Files
Uni-Lab-OS/unilabos/devices/liquid_handling/liquid_handler_abstract.py
ZiWei 5dc81ec9be bump version to 0.10.3
update registry

do not modify axis globally

Prcix9320 (#207)

* 0.10.7 Update (#101)

* Cleanup registry to be easy-understanding (#76)

* delete deprecated mock devices

* rename categories

* combine chromatographic devices

* rename rviz simulation nodes

* organic virtual devices

* parse vessel_id

* run registry completion before merge

---------

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

* fix: workstation handlers and vessel_id parsing

* fix: working dir error when input config path
feat: report publish topic when error

* modify default discovery_interval to 15s

* feat: add trace log level

* feat: 添加ChinWe设备控制类,支持串口通信和电机控制功能 (#79)

* fix: drop_tips not using auto resource select

* fix: discard_tips error

* fix: discard_tips

* fix: prcxi_res

* add: prcxi res
fix: startup slow

* feat: workstation example

* fix pumps and liquid_handler handle

* feat: 优化protocol node节点运行日志

* fix all protocol_compilers and remove deprecated devices

* feat: 新增use_remote_resource参数

* fix and remove redundant info

* bugfixes on organic protocols

* fix filter protocol

* fix protocol node

* 临时兼容错误的driver写法

* fix: prcxi import error

* use call_async in all service to avoid deadlock

* fix: figure_resource

* Update recipe.yaml

* add workstation template and battery example

* feat: add sk & ak

* update workstation base

* Create workstation_architecture.md

* refactor: workstation_base 重构为仅含业务逻辑,通信和子设备管理交给 ProtocolNode

* refactor: ProtocolNode→WorkstationNode

* Add:msgs.action (#83)

* update: Workstation dev 将版本号从 0.10.3 更新为 0.10.4 (#84)

* Add:msgs.action

* update: 将版本号从 0.10.3 更新为 0.10.4

* simplify resource system

* uncompleted refactor

* example for use WorkstationBase

* feat: websocket

* feat: websocket test

* feat: workstation example

* feat: action status

* fix: station自己的方法注册错误

* fix: 还原protocol node处理方法

* fix: build

* fix: missing job_id key

* ws test version 1

* ws test version 2

* ws protocol

* 增加物料关系上传日志

* 增加物料关系上传日志

* 修正物料关系上传

* 修复工站的tracker实例追踪失效问题

* 增加handle检测,增加material edge关系上传

* 修复event loop错误

* 修复edge上报错误

* 修复async错误

* 更新schema的title字段

* 主机节点信息等支持自动刷新

* 注册表编辑器

* 修复status密集发送时,消息出错

* 增加addr参数

* fix: addr param

* fix: addr param

* 取消labid 和 强制config输入

* Add action definitions for LiquidHandlerSetGroup and LiquidHandlerTransferGroup

- Created LiquidHandlerSetGroup.action with fields for group name, wells, and volumes.
- Created LiquidHandlerTransferGroup.action with fields for source and target group names and unit volume.
- Both actions include response fields for return information and success status.

* Add LiquidHandlerSetGroup and LiquidHandlerTransferGroup actions to CMakeLists

* Add set_group and transfer_group methods to PRCXI9300Handler and update liquid_handler.yaml

* result_info改为字典类型

* 新增uat的地址替换

* runze multiple pump support

(cherry picked from commit 49354fcf39)

* remove runze multiple software obtainer

(cherry picked from commit 8bcc92a394)

* support multiple backbone

(cherry picked from commit 4771ff2347)

* Update runze pump format

* Correct runze multiple backbone

* Update runze_multiple_backbone

* Correct runze pump multiple receive method.

* Correct runze pump multiple receive method.

* 对于PRCXI9320的transfer_group,一对多和多对多

* 移除MQTT,更新launch文档,提供注册表示例文件,更新到0.10.5

* fix import error

* fix dupe upload registry

* refactor ws client

* add server timeout

* Fix: run-column with correct vessel id (#86)

* fix run_column

* Update run_column_protocol.py

(cherry picked from commit e5aa4d940a)

* resource_update use resource_add

* 新增版位推荐功能

* 重新规定了版位推荐的入参

* update registry with nested obj

* fix protocol node log_message, added create_resource return value

* fix protocol node log_message, added create_resource return value

* try fix add protocol

* fix resource_add

* 修复移液站错误的aspirate注册表

* Feature/xprbalance-zhida (#80)

* feat(devices): add Zhida GC/MS pretreatment automation workstation

* feat(devices): add mettler_toledo xpr balance

* balance

* 重新补全zhida注册表

* PRCXI9320 json

* PRCXI9320 json

* PRCXI9320 json

* fix resource download

* remove class for resource

* bump version to 0.10.6

* 更新所有注册表

* 修复protocolnode的兼容性

* 修复protocolnode的兼容性

* Update install md

* Add Defaultlayout

* 更新物料接口

* fix dict to tree/nested-dict converter

* coin_cell_station draft

* refactor: rename "station_resource" to "deck"

* add standardized BIOYOND resources: bottle_carrier, bottle

* refactor and add BIOYOND resources tests

* add BIOYOND deck assignment and pass all tests

* fix: update resource with correct structure; remove deprecated liquid_handler set_group action

* feat: 将新威电池测试系统驱动与配置文件并入 workstation_dev_YB2 (#92)

* feat: 新威电池测试系统驱动与注册文件

* feat: bring neware driver & battery.json into workstation_dev_YB2

* add bioyond studio draft

* bioyond station with communication init and resource sync

* fix bioyond station and registry

* fix: update resource with correct structure; remove deprecated liquid_handler set_group action

* frontend_docs

* create/update resources with POST/PUT for big amount/ small amount data

* create/update resources with POST/PUT for big amount/ small amount data

* refactor: add itemized_carrier instead of carrier consists of ResourceHolder

* create warehouse by factory func

* update bioyond launch json

* add child_size for itemized_carrier

* fix bioyond resource io

* Workstation templates: Resources and its CRUD, and workstation tasks (#95)

* coin_cell_station draft

* refactor: rename "station_resource" to "deck"

* add standardized BIOYOND resources: bottle_carrier, bottle

* refactor and add BIOYOND resources tests

* add BIOYOND deck assignment and pass all tests

* fix: update resource with correct structure; remove deprecated liquid_handler set_group action

* feat: 将新威电池测试系统驱动与配置文件并入 workstation_dev_YB2 (#92)

* feat: 新威电池测试系统驱动与注册文件

* feat: bring neware driver & battery.json into workstation_dev_YB2

* add bioyond studio draft

* bioyond station with communication init and resource sync

* fix bioyond station and registry

* create/update resources with POST/PUT for big amount/ small amount data

* refactor: add itemized_carrier instead of carrier consists of ResourceHolder

* create warehouse by factory func

* update bioyond launch json

* add child_size for itemized_carrier

* fix bioyond resource io

---------

Co-authored-by: h840473807 <47357934+h840473807@users.noreply.github.com>
Co-authored-by: Xie Qiming <97236197+Andy6M@users.noreply.github.com>

* 更新物料接口

* Workstation dev yb2 (#100)

* Refactor and extend reaction station action messages

* Refactor dispensing station tasks to enhance parameter clarity and add batch processing capabilities

- Updated `create_90_10_vial_feeding_task` to include detailed parameters for 90%/10% vial feeding, improving clarity and usability.
- Introduced `create_batch_90_10_vial_feeding_task` for batch processing of 90%/10% vial feeding tasks with JSON formatted input.
- Added `create_batch_diamine_solution_task` for batch preparation of diamine solution, also utilizing JSON formatted input.
- Refined `create_diamine_solution_task` to include additional parameters for better task configuration.
- Enhanced schema descriptions and default values for improved user guidance.

* 修复to_plr_resources

* add update remove

* 支持选择器注册表自动生成
支持转运物料

* 修复资源添加

* 修复transfer_resource_to_another生成

* 更新transfer_resource_to_another参数,支持spot入参

* 新增test_resource动作

* fix host_node error

* fix host_node test_resource error

* fix host_node test_resource error

* 过滤本地动作

* 移动内部action以兼容host node

* 修复同步任务报错不显示的bug

* feat: 允许返回非本节点物料,后面可以通过decoration进行区分,就不进行warning了

* update todo

* modify bioyond/plr converter, bioyond resource registry, and tests

* pass the tests

* update todo

* add conda-pack-build.yml

* add auto install script for conda-pack-build.yml

(cherry picked from commit 172599adcf)

* update conda-pack-build.yml

* update conda-pack-build.yml

* update conda-pack-build.yml

* update conda-pack-build.yml

* update conda-pack-build.yml

* Add version in __init__.py
Update conda-pack-build.yml
Add create_zip_archive.py

* Update conda-pack-build.yml

* Update conda-pack-build.yml (with mamba)

* Update conda-pack-build.yml

* Fix FileNotFoundError

* Try fix 'charmap' codec can't encode characters in position 16-23: character maps to <undefined>

* Fix unilabos msgs search error

* Fix environment_check.py

* Update recipe.yaml

* Update registry. Update uuid loop figure method. Update install docs.

* Fix nested conda pack

* Fix one-key installation path error

* Bump version to 0.10.7

* Workshop bj (#99)

* Add LaiYu Liquid device integration and tests

Introduce LaiYu Liquid device implementation, including backend, controllers, drivers, configuration, and resource files. Add hardware connection, tip pickup, and simplified test scripts, as well as experiment and registry configuration for LaiYu Liquid. Documentation and .gitignore for the device are also included.

