@@ -748,7 +805,9 @@ class ROS2DeviceNode:
self.resource_tracker = DeviceNodeResourceTracker()
# use_pylabrobot_creator 使用 cls的包路径检测
use_pylabrobot_creator = driver_class.__module__.startswith("pylabrobot") or driver_class.__name__ == "DPLiquidHandler"
use_pylabrobot_creator = (driver_class.__module__.startswith("pylabrobot")
or driver_class.__name__ == "LiquidHandlerAbstract"
or driver_class.__name__ == "LiquidHandlerBiomek")
# TODO: 要在创建之前预先请求服务器是否有当前id的物料放到resource_tracker中让pylabrobot进行创建
# 创建设备类实例

View File

@@ -12,11 +12,18 @@ from rclpy.action import ActionClient, get_action_server_names_and_types_by_node
from rclpy.callback_groups import ReentrantCallbackGroup
from rclpy.service import Service
from unilabos_msgs.msg import Resource # type: ignore
from unilabos_msgs.srv import ResourceAdd, ResourceGet, ResourceDelete, ResourceUpdate, ResourceList, \
SerialCommand # type: ignore
from unilabos_msgs.srv import (
ResourceAdd,
ResourceGet,
ResourceDelete,
ResourceUpdate,
ResourceList,
SerialCommand,
) # type: ignore
from unique_identifier_msgs.msg import UUID
from unilabos.registry.registry import lab_registry
from unilabos.resources.graphio import initialize_resource
from unilabos.resources.registry import add_schema
from unilabos.ros.initialize_device import initialize_device_from_dict
from unilabos.ros.msgs.message_converter import (
@@ -86,6 +93,7 @@ class HostNode(BaseROS2DeviceNode):
self.__class__._instance = self
# 初始化配置
self.server_latest_timestamp = 0.0 #
self.devices_config = devices_config
self.resources_config = resources_config
self.physical_setup_graph = physical_setup_graph
@@ -99,9 +107,32 @@ class HostNode(BaseROS2DeviceNode):
# 创建设备、动作客户端和目标存储
self.devices_names: Dict[str, str] = {device_id: self.namespace} # 存储设备名称和命名空间的映射
self.devices_instances: Dict[str, ROS2DeviceNode] = {} # 存储设备实例
self.device_machine_names: Dict[str, str] = {device_id: "本地", } # 存储设备ID到机器名称的映射
self._action_clients: Dict[str, ActionClient] = {} # 用来存储多个ActionClient实例
self._action_value_mappings: Dict[str, Dict] = {} # 用来存储多个ActionClient的type, goal, feedback, result的变量名映射关系
self.device_machine_names: Dict[str, str] = {
device_id: "本地",
} # 存储设备ID到机器名称的映射
self._action_clients: Dict[str, ActionClient] = { # 为了方便了解实际的数据类型host的默认写好
"/devices/host_node/create_resource": ActionClient(
self,
lab_registry.ResourceCreateFromOuterEasy,
"/devices/host_node/create_resource",
callback_group=self.callback_group,
),
"/devices/host_node/create_resource_detailed": ActionClient(
self,
lab_registry.ResourceCreateFromOuter,
"/devices/host_node/create_resource_detailed",
callback_group=self.callback_group,
),
"/devices/host_node/test_latency": ActionClient(
self,
lab_registry.EmptyIn,
"/devices/host_node/test_latency",
callback_group=self.callback_group,
),
} # 用来存储多个ActionClient实例
self._action_value_mappings: Dict[str, Dict] = (
{}
) # 用来存储多个ActionClient的type, goal, feedback, result的变量名映射关系
self._goals: Dict[str, Any] = {} # 用来存储多个目标的状态
self._online_devices: Set[str] = {f"{self.namespace}/{device_id}"} # 用于跟踪在线设备
