import requests from typing import List, Sequence, Optional, Union, Literal from geometry_msgs.msg import Point from pylabrobot.liquid_handling import LiquidHandler from unilabos_msgs.msg import Resource from pylabrobot.resources import ( TipRack, Container, Coordinate, ) from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker # type: ignore from .liquid_handler_abstract import LiquidHandlerAbstract import json from typing import Sequence, Optional, List, Union, Literal class LiquidHandlerBiomek(LiquidHandlerAbstract): """ Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。 该类用于处理Biomek液体处理器的特定操作。 """ def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._status = "Idle" # 初始状态为 Idle self._success = False # 初始成功状态为 False self._status_queue = kwargs.get("status_queue", None) # 状态队列 self.temp_protocol = {} self.py32_path = "/opt/py32" # Biomek的Python 3.2路径 self.aspirate_techniques = { 'MC P300 high':{ 'Position': 'P1', 'Height': -2.0, 'Volume': '50', 'liquidtype': 'Well Contents', 'WellsX': 12, 'LabwareClass': 'Matrix96_750uL', 'AutoSelectPrototype': True, 'ColsFirst': True, 'CustomHeight': False, 'DataSetPattern': False, 'HeightFrom': 0, 'LocalPattern': True, 'Operation': 'Aspirate', 'OverrideHeight': False, 'Pattern': (True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True), 'Prototype': 'MC P300 High', 'ReferencedPattern': '', 'RowsFirst': False, 'SectionExpression': '', 'SelectionInfo': (1,), 'SetMark': True, 'Source': True, 'StartAtMark': False, 'StartAtSelection': True, 'UseExpression': False}, } self.dispense_techniques = { 'MC P300 high':{ 'Position': 'P11', 'Height': -2.0, 'Volume': '50', 'liquidtype': 'Tip Contents', 'WellsX': 12, 'LabwareClass': 'Matrix96_750uL', 'AutoSelectPrototype': True, 'ColsFirst': True, 'CustomHeight': False, 'DataSetPattern': False, 'HeightFrom': 0, 'LocalPattern': True, 'Operation': 'Dispense', 'OverrideHeight': False, 'Pattern': (True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True), 'Prototype': 'MC P300 High', 'ReferencedPattern': '', 'RowsFirst': False, 'SectionExpression': '', 'SelectionInfo': (1,), 'SetMark': True, 'Source': False, 'StartAtMark': False, 'StartAtSelection': True, 'UseExpression': False} } @classmethod def deserialize(cls, data: dict, allow_marshal: bool = False) -> LiquidHandler: return LiquidHandler.deserialize(data, allow_marshal) def create_protocol( self, protocol_name: str, protocol_description: str, protocol_version: str, protocol_author: str, protocol_date: str, protocol_type: str, none_keys: List[str] = [], ): """ 创建一个新的协议。 Args: protocol_name (str): 协议名称 protocol_description (str): 协议描述 protocol_version (str): 协议版本 protocol_author (str): 协议作者 protocol_date (str): 协议日期 protocol_type (str): 协议类型 none_keys (List[str]): 需要设置为None的键列表 Returns: dict: 创建的协议字典 """ self.temp_protocol = { "meta": { "name": protocol_name, "description": protocol_description, "version": protocol_version, "author": protocol_author, "date": protocol_date, "type": protocol_type, }, "labwares": [], "steps": [], } return self.temp_protocol def run_protocol(self): """ 执行创建的实验流程。 工作站的完整执行流程是， 从 create_protocol 开始，创建新的 method， 随后执行 transfer_liquid 等操作向实验流程添加步骤， 最后 run_protocol 执行整个方法。 Returns: dict: 执行结果 """ #use popen or subprocess to create py32 process and communicate send the temp protocol to it if not self.temp_protocol: raise ValueError("No protocol created. Please create a protocol first.") # 模拟执行协议 self._status = "Running" self._success = True # 在这里可以添加实际执行协议的逻辑 response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol) def create_resource( self, resource_tracker: DeviceNodeResourceTracker, resources: list[Resource], bind_parent_id: str, bind_location: dict[str, float], liquid_input_slot: list[int], liquid_type: list[str], liquid_volume: list[int], slot_on_deck: int, ): """ 创建一个新的资源。 