* feat(LaiYu_Liquid): 重构设备模块结构并添加硬件文档

refactor: 重新组织LaiYu_Liquid模块目录结构
docs: 添加SOPA移液器和步进电机控制指令文档
fix: 修正设备配置中的最大体积默认值
test: 新增工作台配置测试用例
chore: 删除过时的测试脚本和配置文件

* add

* 重构: 将 LaiYu_Liquid.py 重命名为 laiyu_liquid_main.py 并更新所有导入引用

- 使用 git mv 将 LaiYu_Liquid.py 重命名为 laiyu_liquid_main.py
- 更新所有相关文件中的导入引用
- 保持代码功能不变,仅改善命名一致性
- 测试确认所有导入正常工作

* 修复: 在 core/__init__.py 中添加 LaiYuLiquidBackend 导出

- 添加 LaiYuLiquidBackend 到导入列表
- 添加 LaiYuLiquidBackend 到 __all__ 导出列表
- 确保所有主要类都可以正确导入

* 修复大小写文件夹名字

* 电池装配工站二次开发教程(带目录)上传至dev (#94)

* 电池装配工站二次开发教程

* Update intro.md

* 物料教程

* 更新物料教程,json格式注释

* Update prcxi driver & fix transfer_liquid mix_times (#90)

* Update prcxi driver & fix transfer_liquid mix_times

* fix: correct mix_times type

* Update liquid_handler registry

* test: prcxi.py

* Update registry from pr

* fix ony-key script not exist

* clean files

---------

Co-authored-by: Junhan Chang <changjh@dp.tech>
Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: Xie Qiming <97236197+Andy6M@users.noreply.github.com>
Co-authored-by: h840473807 <47357934+h840473807@users.noreply.github.com>
Co-authored-by: LccLink <1951855008@qq.com>
Co-authored-by: lixinyu1011 <61094742+lixinyu1011@users.noreply.github.com>
Co-authored-by: shiyubo0410 <shiyubo@dp.tech>

* fix startup env check.
add auto install during one-key installation

* Try fix one-key build on linux

* Complete all one key installation

* fix: rename schema field to resource_schema with serialization and validation aliases (#104)

Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>

* Fix one-key installation build

Install conda-pack before pack command

Add conda-pack to base when building one-key installer

Fix param error when using mamba run

Try fix one-key build on linux

* Fix conda pack on windows

* add plr_to_bioyond, and refactor bioyond stations

* modify default config

* Fix one-key installation build for windows

* Fix workstation startup
Update registry

* Fix/resource UUID and doc fix (#109)

* Fix ResourceTreeSet load error

* Raise error when using unsupported type to create ResourceTreeSet

* Fix children key error

* Fix children key error

* Fix workstation resource not tracking

* Fix workstation deck & children resource dupe

* Fix workstation deck & children resource dupe

* Fix multiple resource error

* Fix resource tree update

* Fix resource tree update

* Force confirm uuid

* Tip more error log

* Refactor Bioyond workstation and experiment workflow (#105)

Refactored the Bioyond workstation classes to improve parameter handling and workflow management. Updated experiment.py to use BioyondReactionStation with deck and material mappings, and enhanced workflow step parameter mapping and execution logic. Adjusted JSON experiment configs, improved workflow sequence handling, and added UUID assignment to PLR materials. Removed unused station_config and material cache logic, and added detailed docstrings and debug output for workflow methods.

* Fix resource get.
Fix resource parent not found.
Mapping uuid for all resources.

* mount parent uuid

* Add logging configuration based on BasicConfig in main function

* fix workstation node error

* fix workstation node error

* Update boot example

* temp fix for resource get

* temp fix for resource get

* provide error info when cant find plr type

* pack repo info

* fix to plr type error

* fix to plr type error

* Update regular container method

* support no size init

* fix comprehensive_station.json

* fix comprehensive_station.json

* fix type conversion

* fix state loading for regular container

* Update deploy-docs.yml

* Update deploy-docs.yml

---------

Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>

* Close #107
Update doc url.

* Fix/update resource (#112)

* cancel upload_registry

* Refactor Bioyond workstation and experiment workflow -fix (#111)

* refactor(bioyond_studio): 优化材料缓存加载和参数验证逻辑

改进材料缓存加载逻辑以支持多种材料类型和详细材料处理
更新工作流参数验证中的字段名从key/value改为Key/DisplayValue
移除未使用的merge_workflow_with_parameters方法
添加get_station_info方法获取工作站基础信息
清理实验文件中的注释代码和更新导入路径

* fix: 修复资源移除时的父资源检查问题

在BaseROS2DeviceNode中,移除资源前添加对父资源是否为None的检查,避免空指针异常
同时更新Bottle和BottleCarrier类以支持**kwargs参数
修正测试文件中Liquid_feeding_beaker的大小写拼写错误

* correct return message

---------

Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>

* fix resource_get in action

* fix(reaction_station): 清空工作流序列和参数避免重复执行 (#113)

在创建任务后清空工作流序列和参数,防止下次执行时累积重复

* Update create_resource device_id

* Update ResourceTracker

add more enumeration in POSE

fix converter in resource_tracker

* Update graphio together with workstation design.

fix(reaction_station): 为步骤参数添加Value字段传个BY后端

fix(bioyond/warehouses): 修正仓库尺寸和物品排列参数

调整仓库的x轴和z轴物品数量以及物品尺寸参数,使其符合4x1x4的规格要求

fix warehouse serialize/deserialize

fix bioyond converter

fix itemized_carrier.unassign_child_resource

allow not-loaded MSG in registry

add layout serializer & converter

warehouseuse A1-D4; add warehouse layout

fix(graphio): 修正bioyond到plr资源转换中的坐标计算错误

Fix resource assignment and type mapping issues

Corrects resource assignment in ItemizedCarrier by using the correct spot key from _ordering. Updates graphio to use 'typeName' instead of 'name' for type mapping in resource_bioyond_to_plr. Renames DummyWorkstation to BioyondWorkstation in workstation_http_service for clarity.

* Update workstation & bioyond example

Refine descriptions in Bioyond reaction station YAML

Updated and clarified field and operation descriptions in the reaction_station_bioyond.yaml file for improved accuracy and consistency. Changes include more precise terminology, clearer parameter explanations, and standardized formatting for operation schemas.

refactor(workstation): 更新反应站参数描述并添加分液站配置文件

修正反应站方法参数描述,使其更准确清晰
添加bioyond_dispensing_station.yaml配置文件

add create_workflow script and test

add invisible_slots to carriers

fix(warehouses): 修正bioyond_warehouse_1x4x4仓库的尺寸参数

调整仓库的num_items_x和num_items_z值以匹配实际布局,并更新物品尺寸参数

save resource get data. allow empty value for layout and cross_section_type

More decks&plates support for bioyond (#115)

refactor(registry): 重构反应站设备配置,简化并更新操作命令

移除旧的自动操作命令,新增针对具体化学操作的命令配置
更新模块路径和配置结构,优化参数定义和描述

fix(dispensing_station): 修正物料信息查询方法调用

将直接调用material_id_query改为通过hardware_interface调用,以符合接口设计规范

* PRCXI Update

修改prcxi连线

prcxi样例图

Create example_prcxi.json

* Update resource extra & uuid.

use ordering to convert identifier to idx

convert identifier to site idx

correct extra key

update extra before transfer

fix multiple instance error

add resource_tree_transfer func

fox itemrized carrier assign child resource

support internal device material transfer

remove extra key

use same callback group

support material extra

support material extra
support update_resource_site in extra

* Update workstation.

modify workstation_architecture docs

bioyond_HR (#133)

* feat: Enhance Bioyond synchronization and resource management

- Implemented synchronization for all material types (consumables, samples, reagents) from Bioyond, logging detailed information for each type.
- Improved error handling and logging during synchronization processes.
- Added functionality to save Bioyond material IDs in UniLab resources for future updates.
- Enhanced the `sync_to_external` method to handle material movements correctly, including querying and creating materials in Bioyond.
- Updated warehouse configurations to support new storage types and improved layout for better resource management.
- Introduced new resource types such as reactors and tip boxes, with detailed specifications.
- Modified warehouse factory to support column offsets for naming conventions (e.g., A05-D08).
- Improved resource tracking by merging extra attributes instead of overwriting them.
- Added a new method for updating resources in Bioyond, ensuring better synchronization of resource changes.

* feat: 添加TipBox和Reactor的配置到bottles.yaml

* fix: 修复液体投料方法中的volume参数处理逻辑

修复solid_feeding_vials方法中的volume参数处理逻辑,优化solvents参数的使用条件

更新液体投料方法,支持通过溶剂信息自动计算体积,添加solvents参数并更新文档描述

Add batch creation methods for vial and solution tasks

添加批量创建90%10%小瓶投料任务和二胺溶液配置任务的功能,更新相关参数和默认值

* 封膜仪、撕膜仪、耗材站接口

* 添加Raman和xrd相关代码

* Resource update & asyncio fix

correct bioyond config

prcxi example

fix append_resource

fix regularcontainer

fix cancel error

fix resource_get param

fix json dumps

support name change during materials change

enable slave mode

change uuid logger to trace level

correct remove_resource stats

disable slave connect websocket

adjust with_children param

modify devices to use correct executor (sleep, create_task)

support sleep and create_task in node

fix run async execution error

* bump version to 0.10.9

update registry

* PRCXI Reset Error Correction (#166)

* change 9320 desk row number to 4

* Updated 9320 host address

* Updated 9320 host address

* Add **kwargs in classes: PRCXI9300Deck and PRCXI9300Container

* Removed all sample_id in prcxi_9320.json to avoid KeyError

* 9320 machine testing settings

* Typo

* Rewrite setup logic to clear error code

* 初始化 step_mode 属性

* 1114物料手册定义教程byxinyu (#165)

* 宜宾奔耀工站deck前端by_Xinyu

* 构建物料教程byxinyu

* 1114物料手册定义教程

* 3d sim (#97)

* 修改lh的json启动

* 修改lh的json启动

* 修改backend,做成sim的通用backend

* 修改yaml的地址,3D模型适配网页生产环境

* 添加laiyu硬件连接

* 修改移液枪的状态判断方法,

修改移液枪的状态判断方法,
添加三轴的表定点与零点之间的转换
添加三轴真实移动的backend

* 修改laiyu移液站

简化移动方法,
取消软件限制位置,
修改当值使用Z轴时也需要重新复位Z轴的问题

* 更新lh以及laiyu workshop

1,现在可以直接通过修改backend,适配其他的移液站,主类依旧使用LiquidHandler,不用重新编写

2,修改枪头判断标准,使用枪头自身判断而不是类的判断,

3,将归零参数用毫米计算,方便手动调整,

4,修改归零方式,上电使用机械归零,确定机械零点,手动归零设置工作区域零点方便计算,二者互不干涉

* 修改枪头动作

* 修改虚拟仿真方法

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: Junhan Chang <changjh@dp.tech>