self._last_discovery_time = 0.0 # 上次设备发现的时间
@@ -115,8 +146,11 @@ class HostNode(BaseROS2DeviceNode):
self.device_status_timestamps = {} # 用来存储设备状态最后更新时间
from unilabos.app.mq import mqtt_client
for device_config in lab_registry.obtain_registry_device_info():
mqtt_client.publish_registry(device_config["id"], device_config)
for device_info in lab_registry.obtain_registry_device_info():
mqtt_client.publish_registry(device_info["id"], device_info)
for resource_info in lab_registry.obtain_registry_resource_info():
mqtt_client.publish_registry(resource_info["id"], resource_info)
# 首次发现网络中的设备
self._discover_devices()
@@ -141,12 +175,36 @@ class HostNode(BaseROS2DeviceNode):
].items():
controller_config["update_rate"] = update_rate
self.initialize_controller(controller_id, controller_config)
resources_config.insert(
0,
{
"id": "host_node",
"name": "host_node",
"parent": None,
"type": "device",
"class": "host_node",
"position": {"x": 0, "y": 0, "z": 0},
"config": {},
"data": {},
"children": [],
},
)
resource_with_parent_name = []
resource_ids_to_instance = {i["id"]: i for i in resources_config}
for res in resources_config:
if res.get("parent") and res.get("type") == "device" and res.get("class"):
parent_id = res.get("parent")
parent_res = resource_ids_to_instance[parent_id]
if parent_res.get("type") == "device" and parent_res.get("class"):
resource_with_parent_name.append(copy.deepcopy(res))
resource_with_parent_name[-1]["id"] = f"{parent_res['id']}/{res['id']}"
continue
resource_with_parent_name.append(copy.deepcopy(res))
try:
for bridge in self.bridges:
if hasattr(bridge, "resource_add"):
self.lab_logger().info("[Host Node-Resource] Adding resources to bridge.")
bridge.resource_add(add_schema(resources_config))
resource_add_res = bridge.resource_add(add_schema(resource_with_parent_name))
except Exception as ex:
self.lab_logger().error("[Host Node-Resource] 添加物料出错!")
self.lab_logger().error(traceback.format_exc())
@@ -156,6 +214,10 @@ class HostNode(BaseROS2DeviceNode):
discovery_interval, self._discovery_devices_callback, callback_group=ReentrantCallbackGroup()
)
# 添加ping-pong相关属性
self._ping_responses = {} # 存储ping响应
self._ping_lock = threading.Lock()
self.lab_logger().info("[Host Node] Host node initialized.")
HostNode._ready_event.set()
@@ -191,7 +253,7 @@ class HostNode(BaseROS2DeviceNode):
# 如果是新设备记录并创建ActionClient
if edge_device_id not in self.devices_names:
self.lab_logger().info(f"[Host Node] Discovered new device: {device_key}")
self.lab_logger().info(f"[Host Node] Discovered new device: {edge_device_id}")
self.devices_names[edge_device_id] = namespace
self._create_action_clients_for_device(device_id, namespace)
self._online_devices.add(device_key)
@@ -200,7 +262,7 @@ class HostNode(BaseROS2DeviceNode):
target=self._send_re_register,
args=(sclient,),
daemon=True,
name=f"ROSDevice{self.device_id}_query_host_name_{namespace}"
name=f"ROSDevice{self.device_id}_query_host_name_{namespace}",
).start()
elif device_key not in self._online_devices:
# 设备重新上线
@@ -211,7 +273,7 @@ class HostNode(BaseROS2DeviceNode):
target=self._send_re_register,
args=(sclient,),
daemon=True,
name=f"ROSDevice{self.device_id}_query_host_name_{namespace}"
name=f"ROSDevice{self.device_id}_query_host_name_{namespace}",
).start()
# 检测离线设备
@@ -255,7 +317,7 @@ class HostNode(BaseROS2DeviceNode):
self, action_type, action_id, callback_group=self.callback_group
)
self.lab_logger().debug(f"[Host Node] Created ActionClient (Discovery): {action_id}")
action_name = action_id[len(namespace) + 1:]
action_name = action_id[len(namespace) + 1 :]
edge_device_id = namespace[9:]
# from unilabos.app.mq import mqtt_client
# info_with_schema = ros_action_to_json_schema(action_type)
@@ -268,30 +330,84 @@ class HostNode(BaseROS2DeviceNode):
except Exception as e:
self.lab_logger().error(f"[Host Node] Failed to create ActionClient for {action_id}: {str(e)}")
def add_resource_from_outer(self, resources: list["Resource"], device_ids: list[str], bind_parent_ids: list[str], bind_locations: list[Point], other_calling_params: list[str]):
for resource, device_id, bind_parent_id, bind_location, other_calling_param in zip(resources, device_ids, bind_parent_ids, bind_locations, other_calling_params):
def create_resource_detailed(
self,
resources: list["Resource"],
device_ids: list[str],
bind_parent_ids: list[str],
bind_locations: list[Point],
other_calling_params: list[str],
):
for resource, device_id, bind_parent_id, bind_location, other_calling_param in zip(
resources, device_ids, bind_parent_ids, bind_locations, other_calling_params
):
# 这里要求device_id传入必须是edge_device_id
namespace = "/devices/" + device_id
srv_address = f"/srv{namespace}/append_resource"
sclient = self.create_client(SerialCommand, srv_address)
sclient.wait_for_service()
request = SerialCommand.Request()
request.command = json.dumps({
"resource": resource,
"namespace": namespace,
"edge_device_id": device_id,
"bind_parent_id": bind_parent_id,
"bind_location": {
"x": bind_location.x,
"y": bind_location.y,
"z": bind_location.z,
request.command = json.dumps(
{
"resource": resource, # 单个/单组 可为 list[list[Resource]]
"namespace": namespace,
"edge_device_id": device_id,
"bind_parent_id": bind_parent_id,
"bind_location": {
"x": bind_location.x,
"y": bind_location.y,
"z": bind_location.z,
},
"other_calling_param": json.loads(other_calling_param) if other_calling_param else {},
},
"other_calling_param": json.loads(other_calling_param) if other_calling_param else {},
}, ensure_ascii=False)
ensure_ascii=False,
)
response = sclient.call(request)
pass
pass
def create_resource(
self,
device_id: str,
res_id: str,
class_name: str,
parent: str,
bind_locations: Point,
liquid_input_slot: list[int],
liquid_type: list[str],
liquid_volume: list[int],
slot_on_deck: int,
):
init_new_res = initialize_resource(
{
"name": res_id,
"class": class_name,
"parent": parent,
"position": {
"x": bind_locations.x,
"y": bind_locations.y,
"z": bind_locations.z,
},
}
) # flatten的格式
resources = init_new_res # initialize_resource已经返回list[dict]
