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))