* 标准化opcua设备接入unilab (#78)

* 初始提交,只保留工作区当前状态

* remove redundant arm_slider meshes

---------

Co-authored-by: Junhan Chang <changjh@dp.tech>

* add new laiyu liquid driver, yaml and json files (#164)

* HR物料同步,前端展示位置修复 (#135)

* 更新Bioyond工作站配置,添加新的物料类型映射和载架定义,优化物料查询逻辑

* 添加Bioyond实验配置文件,定义物料类型映射和设备配置

* 更新bioyond_warehouse_reagent_stack方法,修正试剂堆栈尺寸和布局描述

* 更新Bioyond实验配置,修正物料类型映射,优化设备配置

* 更新Bioyond资源同步逻辑,优化物料入库流程,增强错误处理和日志记录

* 更新Bioyond资源,添加配液站和反应站专用载架,优化仓库工厂函数的排序方式

* 更新Bioyond资源,添加配液站和反应站相关载架,优化试剂瓶和样品瓶配置

* 更新Bioyond实验配置,修正试剂瓶载架ID,确保与设备匹配

* 更新Bioyond资源,移除反应站单烧杯载架,添加反应站单烧瓶载架分类

* Refactor Bioyond resource synchronization and update bottle carrier definitions

- Removed traceback printing in error handling for Bioyond synchronization.
- Enhanced logging for existing Bioyond material ID usage during synchronization.
- Added new bottle carrier definitions for single flask and updated existing ones.
- Refactored dispensing station and reaction station bottle definitions for clarity and consistency.
- Improved resource mapping and error handling in graphio for Bioyond resource conversion.
- Introduced layout parameter in warehouse factory for better warehouse configuration.

* 更新Bioyond仓库工厂,添加排序方式支持,优化坐标计算逻辑

* 更新Bioyond载架和甲板配置,调整样品板尺寸和仓库坐标

* 更新Bioyond资源同步,增强占用位置日志信息,修正坐标转换逻辑

* 更新Bioyond反应站和分配站配置,调整材料类型映射和ID,移除不必要的项

* support name change during materials change

* fix json dumps

* correct tip

* 优化调度器API路径,更新相关方法描述

* 更新 BIOYOND 载架相关文档,调整 API 以支持自带试剂瓶的载架类型,修复资源获取时的子物料处理逻辑

* 实现资源删除时的同步处理,优化出库操作逻辑

* 修复 ItemizedCarrier 中的可见性逻辑

* 保存 Bioyond 原始信息到 unilabos_extra,以便出库时查询

* 根据 resource.capacity 判断是试剂瓶(载架)还是多瓶载架,走不同的奔曜转换

* Fix bioyond bottle_carriers ordering

* 优化 Bioyond 物料同步逻辑,增强坐标解析和位置更新处理

* disable slave connect websocket

* correct remove_resource stats

* change uuid logger to trace level

* enable slave mode

* refactor(bioyond): 统一资源命名并优化物料同步逻辑

- 将DispensingStation和ReactionStation资源统一为PolymerStation命名
- 优化物料同步逻辑,支持耗材类型(typeMode=0)的查询
- 添加物料默认参数配置功能
- 调整仓库坐标布局
- 清理废弃资源定义

* feat(warehouses): 为仓库函数添加col_offset和layout参数

* refactor: 更新实验配置中的物料类型映射命名

将DispensingStation和ReactionStation的物料类型映射统一更名为PolymerStation,保持命名一致性

* fix: 更新实验配置中的载体名称从6VialCarrier到6StockCarrier

* feat(bioyond): 实现物料创建与入库分离逻辑

将物料同步流程拆分为两个独立阶段:transfer阶段只创建物料,add阶段执行入库
简化状态检查接口,仅返回连接状态

* fix(reaction_station): 修正液体进料烧杯体积单位并增强返回结果

将液体进料烧杯的体积单位从μL改为g以匹配实际使用场景
在返回结果中添加merged_workflow和order_params字段,提供更完整的工作流信息

* feat(dispensing_station): 在任务创建返回结果中添加order_params信息

在create_order方法返回结果中增加order_params字段,以便调用方获取完整的任务参数

* fix(dispensing_station): 修改90%物料分配逻辑从分成3份改为直接使用

原逻辑将主称固体平均分成3份作为90%物料,现改为直接使用main_portion

* feat(bioyond): 添加任务编码和任务ID的输出,支持批量任务创建后的状态监控

* refactor(registry): 简化设备配置中的任务结果处理逻辑

将多个单独的任务编码和ID字段合并为统一的return_info字段
更新相关描述以反映新的数据结构

* feat(工作站): 添加HTTP报送服务和任务完成状态跟踪

- 在graphio.py中添加API必需字段
- 实现工作站HTTP服务启动和停止逻辑
- 添加任务完成状态跟踪字典和等待方法
- 重写任务完成报送处理方法记录状态
- 支持批量任务完成等待和报告获取

* refactor(dispensing_station): 移除wait_for_order_completion_and_get_report功能

该功能已被wait_for_multiple_orders_and_get_reports替代,简化代码结构

* fix: 更新任务报告API错误

* fix(workstation_http_service): 修复状态查询中device_id获取逻辑

处理状态查询时安全获取device_id,避免因属性不存在导致的异常

* fix(bioyond_studio): 改进物料入库失败时的错误处理和日志记录

在物料入库API调用失败时,添加更详细的错误信息打印
同时修正station.py中对空响应和失败情况的判断逻辑

* refactor(bioyond): 优化瓶架载体的分配逻辑和注释说明

重构瓶架载体的分配逻辑,使用嵌套循环替代硬编码索引分配
添加更详细的坐标映射说明,明确PLR与Bioyond坐标的对应关系

* fix(bioyond_rpc): 修复物料入库成功时无data字段返回空的问题

当API返回成功但无data字段时,返回包含success标识的字典而非空字典

---------

Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com>
Co-authored-by: Junhan Chang <changjh@dp.tech>

* nmr

* Update devices

* bump version to 0.10.10

* Update repo files.

* Add get_resource_with_dir & get_resource method

* fix camera & workstation & warehouse & reaction station driver

* update docs, test examples
fix liquid_handler init bug

* bump version to 0.10.11

* Add startup_json_path, disable_browser, port config

* Update oss config

* feat(bioyond_studio): 添加项目API接口支持及优化物料管理功能

添加通用项目API接口方法(_post_project_api, _delete_project_api)用于与LIMS系统交互
实现compute_experiment_design方法用于实验设计计算
新增brief_step_parameters等订单相关接口方法
优化物料转移逻辑,增加异步任务处理
扩展BioyondV1RPC类,添加批量物料操作、订单状态管理等功能

* feat(bioyond): 添加测量小瓶仓库和更新仓库工厂函数参数

* Support unilabos_samples key

* add session_id and normal_exit

* Add result schema and add TypedDict conversion.

* Fix port error

* Add backend api and update doc

* Add get_regular_container func

* Add get_regular_container func

* Transfer_liquid (#176)

* change 9320 desk row number to 4

* Updated 9320 host address

* Updated 9320 host address

* Add **kwargs in classes: PRCXI9300Deck and PRCXI9300Container

* Removed all sample_id in prcxi_9320.json to avoid KeyError

* 9320 machine testing settings

* Typo

* Typo in base_device_node.py

* Enhance liquid handling functionality by adding support for multiple transfer modes (one-to-many, one-to-one, many-to-one) and improving parameter validation. Default channel usage is set when not specified. Adjusted mixing logic to ensure it only occurs when valid conditions are met. Updated documentation for clarity.

* Auto dump logs, fix workstation input schema

* Fix startup with remote resource error

Resource dict fully change to "pose" key

Update oss link

Reduce pylabrobot conversion warning & force enable log dump.

更新 logo 图片

* signal when host node is ready

* fix ros2 future

print all logs to file
fix resource dict dump error

* update version to 0.10.12

* 修改sample_uuid的返回值

* 修改pose标签设定机制

* 添加 aspiate函数返回值

* 返回dispense后的sample_uuid

* 添加self.pending_liquids_dict的重置方法

* 修改prcxi的json文件,解决trach错误问题

* 修改prcxijson,防止PlateT4的硬件错误

* 对laiyu移液站进行部分修改,取消多次初始化的问题

* 修改根据新的物料格式,修改可视化

* 添加切换枪头方法,添加mock振荡与加热方法

* 夹爪添加

* 删除多余的laiyu部分

* 云端可启动夹爪

* Delete __init__.py

* Enhance PRCXI9300 classes with new Container and TipRack implementations, improving state management and initialization logic. Update JSON configuration to reflect type changes for containers and plates.

* 修改上传数据

---------

Co-authored-by: Junhan Chang <changjh@dp.tech>
Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: Xie Qiming <97236197+Andy6M@users.noreply.github.com>
Co-authored-by: h840473807 <47357934+h840473807@users.noreply.github.com>
Co-authored-by: LccLink <1951855008@qq.com>
Co-authored-by: lixinyu1011 <61094742+lixinyu1011@users.noreply.github.com>
Co-authored-by: shiyubo0410 <shiyubo@dp.tech>
Co-authored-by: hh.(SII) <103566763+Mile-Away@users.noreply.github.com>
Co-authored-by: Xianwei Qi <qxw@stu.pku.edu.cn>
Co-authored-by: WenzheG <wenzheguo32@gmail.com>
Co-authored-by: Harry Liu <113173203+ALITTLELZ@users.noreply.github.com>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>
Co-authored-by: tt <166512503+tt11142023@users.noreply.github.com>
Co-authored-by: xyc <49015816+xiaoyu10031@users.noreply.github.com>
Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: zhangshixiang <554662886@qq.com>
Co-authored-by: ALITTLELZ <l_LZlz@163.com>

Add topic config

add camera driver (#191)

* add camera driver

* add init.py file to cameraSII driver

增强新威电池测试系统 OSS 上传功能 / Enhanced Neware Battery Test System OSS Upload (#196)

* feat: neware-oss-upload-enhancement

* feat(neware): enhance OSS upload with metadata and workflow handles

Add post process station and related resources (#195)

* Add post process station and related resources

- Created JSON configuration for post_process_station and its child post_process_deck.
- Added YAML definitions for post_process_station, bottle carriers, bottles, and deck resources.
- Implemented Python classes for bottle carriers, bottles, decks, and warehouses to manage resources in the post process.
- Established a factory method for creating warehouses with customizable dimensions and layouts.
- Defined the structure and behavior of the post_process_deck and its associated warehouses.