device_ids = [device_id]
bind_parent_id = [parent]
bind_location = [bind_locations]
other_calling_param = [
json.dumps(
{
"ADD_LIQUID_TYPE": liquid_type,
"LIQUID_VOLUME": liquid_volume,
"LIQUID_INPUT_SLOT": liquid_input_slot,
"initialize_full": False,
"slot": slot_on_deck,
}
)
]
return self.create_resource_detailed(resources, device_ids, bind_parent_id, bind_location, other_calling_param)
def initialize_device(self, device_id: str, device_config: Dict[str, Any]) -> None:
"""
根据配置初始化设备,
@@ -319,7 +435,9 @@ class HostNode(BaseROS2DeviceNode):
if action_id not in self._action_clients:
action_type = action_value_mapping["type"]
self._action_clients[action_id] = ActionClient(self, action_type, action_id)
self.lab_logger().debug(f"[Host Node] Created ActionClient (Local): {action_id}") # 子设备再创建用的是Discover发现的
self.lab_logger().debug(
f"[Host Node] Created ActionClient (Local): {action_id}"
) # 子设备再创建用的是Discover发现的
# from unilabos.app.mq import mqtt_client
# info_with_schema = ros_action_to_json_schema(action_type)
# mqtt_client.publish_actions(action_name, {
@@ -419,7 +537,12 @@ class HostNode(BaseROS2DeviceNode):
)
def send_goal(
self, device_id: str, action_name: str, action_kwargs: Dict[str, Any], goal_uuid: Optional[str] = None
self,
device_id: str,
action_name: str,
action_kwargs: Dict[str, Any],
goal_uuid: Optional[str] = None,
server_info: Optional[Dict[str, Any]] = None,
) -> None:
"""
向设备发送目标请求
@@ -431,6 +554,8 @@ class HostNode(BaseROS2DeviceNode):
goal_uuid: 目标UUID如果为None则自动生成
"""
action_id = f"/devices/{device_id}/{action_name}"
if action_name == "test_latency" and server_info is not None:
self.server_latest_timestamp = server_info.get("send_timestamp", 0.0)
if action_id not in self._action_clients:
self.lab_logger().error(f"[Host Node] ActionClient {action_id} not found.")
return
@@ -725,3 +850,148 @@ class HostNode(BaseROS2DeviceNode):
# 这里可以实现返回资源列表的逻辑
self.lab_logger().debug(f"[Host Node-Resource] List parameters: {request}")
return response
def test_latency(self):
"""
测试网络延迟的action实现
通过5次ping-pong机制校对时间误差并计算实际延迟
"""
import time
import uuid as uuid_module
self.lab_logger().info("=" * 60)
self.lab_logger().info("开始网络延迟测试...")
# 记录任务开始执行的时间
task_start_time = time.time()
# 进行5次ping-pong测试
ping_results = []
for i in range(5):
self.lab_logger().info(f"{i+1}/5次ping-pong测试...")
# 生成唯一的ping ID
ping_id = str(uuid_module.uuid4())
# 记录发送时间
send_timestamp = time.time()
# 发送ping
from unilabos.app.mq import mqtt_client
mqtt_client.send_ping(ping_id, send_timestamp)
# 等待pong响应
timeout = 10.0
start_wait_time = time.time()
while time.time() - start_wait_time < timeout:
with self._ping_lock:
if ping_id in self._ping_responses:
pong_data = self._ping_responses.pop(ping_id)
break
time.sleep(0.001)
else:
self.lab_logger().error(f"❌ 第{i+1}次测试超时")
continue
# 计算本次测试结果
receive_timestamp = time.time()
client_timestamp = pong_data["client_timestamp"]
server_timestamp = pong_data["server_timestamp"]
# 往返时间
rtt_ms = (receive_timestamp - send_timestamp) * 1000
