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https://github.com/dptech-corp/Uni-Lab-OS.git
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281 lines
9.3 KiB
Python
281 lines
9.3 KiB
Python
import requests
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from typing import List, Sequence, Optional, Union, Literal
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from geometry_msgs.msg import Point
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from unilabos_msgs.msg import Resource
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from pylabrobot.resources import (
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TipRack,
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Container,
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Coordinate,
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)
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from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker # type: ignore
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from .liquid_handler_abstract import LiquidHandlerAbstract
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import json
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from typing import Sequence, Optional, List, Union, Literal
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class LiquidHandlerBiomek(LiquidHandlerAbstract):
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"""
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Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
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该类用于处理Biomek液体处理器的特定操作。
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"""
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def __init__(self, *args, **kwargs):
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super().__init__(*args, **kwargs)
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self._status = "Idle" # 初始状态为 Idle
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self._success = False # 初始成功状态为 False
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self._status_queue = kwargs.get("status_queue", None) # 状态队列
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self.temp_protocol = {}
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self.py32_path = "/opt/py32" # Biomek的Python 3.2路径
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self.technique = {
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'MC P300 high':{
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"use_channels": "Span8",
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"asp_vols": [50],
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"asp_flow_rates": 50,
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"dis_flow_rates": 50,
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"offsets": None,
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"touch_tip": True,
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"liquid_height": 20,
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"blow_out_air_volume": 20,
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"spread": "wide",
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"is_96_well": True,
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"mix_stage": "none",
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"mix_times": None,
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"mix_vol": None,
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"mix_rate": None,
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"mix_liquid_height": None,
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"delays": None,
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"none_keys": []
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}
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}
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def create_protocol(
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self,
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protocol_name: str,
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protocol_description: str,
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protocol_version: str,
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protocol_author: str,
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protocol_date: str,
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protocol_type: str,
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none_keys: List[str] = [],
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):
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"""
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创建一个新的协议。
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Args:
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protocol_name (str): 协议名称
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protocol_description (str): 协议描述
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protocol_version (str): 协议版本
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protocol_author (str): 协议作者
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protocol_date (str): 协议日期
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protocol_type (str): 协议类型
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none_keys (List[str]): 需要设置为None的键列表
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Returns:
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dict: 创建的协议字典
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"""
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self.temp_protocol = {
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"meta": {
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"name": protocol_name,
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"description": protocol_description,
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"version": protocol_version,
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"author": protocol_author,
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"date": protocol_date,
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"type": protocol_type,
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},
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"labwares": [],
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"steps": [],
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}
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return self.temp_protocol
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def run_protocol(self):
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"""
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执行创建的实验流程。
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工作站的完整执行流程是，
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从 create_protocol 开始，创建新的 method，
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随后执行 transfer_liquid 等操作向实验流程添加步骤，
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最后 run_protocol 执行整个方法。
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Returns:
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dict: 执行结果
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"""
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#use popen or subprocess to create py32 process and communicate send the temp protocol to it
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if not self.temp_protocol:
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raise ValueError("No protocol created. Please create a protocol first.")