* feat(post_process): add post_process_station and related warehouse functionality

- Introduced post_process_station.json to define the post-processing station structure.
- Implemented post_process_warehouse.py to create warehouse configurations with customizable layouts.
- Added warehouses.py for specific warehouse configurations (4x3x1).
- Updated post_process_station.yaml to reflect new module paths for OpcUaClient.
- Refactored bottle carriers and bottles YAML files to point to the new module paths.
- Adjusted deck.yaml to align with the new organizational structure for post_process_deck.

prcxi resource (#202)

* prcxi resource

* prcxi_resource

* Fix upload error not showing.
Support str type category.

---------

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

Fix upload error not showing.
Support str type category.

feat: introduce `wait_time` command and configurable device communication timeout.

feat: Add `SyringePump` (SY-03B) driver with unified serial/TCP transport for `chinwe` device, including registry and test configurations.
2025-12-26 03:36:48 +08:00

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from __future__ import annotations
import asyncio
import time
import traceback
from collections import Counter
from typing import List, Sequence, Optional, Literal, Union, Iterator, Dict, Any, Callable, Set, cast
from typing_extensions import TypedDict
from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, LiquidHandlerChatterboxBackend, Strictness
from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
from unilabos.devices.liquid_handling.laiyu.backend.laiyu_v_backend import UniLiquidHandlerLaiyuBackend
from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod
from pylabrobot.liquid_handling.standard import GripDirection
from pylabrobot.resources import (
Resource,
TipRack,
Container,
Coordinate,
Well,
Deck,
TipSpot,
Plate,
ResourceStack,
ResourceHolder,
Lid,
Trash,
Tip,
)
from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
class SimpleReturn(TypedDict):
samples: list
volumes: list
class LiquidHandlerMiddleware(LiquidHandler):
def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool = False, channel_num: int = 8, **kwargs):
self._simulator = simulator
self.channel_num = channel_num
self.pending_liquids_dict = {}
joint_config = kwargs.get("joint_config", None)
if simulator:
if joint_config:
self._simulate_backend = UniLiquidHandlerRvizBackend(channel_num, kwargs["total_height"],
joint_config=joint_config, lh_device_id=deck.name)
else:
self._simulate_backend = LiquidHandlerChatterboxBackend(channel_num)
self._simulate_handler = LiquidHandlerAbstract(self._simulate_backend, deck, False)
super().__init__(backend, deck)
async def setup(self, **backend_kwargs):
if self._simulator:
return await self._simulate_handler.setup(**backend_kwargs)
return await super().setup(**backend_kwargs)
def serialize_state(self) -> Dict[str, Any]:
if self._simulator:
self._simulate_handler.serialize_state()
return super().serialize_state()
def load_state(self, state: Dict[str, Any]):
if self._simulator:
self._simulate_handler.load_state(state)
super().load_state(state)
def update_head_state(self, state: Dict[int, Optional[Tip]]):
if self._simulator:
self._simulate_handler.update_head_state(state)
super().update_head_state(state)
def clear_head_state(self):
if self._simulator:
self._simulate_handler.clear_head_state()
super().clear_head_state()
def _run_async_in_thread(self, func, *args, **kwargs):
super()._run_async_in_thread(func, *args, **kwargs)
def _send_assigned_resource_to_backend(self, resource: Resource):
if self._simulator:
self._simulate_handler._send_assigned_resource_to_backend(resource)
super()._send_assigned_resource_to_backend(resource)
def _send_unassigned_resource_to_backend(self, resource: Resource):
if self._simulator:
self._simulate_handler._send_unassigned_resource_to_backend(resource)
super()._send_unassigned_resource_to_backend(resource)
def summary(self):
if self._simulator:
self._simulate_handler.summary()
super().summary()
def _assert_positions_unique(self, positions: List[str]):
super()._assert_positions_unique(positions)
def _assert_resources_exist(self, resources: Sequence[Resource]):
super()._assert_resources_exist(resources)
def _check_args(
self, method: Callable, backend_kwargs: Dict[str, Any], default: Set[str], strictness: Strictness
) -> Set[str]:
return super()._check_args(method, backend_kwargs, default, strictness)
def _make_sure_channels_exist(self, channels: List[int]):
super()._make_sure_channels_exist(channels)
def _format_param(self, value: Any) -> Any:
return super()._format_param(value)
def _log_command(self, name: str, **kwargs) -> None:
super()._log_command(name, **kwargs)
async def pick_up_tips(
self,
tip_spots: List[TipSpot],
use_channels: Optional[List[int]] = None,
offsets: Optional[List[Coordinate]] = None,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.pick_up_tips(tip_spots, use_channels, offsets, **backend_kwargs)
return await super().pick_up_tips(tip_spots, use_channels, offsets, **backend_kwargs)
async def drop_tips(
self,
tip_spots: Sequence[Union[TipSpot, Trash]],
use_channels: Optional[List[int]] = None,
offsets: Optional[List[Coordinate]] = None,
allow_nonzero_volume: bool = False,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.drop_tips(
tip_spots, use_channels, offsets, allow_nonzero_volume, **backend_kwargs
)
await super().drop_tips(tip_spots, use_channels, offsets, allow_nonzero_volume, **backend_kwargs)
self.pending_liquids_dict = {}
return
async def return_tips(
self, use_channels: Optional[list[int]] = None, allow_nonzero_volume: bool = False, **backend_kwargs
):
if self._simulator:
return await self._simulate_handler.return_tips(use_channels, allow_nonzero_volume, **backend_kwargs)
return await super().return_tips(use_channels, allow_nonzero_volume, **backend_kwargs)
async def discard_tips(
self,
use_channels: Optional[List[int]] = None,
allow_nonzero_volume: bool = True,
offsets: Optional[List[Coordinate]] = None,
**backend_kwargs,
):
# 如果 use_channels 为 None使用默认值所有通道
if use_channels is None:
use_channels = list(range(self.channel_num))
if not offsets or (isinstance(offsets, list) and len(offsets) != len(use_channels)):
offsets = [Coordinate.zero()] * len(use_channels)
if self._simulator:
return await self._simulate_handler.discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs)
await super().discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs)
self.pending_liquids_dict = {}
return
def _check_containers(self, resources: Sequence[Resource]):
super()._check_containers(resources)
async def aspirate(
self,
resources: Sequence[Container],
vols: List[float],
use_channels: Optional[List[int]] = None,
flow_rates: Optional[List[Optional[float]]] = None,
offsets: Optional[List[Coordinate]] = None,
liquid_height: Optional[List[Optional[float]]] = None,
blow_out_air_volume: Optional[List[Optional[float]]] = None,
spread: Literal["wide", "tight", "custom"] = "wide",
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.aspirate(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
await super().aspirate(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
res_samples = []
res_volumes = []
for resource, volume, channel in zip(resources, vols, use_channels):
res_samples.append({"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)})
res_volumes.append(volume)
self.pending_liquids_dict[channel] = {
"sample_uuid": resource.unilabos_extra.get("sample_uuid", None),
"volume": volume
}
return SimpleReturn(samples=res_samples, volumes=res_volumes)
async def dispense(
self,
resources: Sequence[Container],
vols: List[float],
use_channels: Optional[List[int]] = None,
flow_rates: Optional[List[Optional[float]]] = None,
offsets: Optional[List[Coordinate]] = None,
liquid_height: Optional[List[Optional[float]]] = None,
blow_out_air_volume: Optional[List[Optional[float]]] = None,
spread: Literal["wide", "tight", "custom"] = "wide",
**backend_kwargs,
) -> SimpleReturn:
if self._simulator:
return await self._simulate_handler.dispense(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
await super().dispense(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
**backend_kwargs,
)
res_samples = []
res_volumes = []
for resource, volume, channel in zip(resources, vols, use_channels):
res_uuid = self.pending_liquids_dict[channel]["sample_uuid"]
self.pending_liquids_dict[channel]["volume"] -= volume
resource.unilabos_extra["sample_uuid"] = res_uuid
res_samples.append({"name": resource.name, "sample_uuid": res_uuid})
res_volumes.append(volume)
return SimpleReturn(samples=res_samples, volumes=res_volumes)
async def transfer(
self,
source: Well,
targets: List[Well],
source_vol: Optional[float] = None,
ratios: Optional[List[float]] = None,
target_vols: Optional[List[float]] = None,
aspiration_flow_rate: Optional[float] = None,
dispense_flow_rates: Optional[List[Optional[float]]] = None,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.transfer(
source,
targets,
source_vol,
ratios,
target_vols,
aspiration_flow_rate,
dispense_flow_rates,
**backend_kwargs,
)
return await super().transfer(
source,
targets,
source_vol,
ratios,
target_vols,
aspiration_flow_rate,
dispense_flow_rates,
**backend_kwargs,
)
def use_channels(self, channels: List[int]):
if self._simulator:
self._simulate_handler.use_channels(channels)
return super().use_channels(channels)
async def pick_up_tips96(self, tip_rack: TipRack, offset: Coordinate = Coordinate.zero(), **backend_kwargs):
if self._simulator:
return await self._simulate_handler.pick_up_tips96(tip_rack, offset, **backend_kwargs)
return await super().pick_up_tips96(tip_rack, offset, **backend_kwargs)
async def drop_tips96(
self,
resource: Union[TipRack, Trash],
offset: Coordinate = Coordinate.zero(),
allow_nonzero_volume: bool = False,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.drop_tips96(resource, offset, allow_nonzero_volume, **backend_kwargs)
return await super().drop_tips96(resource, offset, allow_nonzero_volume, **backend_kwargs)