# 客户端与服务端时间差(客户端时间 - 服务端时间)
# 假设网络延迟对称,取中间点的服务端时间
mid_point_time = send_timestamp + (receive_timestamp - send_timestamp) / 2
time_diff_ms = (mid_point_time - server_timestamp) * 1000
ping_results.append({"rtt_ms": rtt_ms, "time_diff_ms": time_diff_ms})
self.lab_logger().info(f"✅ 第{i+1}次: 往返时间={rtt_ms:.2f}ms, 时间差={time_diff_ms:.2f}ms")
time.sleep(0.1)
if not ping_results:
self.lab_logger().error("❌ 所有ping-pong测试都失败了")
return {"status": "all_timeout"}
# 统计分析
rtts = [r["rtt_ms"] for r in ping_results]
time_diffs = [r["time_diff_ms"] for r in ping_results]
avg_rtt_ms = sum(rtts) / len(rtts)
avg_time_diff_ms = sum(time_diffs) / len(time_diffs)
max_time_diff_error_ms = max(abs(min(time_diffs)), abs(max(time_diffs)))
self.lab_logger().info("-" * 50)
self.lab_logger().info("[测试统计]")
self.lab_logger().info(f"有效测试次数: {len(ping_results)}/5")
self.lab_logger().info(f"平均往返时间: {avg_rtt_ms:.2f}ms")
self.lab_logger().info(f"平均时间差: {avg_time_diff_ms:.2f}ms")
self.lab_logger().info(f"时间差范围: {min(time_diffs):.2f}ms ~ {max(time_diffs):.2f}ms")
self.lab_logger().info(f"最大时间误差: ±{max_time_diff_error_ms:.2f}ms")
# 计算任务执行延迟
if hasattr(self, "server_latest_timestamp") and self.server_latest_timestamp > 0:
self.lab_logger().info("-" * 50)
self.lab_logger().info("[任务执行延迟分析]")
self.lab_logger().info(f"服务端任务下发时间: {self.server_latest_timestamp:.6f}")
self.lab_logger().info(f"客户端任务开始时间: {task_start_time:.6f}")
# 原始时间差(不考虑时间同步误差)
raw_delay_ms = (task_start_time - self.server_latest_timestamp) * 1000
# 考虑时间同步误差后的延迟(用平均时间差校正)
corrected_delay_ms = raw_delay_ms - avg_time_diff_ms
self.lab_logger().info(f"📊 原始时间差: {raw_delay_ms:.2f}ms")
self.lab_logger().info(f"🔧 时间同步校正: {avg_time_diff_ms:.2f}ms")
self.lab_logger().info(f"⏰ 实际任务延迟: {corrected_delay_ms:.2f}ms")
self.lab_logger().info(f"📏 误差范围: ±{max_time_diff_error_ms:.2f}ms")
# 给出延迟范围
min_delay = corrected_delay_ms - max_time_diff_error_ms
max_delay = corrected_delay_ms + max_time_diff_error_ms
self.lab_logger().info(f"📋 延迟范围: {min_delay:.2f}ms ~ {max_delay:.2f}ms")
else:
self.lab_logger().warning("⚠️ 无法获取服务端任务下发时间,跳过任务延迟分析")
corrected_delay_ms = -1
self.lab_logger().info("=" * 60)
return {
"avg_rtt_ms": avg_rtt_ms,
"avg_time_diff_ms": avg_time_diff_ms,
"max_time_error_ms": max_time_diff_error_ms,
"task_delay_ms": corrected_delay_ms if corrected_delay_ms > 0 else -1,
"raw_delay_ms": (
raw_delay_ms if hasattr(self, "server_latest_timestamp") and self.server_latest_timestamp > 0 else -1
),
"test_count": len(ping_results),
"status": "success",
}
def handle_pong_response(self, pong_data: dict):
"""
处理pong响应
"""
ping_id = pong_data.get("ping_id")
if ping_id:
with self._ping_lock:
self._ping_responses[ping_id] = pong_data
# 详细信息合并为一条日志
client_timestamp = pong_data.get("client_timestamp", 0)
server_timestamp = pong_data.get("server_timestamp", 0)
current_time = time.time()
self.lab_logger().debug(
f"📨 Pong | ID:{ping_id[:8]}.. | C→S→C: {client_timestamp:.3f}{server_timestamp:.3f}{current_time:.3f}"
)
else:
self.lab_logger().warning("⚠️ 收到无效的Pong响应缺少ping_id")

