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Biomek test

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This commit is contained in:
Guangxin Zhang
2025-06-04 16:38:18 +08:00
parent 6d2489af5f
commit 147b8f47c0
2 changed files with 623 additions and 7 deletions
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58
unilabos/devices/liquid_handling/biomek.py
View File

@@ -15,8 +15,8 @@ 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。
@@ -29,6 +29,28 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
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.technique = {
'MC P300 high':{
"use_channels": "Span8",
"asp_vols": [50],
"asp_flow_rates": 50,
"dis_flow_rates": 50,
"offsets": None,
"touch_tip": True,
"liquid_height": 20,
"blow_out_air_volume": 20,
"spread": "wide",
"is_96_well": True,
"mix_stage": "none",
"mix_times": None,
"mix_vol": None,
"mix_rate": None,
"mix_liquid_height": None,
"delays": None,
"none_keys": []
}
}
def create_protocol(
self,
@@ -143,7 +165,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
targets: Sequence[Container],
tip_racks: Sequence[TipRack],
solvent: Optional[str] = None,
TipLocation: Optional[str] = None,
TipLocation :str = None,
*,
use_channels: Optional[List[int]] = None,
asp_vols: Union[List[float], float],
@@ -157,7 +179,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
spread: Literal["wide", "tight", "custom"] = "wide",
is_96_well: bool = False,
mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
mix_times: Optional[List(int)] = None,
mix_times: Optional[int] = None,
mix_vol: Optional[int] = None,
mix_rate: Optional[int] = None,
mix_liquid_height: Optional[float] = None,
@@ -208,14 +230,14 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
items[str(idx)] = {
"Source": str(src),
"Destination": str(dst),
"Volume": asp_vols[idx]
"Volume": dis_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
transfer_params['UseCurrentTips'] = True
elif len(tip_racks) > 1:
transfer_params["ChangeTipsBetweenDests"] = True
@@ -223,3 +245,29 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
return
def transfer_biomek(
self,
parameters: dict,
technique: str,
):
"""
处理Biomek的液体转移操作。
"""
sources = parameters.get("source")
targets = parameters.get("target")
tip_rack = parameters.get("tip_rack")
volume = parameters.get("volume")
liquid_type = parameters.get("liquid_type", "Well Content")
other_params = self.technique.get(technique, {})
self.transfer_liquid(
sources=[sources],
targets=[targets],
TipLocation=tip_rack,
tip_racks=[tip_rack],
solvent=liquid_type,
dis_vols=[volume],
**other_params
)
return

568
unilabos/devices/liquid_handling/biomek_test.py Normal file
View File

@@ -0,0 +1,568 @@
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（700-900rpm，300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.technique = {
'MC P300 high':{
"use_channels": "Span8",
"asp_vols": [50],
"asp_flow_rates": 50,
"dis_flow_rates": 50,
"offsets": None,
"touch_tip": True,
"liquid_height": 20,
"blow_out_air_volume": 20,
"spread": "wide",
"is_96_well": True,
"mix_stage": "none",
"mix_times": None,
"mix_vol": None,
"mix_rate": None,
"mix_liquid_height": None,
"delays": None,
"none_keys": []
}
}
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_liquid(
self,
sources: Sequence[Container],
targets: Sequence[Container],
tip_racks: Sequence[TipRack],
solvent: Optional[str] = None,
TipLocation :str = None,
*,
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": "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": dis_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
self.temp_protocol["steps"].append(transfer_params)
return
def transfer_biomek(
self,
parameters: dict,
technique: str,
):
"""
创建一个Biomek液体处理器的转移步骤。
Args:
step_number (int): 步骤编号
operation (str): 操作类型
description (str): 步骤描述
parameters (dict): 步骤参数
Returns:
dict: 创建的转移步骤字典
"""
sources = parameters.get("source")
targets = parameters.get("target")
tip_rack = parameters.get("tip_rack")
volume = parameters.get("volume")
liquid_type = parameters.get("liquid_type", "Well Content")
other_params = self.technique.get(technique, {})
self.transfer_liquid(
sources=[sources],
targets=[targets],
TipLocation=tip_rack,
tip_racks=[tip_rack],
solvent=liquid_type,
dis_vols=[volume],
**other_params
)
return
handler = LiquidHandlerBiomek()
handler.temp_protocol = {
"meta": {},
"labwares": [],
"steps": []
}
input_steps = json.loads(steps_info)
for step in input_steps['steps']:
if step['operation'] != 'transfer':
continue
parameters = step['parameters']
handler.transfer_biomek(parameters, technique='MC P300 high')
print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))