def _get_96_head_origin_tip_rack(self) -> Optional[TipRack]:
return super()._get_96_head_origin_tip_rack()
async def return_tips96(self, allow_nonzero_volume: bool = False, **backend_kwargs):
if self._simulator:
return await self._simulate_handler.return_tips96(allow_nonzero_volume, **backend_kwargs)
return await super().return_tips96(allow_nonzero_volume, **backend_kwargs)
async def discard_tips96(self, allow_nonzero_volume: bool = True, **backend_kwargs):
if self._simulator:
return await self._simulate_handler.discard_tips96(allow_nonzero_volume, **backend_kwargs)
return await super().discard_tips96(allow_nonzero_volume, **backend_kwargs)
async def aspirate96(
self,
resource: Union[Plate, Container, List[Well]],
volume: float,
offset: Coordinate = Coordinate.zero(),
flow_rate: Optional[float] = None,
blow_out_air_volume: Optional[float] = None,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.aspirate96(
resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs
)
return await super().aspirate96(resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs)
async def dispense96(
self,
resource: Union[Plate, Container, List[Well]],
volume: float,
offset: Coordinate = Coordinate.zero(),
flow_rate: Optional[float] = None,
blow_out_air_volume: Optional[float] = None,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.dispense96(
resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs
)
return await super().dispense96(resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs)
async def stamp(
self,
source: Plate,
target: Plate,
volume: float,
aspiration_flow_rate: Optional[float] = None,
dispense_flow_rate: Optional[float] = None,
):
if self._simulator:
return await self._simulate_handler.stamp(source, target, volume, aspiration_flow_rate, dispense_flow_rate)
return await super().stamp(source, target, volume, aspiration_flow_rate, dispense_flow_rate)
async def pick_up_resource(
self,
resource: Resource,
offset: Coordinate = Coordinate.zero(),
pickup_distance_from_top: float = 0,
direction: GripDirection = GripDirection.FRONT,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.pick_up_resource(
resource, offset, pickup_distance_from_top, direction, **backend_kwargs
)
return await super().pick_up_resource(resource, offset, pickup_distance_from_top, direction, **backend_kwargs)
async def move_picked_up_resource(
self,
to: Coordinate,
offset: Coordinate = Coordinate.zero(),
direction: Optional[GripDirection] = None,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.move_picked_up_resource(to, offset, direction, **backend_kwargs)
return await super().move_picked_up_resource(to, offset, direction, **backend_kwargs)
async def drop_resource(
self,
destination: Union[ResourceStack, ResourceHolder, Resource, Coordinate],
offset: Coordinate = Coordinate.zero(),
direction: GripDirection = GripDirection.FRONT,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.drop_resource(destination, offset, direction, **backend_kwargs)
return await super().drop_resource(destination, offset, direction, **backend_kwargs)
async def move_resource(
self,
resource: Resource,
to: Union[ResourceStack, ResourceHolder, Resource, Coordinate],
intermediate_locations: Optional[List[Coordinate]] = None,
pickup_offset: Coordinate = Coordinate.zero(),
destination_offset: Coordinate = Coordinate.zero(),
pickup_distance_from_top: float = 0,
pickup_direction: GripDirection = GripDirection.FRONT,
drop_direction: GripDirection = GripDirection.FRONT,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.move_resource(
resource,
to,
intermediate_locations,
pickup_offset,
destination_offset,
pickup_distance_from_top,
pickup_direction,
drop_direction,
**backend_kwargs,
)
return await super().move_resource(
resource,
to,
intermediate_locations,
pickup_offset,
destination_offset,
pickup_distance_from_top,
pickup_direction,
drop_direction,
**backend_kwargs,
)
async def move_lid(
self,
lid: Lid,
to: Union[Plate, ResourceStack, Coordinate],
intermediate_locations: Optional[List[Coordinate]] = None,
pickup_offset: Coordinate = Coordinate.zero(),
destination_offset: Coordinate = Coordinate.zero(),
pickup_direction: GripDirection = GripDirection.FRONT,
drop_direction: GripDirection = GripDirection.FRONT,
pickup_distance_from_top: float = 5.7 - 3.33,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.move_lid(
lid,
to,
intermediate_locations,
pickup_offset,
destination_offset,
pickup_direction,
drop_direction,
pickup_distance_from_top,
**backend_kwargs,
)
return await super().move_lid(
lid,
to,
intermediate_locations,
pickup_offset,
destination_offset,
pickup_direction,
drop_direction,
pickup_distance_from_top,
**backend_kwargs,
)
async def move_plate(
self,
plate: Plate,
to: Union[ResourceStack, ResourceHolder, Resource, Coordinate],
intermediate_locations: Optional[List[Coordinate]] = None,
pickup_offset: Coordinate = Coordinate.zero(),
destination_offset: Coordinate = Coordinate.zero(),
drop_direction: GripDirection = GripDirection.FRONT,
pickup_direction: GripDirection = GripDirection.FRONT,
pickup_distance_from_top: float = 13.2 - 3.33,
**backend_kwargs,
):
if self._simulator:
return await self._simulate_handler.move_plate(
plate,
to,
intermediate_locations,
pickup_offset,
destination_offset,
drop_direction,
pickup_direction,
pickup_distance_from_top,
**backend_kwargs,
)
return await super().move_plate(
plate,
to,
intermediate_locations,
pickup_offset,
destination_offset,
drop_direction,
pickup_direction,
pickup_distance_from_top,
**backend_kwargs,
)
def serialize(self):
if self._simulator:
self._simulate_handler.serialize()
return super().serialize()
@classmethod
def deserialize(cls, data: dict, allow_marshal: bool = False) -> LiquidHandler:
return super().deserialize(data, allow_marshal)
@classmethod
def load(cls, path: str) -> LiquidHandler:
return super().load(path)
async def prepare_for_manual_channel_operation(self, channel: int):
if self._simulator:
return await self._simulate_handler.prepare_for_manual_channel_operation(channel)
return await super().prepare_for_manual_channel_operation(channel)
async def move_channel_x(self, channel: int, x: float):
if self._simulator:
return await self._simulate_handler.move_channel_x(channel, x)
return await super().move_channel_x(channel, x)
async def move_channel_y(self, channel: int, y: float):
if self._simulator:
return await self._simulate_handler.move_channel_y(channel, y)
return await super().move_channel_y(channel, y)
async def move_channel_z(self, channel: int, z: float):
if self._simulator:
return await self._simulate_handler.move_channel_z(channel, z)
return await super().move_channel_z(channel, z)
def assign_child_resource(self, resource: Resource, location: Optional[Coordinate], reassign: bool = True):
if self._simulator:
self._simulate_handler.assign_child_resource(resource, location, reassign)
pass
async def probe_tip_presence_via_pickup(
self, tip_spots: List[TipSpot], use_channels: Optional[List[int]] = None
) -> Dict[str, bool]:
if self._simulator:
return await self._simulate_handler.probe_tip_presence_via_pickup(tip_spots, use_channels)
return await super().probe_tip_presence_via_pickup(tip_spots, use_channels)
async def probe_tip_inventory(
self,
tip_spots: List[TipSpot],
probing_fn: Optional[TipPresenceProbingMethod] = None,
use_channels: Optional[List[int]] = None,
) -> Dict[str, bool]:
if self._simulator:
return await self._simulate_handler.probe_tip_inventory(tip_spots, probing_fn, use_channels)
return await super().probe_tip_inventory(tip_spots, probing_fn, use_channels)
async def consolidate_tip_inventory(self, tip_racks: List[TipRack], use_channels: Optional[List[int]] = None):
if self._simulator:
return await self._simulate_handler.consolidate_tip_inventory(tip_racks, use_channels)
return await super().consolidate_tip_inventory(tip_racks, use_channels)
class LiquidHandlerAbstract(LiquidHandlerMiddleware):
"""Extended LiquidHandler with additional operations."""
support_touch_tip = True
_ros_node: BaseROS2DeviceNode
def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool=False, channel_num:int = 8, total_height:float = 310):
"""Initialize a LiquidHandler.
Args:
backend: Backend to use.
deck: Deck to use.
"""
backend_type = None
if isinstance(backend, dict) and "type" in backend:
backend_dict = backend.copy()
type_str = backend_dict.pop("type")
try:
# Try to get class from string using globals (current module), or fallback to pylabrobot or unilabos namespaces
backend_cls = None
if type_str in globals():
backend_cls = globals()[type_str]
else:
# Try resolving dotted notation, e.g. "xxx.yyy.ClassName"
components = type_str.split(".")
mod = None
if len(components) > 1:
module_name = ".".join(components[:-1])
try:
import importlib
mod = importlib.import_module(module_name)
except ImportError:
mod = None
if mod is not None:
backend_cls = getattr(mod, components[-1], None)
if backend_cls is None:
# Try pylabrobot style import (if available)
try:
import pylabrobot
backend_cls = getattr(pylabrobot, type_str, None)
except Exception:
backend_cls = None
if backend_cls is not None and isinstance(backend_cls, type):
backend_type = backend_cls(**backend_dict) # pass the rest of dict as kwargs
except Exception as exc:
raise RuntimeError(f"Failed to convert backend type '{type_str}' to class: {exc}")
else:
backend_type = backend
self._simulator = simulator
self.group_info = dict()
super().__init__(backend_type, deck, simulator, channel_num)
def post_init(self, ros_node: BaseROS2DeviceNode):
self._ros_node = ros_node
@classmethod
def set_liquid(cls, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SimpleReturn:
"""Set the liquid in a well."""
res_samples = []
res_volumes = []
for well, liquid_name, volume in zip(wells, liquid_names, volumes):
well.set_liquids([(liquid_name, volume)]) # type: ignore
res_samples.append({"name": well.name, "sample_uuid": well.unilabos_extra.get("sample_uuid", None)})
res_volumes.append(volume)
return SimpleReturn(samples=res_samples, volumes=res_volumes)