View File

@@ -13,6 +13,7 @@ endif()
if(CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
add_compile_options(-Wall -Wextra -Wpedantic)
add_compile_options(-include cstdint)
endif()
# find dependencies
@@ -28,6 +29,8 @@ set(action_files
"action/HeatChillStart.action"
"action/HeatChillStop.action"
"action/LiquidHandlerProtocolCreation.action"
"action/LiquidHandlerAspirate.action"
"action/LiquidHandlerDiscardTips.action"
"action/LiquidHandlerDispense.action"
@@ -42,15 +45,12 @@ set(action_files
"action/LiquidHandlerReturnTips96.action"
"action/LiquidHandlerStamp.action"
"action/LiquidHandlerTransfer.action"
"action/LiquidHandlerTransferBiomek.action"
"action/DPLiquidHandlerAddLiquid.action"
"action/DPLiquidHandlerCustomDelay.action"
"action/DPLiquidHandlerMix.action"
"action/DPLiquidHandlerMoveTo.action"
"action/DPLiquidHandlerRemoveLiquid.action"
"action/DPLiquidHandlerSetTiprack.action"
"action/DPLiquidHandlerTouchTip.action"
"action/DPLiquidHandlerTransferLiquid.action"
"action/LiquidHandlerAdd.action"
"action/LiquidHandlerMix.action"
"action/LiquidHandlerMoveTo.action"
"action/LiquidHandlerRemove.action"
"action/EmptyIn.action"
"action/FloatSingleInput.action"
@@ -59,9 +59,10 @@ set(action_files
"action/Point3DSeparateInput.action"
"action/ResourceCreateFromOuter.action"
"action/ResourceCreateFromOuterEasy.action"
"action/SolidDispenseAddPowderTube.action"
"action/PumpTransfer.action"
"action/Clean.action"
"action/Separate.action"

View File

@@ -1,6 +0,0 @@
float64 seconds
string msg
---
bool success
---
# 反馈

View File

@@ -1,5 +0,0 @@
Resource[] tip_racks
---
bool success
---
# 反馈

View File

@@ -1,5 +0,0 @@
Resource[] targets
---
bool success
---
# 反馈

View File

@@ -1,25 +0,0 @@
float64[] asp_vols
float64[] dis_vols
Resource[] sources
Resource[] targets
Resource[] tip_racks
int32[] use_channels
float64[] asp_flow_rates
float64[] dis_flow_rates
geometry_msgs/Point[] offsets
bool touch_tip
float64[] liquid_height
float64[] blow_out_air_volume
string spread
bool is_96_well
string mix_stage
int32[] mix_times
int32 mix_vol
int32 mix_rate
float64 mix_liquid_height
int32[] delays
string[] none_keys
---
bool success
---
# 反馈

View File

@@ -5,7 +5,7 @@ float64[] flow_rates
geometry_msgs/Point[] offsets
float64[] liquid_height
float64[] blow_out_air_volume
string spread="wide"
string spread
---
bool success
---

View File

@@ -5,7 +5,7 @@ int32[] use_channels
float64[] flow_rates
geometry_msgs/Point[] offsets
int32[] blow_out_air_volume
string spread="wide"
string spread
---
# 结果字段
bool success

View File

@@ -0,0 +1,9 @@
string protocol_name
string protocol_description
string protocol_version
string protocol_author
string protocol_date
string protocol_type
string[] none_keys
---
---

View File

@@ -1,11 +1,25 @@
# Bio
Resource source
float64[] asp_vols
float64[] dis_vols
Resource[] sources
Resource[] targets
float64 source_vol
float64[] ratios
float64[] target_vols
float64 aspiration_flow_rate
float64[] dispense_flow_rates
Resource[] tip_racks
int32[] use_channels
float64[] asp_flow_rates
float64[] dis_flow_rates
geometry_msgs/Point[] offsets
bool touch_tip
float64[] liquid_height
float64[] blow_out_air_volume
string spread
bool is_96_well
string mix_stage
int32[] mix_times
int32 mix_vol
int32 mix_rate
float64 mix_liquid_height
int32[] delays
string[] none_keys
---
bool success
---
---
# 反馈

View File

@@ -0,0 +1,10 @@
string source
string target
string tip_rack
float64 volume
string aspirate_technique
string dispense_technique
---
---

View File

@@ -0,0 +1,12 @@
string res_id
string device_id
string class_name
string parent
geometry_msgs/Point bind_locations
int32[] liquid_input_slot
string[] liquid_type
float32[] liquid_volume
int32 slot_on_deck
---
bool success
---