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# 模拟执行协议
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self._status = "Running"
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self._success = True
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# 在这里可以添加实际执行协议的逻辑
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response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
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def create_resource(
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self,
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resource_tracker: DeviceNodeResourceTracker,
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resources: list[Resource],
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bind_parent_id: str,
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bind_location: dict[str, float],
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liquid_input_slot: list[int],
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liquid_type: list[str],
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liquid_volume: list[int],
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slot_on_deck: int,
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):
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"""
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创建一个新的资源。
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Args:
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device_id (str): 设备ID
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res_id (str): 资源ID
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class_name (str): 资源类名
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parent (str): 父级ID
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bind_locations (Point): 绑定位置
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liquid_input_slot (list[int]): 液体输入槽列表
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liquid_type (list[str]): 液体类型列表
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liquid_volume (list[int]): 液体体积列表
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slot_on_deck (int): 甲板上的槽位
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Returns:
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dict: 创建的资源字典
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"""
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# TODO：需要对好接口，下面这个是临时的
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for resource in resources:
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res_id = resource.id
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class_name = resource.class_name
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parent = bind_parent_id
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bind_locations = Coordinate.from_point(resource.bind_location)
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liquid_input_slot = liquid_input_slot
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liquid_type = liquid_type
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liquid_volume = liquid_volume
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slot_on_deck = slot_on_deck
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resource = {
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"id": res_id,
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"class": class_name,
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"parent": parent,
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"bind_locations": bind_locations.to_dict(),
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"liquid_input_slot": liquid_input_slot,
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"liquid_type": liquid_type,
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"liquid_volume": liquid_volume,
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"slot_on_deck": slot_on_deck,
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}
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self.temp_protocol["labwares"].append(resource)
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return resource
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def transfer_liquid(
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self,
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sources: Sequence[Container],
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targets: Sequence[Container],
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tip_racks: Sequence[TipRack],
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solvent: Optional[str] = None,
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TipLocation :str = None,
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*,
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use_channels: Optional[List[int]] = None,
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asp_vols: Union[List[float], float],
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dis_vols: Union[List[float], float],
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asp_flow_rates: Optional[List[Optional[float]]] = None,
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dis_flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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touch_tip: bool = False,
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liquid_height: Optional[List[Optional[float]]] = None,
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blow_out_air_volume: Optional[List[Optional[float]]] = None,
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spread: Literal["wide", "tight", "custom"] = "wide",
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is_96_well: bool = False,
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mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
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mix_times: Optional[int] = None,
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mix_vol: Optional[int] = None,
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mix_rate: Optional[int] = None,
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mix_liquid_height: Optional[float] = None,
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delays: Optional[List[int]] = None,
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none_keys: List[str] = []
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):
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transfer_params = {
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"Span8": False,
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"Pod": "Pod1",
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"items": {},
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"Wash": False,
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"Dynamic?": True,
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"AutoSelectActiveWashTechnique": False,
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"ActiveWashTechnique": "",
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"ChangeTipsBetweenDests": False,
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"ChangeTipsBetweenSources": False,
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"DefaultCaption": "",
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"UseExpression": False,
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"LeaveTipsOn": False,
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"MandrelExpression": "",
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"Repeats": "1",
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"RepeatsByVolume": False,
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"Replicates": "1",
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"ShowTipHandlingDetails": False,
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"ShowTransferDetails": True,
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"Solvent": "Water",
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"Span8Wash": False,
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"Span8WashVolume": "2",
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"Span8WasteVolume": "1",
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"SplitVolume": False,
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"SplitVolumeCleaning": False,
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"Stop": "Destinations",
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"TipLocation": "BC1025F",
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"UseCurrentTips": False,
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"UseDisposableTips": True,
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"UseFixedTips": False,
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"UseJIT": True,
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"UseMandrelSelection": True,
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"UseProbes": [True, True, True, True, True, True, True, True],
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"WashCycles": "1",
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"WashVolume": "110%",
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"Wizard": False
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}
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items: dict = {}
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for idx, (src, dst) in enumerate(zip(sources, targets)):
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items[str(idx)] = {
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"Source": str(src),
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"Destination": str(dst),
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"Volume": dis_vols[idx]
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}
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transfer_params["items"] = items
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transfer_params["Solvent"] = solvent if solvent else "Water"
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transfer_params["TipLocation"] = TipLocation
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if len(tip_racks) == 1:
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transfer_params['UseCurrentTips'] = True
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elif len(tip_racks) > 1:
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transfer_params["ChangeTipsBetweenDests"] = True
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self.temp_protocol["steps"].append(transfer_params)
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return
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def transfer_biomek(
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self,
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parameters: dict,
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technique: str,
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):
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"""
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处理Biomek的液体转移操作。
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"""
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sources = parameters.get("source")
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targets = parameters.get("target")
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tip_rack = parameters.get("tip_rack")
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volume = parameters.get("volume")
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liquid_type = parameters.get("liquid_type", "Well Content")
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other_params = self.technique.get(technique, {})
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self.transfer_liquid(
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sources=[sources],
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targets=[targets],
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TipLocation=tip_rack,
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tip_racks=[tip_rack],
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solvent=liquid_type,
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dis_vols=[volume],
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**other_params
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)
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return
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