# ---------------------------------------------------------------
# REMOVE LIQUID --------------------------------------------------
# ---------------------------------------------------------------
def set_group(self, group_name: str, wells: List[Well], volumes: List[float]):
if self.channel_num == 8 and len(wells) != 8:
raise RuntimeError(f"Expected 8 wells, got {len(wells)}")
self.group_info[group_name] = wells
self.set_liquid(wells, [group_name] * len(wells), volumes)
async def transfer_group(self, source_group_name: str, target_group_name: str, unit_volume: float):
source_wells = self.group_info.get(source_group_name, [])
target_wells = self.group_info.get(target_group_name, [])
rack_info = dict()
for child in self.deck.children:
if issubclass(child.__class__, TipRack):
rack: TipRack = cast(TipRack, child)
if "plate" not in rack.name.lower():
for tip in rack.get_all_tips():
if unit_volume > tip.maximal_volume:
break
else:
rack_info[rack.name] = (rack, tip.maximal_volume - unit_volume)
if len(rack_info) == 0:
raise ValueError(f"No tip rack can support volume {unit_volume}.")
rack_info = sorted(rack_info.items(), key=lambda x: x[1][1])
for child in self.deck.children:
if child.name == rack_info[0][0]:
target_rack = child
target_rack = cast(TipRack, target_rack)
available_tips = {}
for (idx, tipSpot) in enumerate(target_rack.get_all_items()):
if tipSpot.has_tip():
available_tips[idx] = tipSpot
continue
# 一般移动液体有两种方式,一对多和多对多
print("channel_num", self.channel_num)
if self.channel_num == 8:
tip_prefix = list(available_tips.values())[0].name.split('_')[0]
colnum_list = [int(tip.name.split('_')[-1][1:]) for tip in available_tips.values()]
available_cols = [colnum for colnum, count in dict(Counter(colnum_list)).items() if count == 8]
available_cols.sort()
available_tips_dict = {tip.name: tip for tip in available_tips.values()}
tips_to_use = [available_tips_dict[f"{tip_prefix}_{chr(65 + i)}{available_cols[0]}"] for i in range(8)]
print("tips_to_use", tips_to_use)
await self.pick_up_tips(tips_to_use, use_channels=list(range(0, 8)))
print("source_wells", source_wells)
await self.aspirate(source_wells, [unit_volume] * 8, use_channels=list(range(0, 8)))
print("target_wells", target_wells)
await self.dispense(target_wells, [unit_volume] * 8, use_channels=list(range(0, 8)))
await self.discard_tips(use_channels=list(range(0, 8)))
elif self.channel_num == 1:
for num_well in range(len(target_wells)):
tip_to_use = available_tips[list(available_tips.keys())[num_well]]
print("tip_to_use", tip_to_use)
await self.pick_up_tips([tip_to_use], use_channels=[0])
print("source_wells", source_wells)
print("target_wells", target_wells)
if len(source_wells) == 1:
await self.aspirate([source_wells[0]], [unit_volume], use_channels=[0])
else:
await self.aspirate([source_wells[num_well]], [unit_volume], use_channels=[0])
await self.dispense([target_wells[num_well]], [unit_volume], use_channels=[0])
await self.discard_tips(use_channels=[0])
else:
raise ValueError(f"Unsupported channel number {self.channel_num}.")
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],
sources: Sequence[Container],
waste_liquid: Optional[Container] = None,
*,
use_channels: Optional[List[int]] = None,
flow_rates: Optional[List[Optional[float]]] = None,
offsets: Optional[List[Coordinate]] = None,
liquid_height: Optional[List[Optional[float]]] = None,
blow_out_air_volume: Optional[List[Optional[float]]] = None,
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] = [],
):
"""A complete *remove* (aspirate → waste) operation."""
try:
if is_96_well:
pass # This mode is not verified.
else:
# 首先应该对任务分组然后每次1个/8个进行操作处理
if len(use_channels) == 1 and self.backend.num_channels == 1:
for _ in range(len(sources)):
tip = []
for __ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
await self.aspirate(
resources=[sources[_]],
vols=[vols[_]],
use_channels=use_channels,
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,
blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
await self.dispense(
resources=[waste_liquid],
vols=[vols[_]],
use_channels=use_channels,
flow_rates=[flow_rates[1]] if flow_rates else None,
offsets=[offsets[1]] if offsets else None,
blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
liquid_height=[liquid_height[1]] if liquid_height else None,
spread=spread,
)
await self.discard_tips()
elif len(use_channels) == 8 and self.backend.num_channels == 8:
# 对于8个的情况需要判断此时任务是不是能被8通道移液站来成功处理
if len(sources) % 8 != 0:
raise ValueError(f"Length of `sources` {len(sources)} must be a multiple of 8 for 8-channel mode.")
# 8个8个来取任务序列
for i in range(0, len(sources), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
current_targets = waste_liquid[i:i + 8]
current_reagent_sources = sources[i:i + 8]
current_asp_vols = vols[i:i + 8]
current_dis_vols = vols[i:i + 8]
current_asp_flow_rates = flow_rates[i:i + 8] if flow_rates else [None] * 8
current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8
current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8
current_dis_offset = offsets[-i*8-8:len(offsets)-i*8] if offsets else [None] * 8
current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8
current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
current_dis_blow_out_air_volume = blow_out_air_volume[-i*8-8:len(blow_out_air_volume)-i*8] if blow_out_air_volume else [None] * 8
await self.aspirate(
resources=current_reagent_sources,
vols=current_asp_vols,
use_channels=use_channels,
flow_rates=current_asp_flow_rates,
offsets=current_asp_offset,
liquid_height=current_asp_liquid_height,
blow_out_air_volume=current_asp_blow_out_air_volume,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
await self.dispense(
resources=current_targets,
vols=current_dis_vols,
use_channels=use_channels,
flow_rates=current_dis_flow_rates,
offsets=current_dis_offset,
liquid_height=current_dis_liquid_height,
blow_out_air_volume=current_dis_blow_out_air_volume,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
await self.touch_tip(current_targets)
await self.discard_tips()
except Exception as e:
traceback.print_exc()
raise RuntimeError(f"Liquid addition failed: {e}") from e
# ---------------------------------------------------------------
# ADD LIQUID -----------------------------------------------------
# ---------------------------------------------------------------
async def add_liquid(
self,
asp_vols: Union[List[float], float],
dis_vols: Union[List[float], float],
reagent_sources: Sequence[Container],
targets: Sequence[Container],
*,
use_channels: Optional[List[int]] = None,
flow_rates: Optional[List[Optional[float]]] = None,
offsets: Optional[List[Coordinate]] = None,
liquid_height: Optional[List[Optional[float]]] = None,
blow_out_air_volume: Optional[List[Optional[float]]] = None,
spread: Optional[Literal["wide", "tight", "custom"]] = "wide",
is_96_well: bool = False,
delays: Optional[List[int]] = None,
mix_time: Optional[int] = None,
mix_vol: Optional[int] = None,
mix_rate: Optional[int] = None,
mix_liquid_height: Optional[float] = None,
none_keys: List[str] = [],
):
# """A complete *add* (aspirate reagent → dispense into targets) operation."""
# # try:
if is_96_well:
pass # This mode is not verified.
else:
if len(asp_vols) != len(targets):
raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.")
# 首先应该对任务分组然后每次1个/8个进行操作处理
if len(use_channels) == 1:
for _ in range(len(targets)):
tip = []
for x in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
await self.aspirate(
resources=[reagent_sources[_]],
vols=[asp_vols[_]],
use_channels=use_channels,
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,
blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
await self.dispense(
resources=[targets[_]],
vols=[dis_vols[_]],
use_channels=use_channels,
flow_rates=[flow_rates[1]] if flow_rates else None,
offsets=[offsets[1]] if offsets else None,
blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
liquid_height=[liquid_height[1]] if liquid_height else None,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
# 只有在 mix_time 有效时才调用 mix
if mix_time is not None and mix_time > 0:
await self.mix(
targets=[targets[_]],
mix_time=mix_time,
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,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
await self.touch_tip(targets[_])
await self.discard_tips()
elif len(use_channels) == 8:
# 对于8个的情况需要判断此时任务是不是能被8通道移液站来成功处理
if len(targets) % 8 != 0:
raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.")
for i in range(0, len(targets), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
current_targets = targets[i:i + 8]
current_reagent_sources = reagent_sources[i:i + 8]
current_asp_vols = asp_vols[i:i + 8]
current_dis_vols = dis_vols[i:i + 8]
current_asp_flow_rates = flow_rates[i:i + 8] if flow_rates else [None] * 8
current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8
current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8
current_dis_offset = offsets[-i*8-8:len(offsets)-i*8] if offsets else [None] * 8
current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8
current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
current_dis_blow_out_air_volume = blow_out_air_volume[-i*8-8:len(blow_out_air_volume)-i*8] if blow_out_air_volume else [None] * 8
await self.aspirate(
resources=current_reagent_sources,
vols=current_asp_vols,
use_channels=use_channels,
flow_rates=current_asp_flow_rates,
offsets=current_asp_offset,
liquid_height=current_asp_liquid_height,
blow_out_air_volume=current_asp_blow_out_air_volume,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
await self.dispense(
resources=current_targets,
vols=current_dis_vols,
use_channels=use_channels,
flow_rates=current_dis_flow_rates,
offsets=current_dis_offset,
liquid_height=current_dis_liquid_height,
blow_out_air_volume=current_dis_blow_out_air_volume,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
# 只有在 mix_time 有效时才调用 mix
if mix_time is not None and mix_time > 0:
await self.mix(
targets=current_targets,
mix_time=mix_time,
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,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
await self.touch_tip(current_targets)
await self.discard_tips()
# except Exception as e:
# traceback.print_exc()
# raise RuntimeError(f"Liquid addition failed: {e}") from e
# ---------------------------------------------------------------
# TRANSFER LIQUID ------------------------------------------------
# ---------------------------------------------------------------
async 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 liquid with automatic mode detection.
Supports three transfer modes:
1. One-to-many (1 source -> N targets): Distribute from one source to multiple targets
2. One-to-one (N sources -> N targets): Standard transfer, each source to corresponding target
3. Many-to-one (N sources -> 1 target): Combine multiple sources into one target
Parameters
----------
asp_vols, dis_vols
Single volume (µL) or list. Automatically expanded based on transfer mode.
sources, targets
Containers (wells or plates). Length determines transfer mode:
- len(sources) == 1, len(targets) > 1: One-to-many mode
- len(sources) == len(targets): One-to-one mode
- len(sources) > 1, len(targets) == 1: Many-to-one mode
tip_racks
One or more TipRacks providing fresh tips.
is_96_well
Set *True* to use the 96channel head.
"""
# 确保 use_channels 有默认值
if use_channels is None:
use_channels = [0] if self.channel_num >= 1 else list(range(self.channel_num))
if is_96_well:
pass # This mode is not verified.
else:
# 转换体积参数为列表
if isinstance(asp_vols, (int, float)):
asp_vols = [float(asp_vols)]
else:
asp_vols = [float(v) for v in asp_vols]
if isinstance(dis_vols, (int, float)):
dis_vols = [float(dis_vols)]
else:
dis_vols = [float(v) for v in dis_vols]
# 统一混合次数为标量,防止数组/列表与 int 比较时报错
if mix_times is not None and not isinstance(mix_times, (int, float)):
try:
mix_times = mix_times[0] if len(mix_times) > 0 else None
except Exception:
try:
mix_times = next(iter(mix_times))
except Exception:
pass
if mix_times is not None:
mix_times = int(mix_times)
# 识别传输模式
num_sources = len(sources)
num_targets = len(targets)
if num_sources == 1 and num_targets > 1:
# 模式1: 一对多 (1 source -> N targets)
await self._transfer_one_to_many(
sources[0], targets, tip_racks, use_channels,
asp_vols, dis_vols, asp_flow_rates, dis_flow_rates,
offsets, touch_tip, liquid_height, blow_out_air_volume,
spread, mix_stage, mix_times, mix_vol, mix_rate,
mix_liquid_height, delays
)
elif num_sources > 1 and num_targets == 1:
# 模式2: 多对一 (N sources -> 1 target)
await self._transfer_many_to_one(
sources, targets[0], tip_racks, use_channels,
asp_vols, dis_vols, asp_flow_rates, dis_flow_rates,
offsets, touch_tip, liquid_height, blow_out_air_volume,
spread, mix_stage, mix_times, mix_vol, mix_rate,
mix_liquid_height, delays
)
elif num_sources == num_targets:
# 模式3: 一对一 (N sources -> N targets) - 原有逻辑
await self._transfer_one_to_one(
sources, targets, tip_racks, use_channels,
asp_vols, dis_vols, asp_flow_rates, dis_flow_rates,
offsets, touch_tip, liquid_height, blow_out_air_volume,
spread, mix_stage, mix_times, mix_vol, mix_rate,
mix_liquid_height, delays
)
else:
raise ValueError(
f"Unsupported transfer mode: {num_sources} sources -> {num_targets} targets. "
"Supported modes: 1->N, N->1, or N->N."
)
async def _transfer_one_to_one(
self,
sources: Sequence[Container],
targets: Sequence[Container],
tip_racks: Sequence[TipRack],
use_channels: List[int],
asp_vols: List[float],
dis_vols: List[float],
asp_flow_rates: Optional[List[Optional[float]]],
dis_flow_rates: Optional[List[Optional[float]]],
offsets: Optional[List[Coordinate]],
touch_tip: bool,
liquid_height: Optional[List[Optional[float]]],
blow_out_air_volume: Optional[List[Optional[float]]],
spread: Literal["wide", "tight", "custom"],
mix_stage: Optional[Literal["none", "before", "after", "both"]],
mix_times: Optional[int],
mix_vol: Optional[int],
mix_rate: Optional[int],
mix_liquid_height: Optional[float],
delays: Optional[List[int]],
):
"""一对一传输模式N sources -> N targets"""
# 验证参数长度
if len(asp_vols) != len(targets):
raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.")
if len(dis_vols) != len(targets):
raise ValueError(f"Length of `dis_vols` {len(dis_vols)} must match `targets` {len(targets)}.")
if len(sources) != len(targets):
raise ValueError(f"Length of `sources` {len(sources)} must match `targets` {len(targets)}.")
if len(use_channels) == 1:
for _ in range(len(targets)):
tip = []
for ___ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
await self.aspirate(
resources=[sources[_]],
vols=[asp_vols[_]],
use_channels=use_channels,
flow_rates=[asp_flow_rates[_]] if asp_flow_rates and len(asp_flow_rates) > _ else None,
offsets=[offsets[_]] if offsets and len(offsets) > _ else None,
liquid_height=[liquid_height[_]] if liquid_height and len(liquid_height) > _ else None,
blow_out_air_volume=[blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
await self.dispense(
resources=[targets[_]],
vols=[dis_vols[_]],
use_channels=use_channels,
flow_rates=[dis_flow_rates[_]] if dis_flow_rates and len(dis_flow_rates) > _ else None,
offsets=[offsets[_]] if offsets and len(offsets) > _ else None,
blow_out_air_volume=[blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None,
liquid_height=[liquid_height[_]] if liquid_height and len(liquid_height) > _ else None,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=[targets[_]],
mix_time=mix_times,
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,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
await self.touch_tip(targets[_])
await self.discard_tips(use_channels=use_channels)
elif len(use_channels) == 8:
if len(targets) % 8 != 0:
raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.")
for i in range(0, len(targets), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
current_targets = targets[i:i + 8]
current_reagent_sources = sources[i:i + 8]
current_asp_vols = asp_vols[i:i + 8]
current_dis_vols = dis_vols[i:i + 8]
current_asp_flow_rates = asp_flow_rates[i:i + 8] if asp_flow_rates else None
current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8
current_dis_offset = offsets[i:i + 8] if offsets else [None] * 8
current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
current_dis_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
current_dis_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else None
await self.aspirate(
resources=current_reagent_sources,
vols=current_asp_vols,
use_channels=use_channels,
flow_rates=current_asp_flow_rates,
offsets=current_asp_offset,
blow_out_air_volume=current_asp_blow_out_air_volume,
liquid_height=current_asp_liquid_height,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
await self.dispense(
resources=current_targets,
vols=current_dis_vols,
use_channels=use_channels,
flow_rates=current_dis_flow_rates,
offsets=current_dis_offset,
blow_out_air_volume=current_dis_blow_out_air_volume,
liquid_height=current_dis_liquid_height,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=current_targets,
mix_time=mix_times,
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,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
await self.touch_tip(current_targets)
await self.discard_tips([0,1,2,3,4,5,6,7])
async def _transfer_one_to_many(
self,
source: Container,
targets: Sequence[Container],
tip_racks: Sequence[TipRack],
use_channels: List[int],
asp_vols: List[float],
dis_vols: List[float],
asp_flow_rates: Optional[List[Optional[float]]],
dis_flow_rates: Optional[List[Optional[float]]],
offsets: Optional[List[Coordinate]],
touch_tip: bool,
liquid_height: Optional[List[Optional[float]]],
blow_out_air_volume: Optional[List[Optional[float]]],
spread: Literal["wide", "tight", "custom"],
mix_stage: Optional[Literal["none", "before", "after", "both"]],
mix_times: Optional[int],
mix_vol: Optional[int],
mix_rate: Optional[int],
mix_liquid_height: Optional[float],
delays: Optional[List[int]],
):
"""一对多传输模式1 source -> N targets"""
# 验证和扩展体积参数
if len(asp_vols) == 1:
# 如果只提供一个吸液体积,计算总吸液体积(所有分液体积之和)
total_asp_vol = sum(dis_vols)
asp_vol = asp_vols[0] if asp_vols[0] >= total_asp_vol else total_asp_vol
else:
raise ValueError("For one-to-many mode, `asp_vols` should be a single value or list with one element.")
if len(dis_vols) != len(targets):
raise ValueError(f"Length of `dis_vols` {len(dis_vols)} must match `targets` {len(targets)}.")
if len(use_channels) == 1:
# 单通道模式:一次吸液,多次分液
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
# 从源容器吸液(总体积)
await self.aspirate(
resources=[source],
vols=[asp_vol],
use_channels=use_channels,
flow_rates=[asp_flow_rates[0]] if asp_flow_rates and len(asp_flow_rates) > 0 else None,
offsets=[offsets[0]] if offsets and len(offsets) > 0 else None,
liquid_height=[liquid_height[0]] if liquid_height and len(liquid_height) > 0 else None,
blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
# 分多次分液到不同的目标容器
for idx, target in enumerate(targets):
await self.dispense(
resources=[target],
vols=[dis_vols[idx]],
use_channels=use_channels,
flow_rates=[dis_flow_rates[idx]] if dis_flow_rates and len(dis_flow_rates) > idx else None,
offsets=[offsets[idx]] if offsets and len(offsets) > idx else None,
blow_out_air_volume=[blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None,
liquid_height=[liquid_height[idx]] if liquid_height and len(liquid_height) > idx else None,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=[target],
mix_time=mix_times,
mix_vol=mix_vol,
offsets=offsets[idx:idx+1] 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,
)
if touch_tip:
await self.touch_tip([target])
await self.discard_tips(use_channels=use_channels)
elif len(use_channels) == 8:
# 8通道模式需要确保目标数量是8的倍数
if len(targets) % 8 != 0:
raise ValueError(f"For 8-channel mode, number of targets {len(targets)} must be a multiple of 8.")
# 每次处理8个目标
for i in range(0, len(targets), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
current_targets = targets[i:i + 8]
current_dis_vols = dis_vols[i:i + 8]
# 8个通道都从同一个源容器吸液每个通道的吸液体积等于对应的分液体积
current_asp_flow_rates = asp_flow_rates[0:1] * 8 if asp_flow_rates and len(asp_flow_rates) > 0 else None
current_asp_offset = offsets[0:1] * 8 if offsets and len(offsets) > 0 else [None] * 8
current_asp_liquid_height = liquid_height[0:1] * 8 if liquid_height and len(liquid_height) > 0 else [None] * 8
current_asp_blow_out_air_volume = blow_out_air_volume[0:1] * 8 if blow_out_air_volume and len(blow_out_air_volume) > 0 else [None] * 8
# 从源容器吸液8个通道都从同一个源但每个通道的吸液体积不同
await self.aspirate(
resources=[source] * 8, # 8个通道都从同一个源
vols=current_dis_vols, # 每个通道的吸液体积等于对应的分液体积
use_channels=use_channels,
flow_rates=current_asp_flow_rates,
offsets=current_asp_offset,
liquid_height=current_asp_liquid_height,
blow_out_air_volume=current_asp_blow_out_air_volume,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
# 分液到8个目标
current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else None
current_dis_offset = offsets[i:i + 8] if offsets else [None] * 8
current_dis_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
current_dis_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
await self.dispense(
resources=current_targets,
vols=current_dis_vols,
use_channels=use_channels,
flow_rates=current_dis_flow_rates,
offsets=current_dis_offset,
blow_out_air_volume=current_dis_blow_out_air_volume,
liquid_height=current_dis_liquid_height,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=current_targets,
mix_time=mix_times,
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,
)
if touch_tip:
await self.touch_tip(current_targets)
await self.discard_tips([0,1,2,3,4,5,6,7])
async def _transfer_many_to_one(
self,
sources: Sequence[Container],
target: Container,
tip_racks: Sequence[TipRack],
use_channels: List[int],
asp_vols: List[float],
dis_vols: List[float],
asp_flow_rates: Optional[List[Optional[float]]],
dis_flow_rates: Optional[List[Optional[float]]],
offsets: Optional[List[Coordinate]],
touch_tip: bool,
liquid_height: Optional[List[Optional[float]]],
blow_out_air_volume: Optional[List[Optional[float]]],
spread: Literal["wide", "tight", "custom"],
mix_stage: Optional[Literal["none", "before", "after", "both"]],
mix_times: Optional[int],
mix_vol: Optional[int],
mix_rate: Optional[int],
mix_liquid_height: Optional[float],
delays: Optional[List[int]],
):
"""多对一传输模式N sources -> 1 target汇总/混合)"""
# 验证和扩展体积参数
if len(asp_vols) != len(sources):
raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `sources` {len(sources)}.")
# 支持两种模式:
# 1. dis_vols 为单个值:所有源汇总,使用总吸液体积或指定分液体积
# 2. dis_vols 长度等于 asp_vols每个源按不同比例分液按比例混合
if len(dis_vols) == 1:
# 模式1使用单个分液体积
total_dis_vol = sum(asp_vols)
dis_vol = dis_vols[0] if dis_vols[0] >= total_dis_vol else total_dis_vol
use_proportional_mixing = False
elif len(dis_vols) == len(asp_vols):
# 模式2按不同比例混合
use_proportional_mixing = True
else:
raise ValueError(
f"For many-to-one mode, `dis_vols` should be a single value or list with length {len(asp_vols)} "
f"(matching `asp_vols`). Got length {len(dis_vols)}."
)
if len(use_channels) == 1:
# 单通道模式:多次吸液,一次分液
# 先混合前(如果需要)
if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0:
# 注意:在吸液前混合源容器通常不常见,这里跳过
pass
# 从每个源容器吸液并分液到目标容器
for idx, source in enumerate(sources):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
await self.aspirate(
resources=[source],
vols=[asp_vols[idx]],
use_channels=use_channels,
flow_rates=[asp_flow_rates[idx]] if asp_flow_rates and len(asp_flow_rates) > idx else None,
offsets=[offsets[idx]] if offsets and len(offsets) > idx else None,
liquid_height=[liquid_height[idx]] if liquid_height and len(liquid_height) > idx else None,
blow_out_air_volume=[blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
# 分液到目标容器
if use_proportional_mixing:
# 按不同比例混合:使用对应的 dis_vols
dis_vol = dis_vols[idx]
dis_flow_rate = dis_flow_rates[idx] if dis_flow_rates and len(dis_flow_rates) > idx else None
dis_offset = offsets[idx] if offsets and len(offsets) > idx else None
dis_liquid_height = liquid_height[idx] if liquid_height and len(liquid_height) > idx else None
dis_blow_out = blow_out_air_volume[idx] if blow_out_air_volume and len(blow_out_air_volume) > idx else None
else:
# 标准模式:分液体积等于吸液体积
dis_vol = asp_vols[idx]
dis_flow_rate = dis_flow_rates[0] if dis_flow_rates and len(dis_flow_rates) > 0 else None
dis_offset = offsets[0] if offsets and len(offsets) > 0 else None
dis_liquid_height = liquid_height[0] if liquid_height and len(liquid_height) > 0 else None
dis_blow_out = blow_out_air_volume[0] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None
await self.dispense(
resources=[target],
vols=[dis_vol],
use_channels=use_channels,
flow_rates=[dis_flow_rate] if dis_flow_rate is not None else None,
offsets=[dis_offset] if dis_offset is not None else None,
blow_out_air_volume=[dis_blow_out] if dis_blow_out is not None else None,
liquid_height=[dis_liquid_height] if dis_liquid_height is not None else None,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
await self.discard_tips(use_channels=use_channels)
# 最后在目标容器中混合(如果需要)
if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=[target],
mix_time=mix_times,
mix_vol=mix_vol,
offsets=offsets[0:1] 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,
)
if touch_tip:
await self.touch_tip([target])
elif len(use_channels) == 8:
# 8通道模式需要确保源数量是8的倍数
if len(sources) % 8 != 0:
raise ValueError(f"For 8-channel mode, number of sources {len(sources)} must be a multiple of 8.")
# 每次处理8个源
for i in range(0, len(sources), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
await self.pick_up_tips(tip)
current_sources = sources[i:i + 8]
current_asp_vols = asp_vols[i:i + 8]
current_asp_flow_rates = asp_flow_rates[i:i + 8] if asp_flow_rates else None
current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8
current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
# 从8个源容器吸液
await self.aspirate(
resources=current_sources,
vols=current_asp_vols,
use_channels=use_channels,
flow_rates=current_asp_flow_rates,
offsets=current_asp_offset,
blow_out_air_volume=current_asp_blow_out_air_volume,
liquid_height=current_asp_liquid_height,
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
# 分液到目标容器(每个通道分液到同一个目标)
if use_proportional_mixing:
# 按比例混合:使用对应的 dis_vols
current_dis_vols = dis_vols[i:i + 8]
current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else None
current_dis_offset = offsets[i:i + 8] if offsets else [None] * 8
current_dis_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
current_dis_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
else:
# 标准模式:每个通道分液体积等于其吸液体积
current_dis_vols = current_asp_vols
current_dis_flow_rates = dis_flow_rates[0:1] * 8 if dis_flow_rates else None
current_dis_offset = offsets[0:1] * 8 if offsets else [None] * 8
current_dis_liquid_height = liquid_height[0:1] * 8 if liquid_height else [None] * 8
current_dis_blow_out_air_volume = blow_out_air_volume[0:1] * 8 if blow_out_air_volume else [None] * 8
await self.dispense(
resources=[target] * 8, # 8个通道都分到同一个目标
vols=current_dis_vols,
use_channels=use_channels,
flow_rates=current_dis_flow_rates,
offsets=current_dis_offset,
blow_out_air_volume=current_dis_blow_out_air_volume,
liquid_height=current_dis_liquid_height,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
await self.discard_tips([0,1,2,3,4,5,6,7])
# 最后在目标容器中混合(如果需要)
if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=[target],
mix_time=mix_times,
mix_vol=mix_vol,
offsets=offsets[0:1] 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,
)
if touch_tip:
await self.touch_tip([target])
# except Exception as e:
# traceback.print_exc()
# raise RuntimeError(f"Liquid addition failed: {e}") from e
# ---------------------------------------------------------------
# Helper utilities
# ---------------------------------------------------------------
async def custom_delay(self, seconds=0, msg=None):
"""
seconds: seconds to wait
msg: information to be printed
"""
if seconds != None and seconds > 0:
if msg:
print(f"Waiting time: {msg}")
print(f"Current time: {time.strftime('%H:%M:%S')}")
print(f"Time to finish: {time.strftime('%H:%M:%S', time.localtime(time.time() + seconds))}")
await self._ros_node.sleep(seconds)
if msg:
print(f"Done: {msg}")
print(f"Current time: {time.strftime('%H:%M:%S')}")
async def touch_tip(self, targets: Sequence[Container]):
"""Touch the tip to the side of the well."""
if not self.support_touch_tip:
return
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)],
liquid_height=None,
blow_out_air_volume=None,
)
# 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)],
liquid_height=None,
blow_out_air_volume=None,
)
async def mix(
self,
targets: Sequence[Container],
mix_time: int = None,
mix_vol: Optional[int] = None,
height_to_bottom: Optional[float] = None,
offsets: Optional[Coordinate] = None,
mix_rate: Optional[float] = None,
none_keys: List[str] = [],
):
if mix_time is None: # No mixing required
return
"""Mix the liquid in the target wells."""
for _ in range(mix_time):
await self.aspirate(
resources=[targets],
vols=[mix_vol],
flow_rates=[mix_rate] if mix_rate else None,
offsets=[offsets] if offsets else None,
liquid_height=[height_to_bottom] if height_to_bottom else None,
)
await self.custom_delay(seconds=1)
await self.dispense(
resources=[targets],
vols=[mix_vol],
flow_rates=[mix_rate] if mix_rate else None,
offsets=[offsets] if offsets else None,
liquid_height=[height_to_bottom] if height_to_bottom else None,
)
def iter_tips(self, tip_racks: Sequence[TipRack]) -> Iterator[Resource]:
"""Yield tips from a list of TipRacks one-by-one until depleted."""
for rack in tip_racks:
for tip in rack:
yield tip
raise RuntimeError("Out of tips!")
def set_tiprack(self, tip_racks: Sequence[TipRack]):
"""Set the tip racks for the liquid handler."""
self.tip_racks = tip_racks
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):
"""
Move a single channel to a specific well with a given z-height.
Parameters
----------
well : Well
The target well.
dis_to_top : float
Height in mm to move to relative to the well top.
channel : int
Pipetting channel to move (default: 0).
"""
await self.prepare_for_manual_channel_operation(channel=channel)
abs_loc = well.get_absolute_location()
well_height = well.get_absolute_size_z()
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)