Args: device_id (str): 设备ID res_id (str): 资源ID class_name (str): 资源类名 parent (str): 父级ID bind_locations (Point): 绑定位置 liquid_input_slot (list[int]): 液体输入槽列表 liquid_type (list[str]): 液体类型列表 liquid_volume (list[int]): 液体体积列表 slot_on_deck (int): 甲板上的槽位 Returns: dict: 创建的资源字典 """ # TODO：需要对好接口，下面这个是临时的 for resource in resources: res_id = resource.id class_name = resource.class_name parent = bind_parent_id bind_locations = Coordinate.from_point(resource.bind_location) liquid_input_slot = liquid_input_slot liquid_type = liquid_type liquid_volume = liquid_volume slot_on_deck = slot_on_deck resource = { "id": res_id, "class": class_name, "parent": parent, "bind_locations": bind_locations.to_dict(), "liquid_input_slot": liquid_input_slot, "liquid_type": liquid_type, "liquid_volume": liquid_volume, "slot_on_deck": slot_on_deck, } self.temp_protocol["labwares"].append(resource) return resource def transfer_liquid( self, sources: Sequence[Container], targets: Sequence[Container], tip_racks: Sequence[TipRack], *, use_channels: Optional[List[int]] = None, asp_vols: Union[List[float], float], dis_vols: Union[List[float], float], asp_flow_rates: Optional[List[Optional[float]]] = None, dis_flow_rates: Optional[List[Optional[float]]] = None, offsets: Optional[List[Coordinate]] = None, touch_tip: bool = False, liquid_height: Optional[List[Optional[float]]] = None, blow_out_air_volume: Optional[List[Optional[float]]] = None, spread: Literal["wide", "tight", "custom"] = "wide", is_96_well: bool = False, mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none", mix_times: Optional[int] = None, mix_vol: Optional[int] = None, mix_rate: Optional[int] = None, mix_liquid_height: Optional[float] = None, delays: Optional[List[int]] = None, none_keys: List[str] = [] ): transfer_params = { "Span8": False, "Pod": "Pod1", "items": {}, "Wash": False, "Dynamic?": True, "AutoSelectActiveWashTechnique": False, "ActiveWashTechnique": "", "ChangeTipsBetweenDests": False, "ChangeTipsBetweenSources": False, "DefaultCaption": "", "UseExpression": False, "LeaveTipsOn": False, "MandrelExpression": "", "Repeats": "1", "RepeatsByVolume": False, "Replicates": "1", "ShowTipHandlingDetails": False, "ShowTransferDetails": True, "Solvent": "Well Content", "Span8Wash": False, "Span8WashVolume": "2", "Span8WasteVolume": "1", "SplitVolume": False, "SplitVolumeCleaning": False, "Stop": "Destinations", "TipLocation": "BC1025F", "UseCurrentTips": False, "UseDisposableTips": True, "UseFixedTips": False, "UseJIT": True, "UseMandrelSelection": True, "UseProbes": [True, True, True, True, True, True, True, True], "WashCycles": "1", "WashVolume": "110%", "Wizard": False } items: dict = {} for idx, (src, dst) in enumerate(zip(sources, targets)): items[str(idx)] = { "Source": str(src), "Destination": str(dst), "Volume": dis_vols[idx] } transfer_params["items"] = items transfer_params["Solvent"] = "Water" TipLocation = tip_racks[0].name transfer_params["TipLocation"] = TipLocation if len(tip_racks) == 1: transfer_params['UseCurrentTips'] = True elif len(tip_racks) > 1: transfer_params["ChangeTipsBetweenDests"] = True self.temp_protocol["steps"].append(transfer_params) return def transfer_biomek( self, source: str, target: str, tip_rack: str, volume: float, aspirate_techniques: str, dispense_techniques: str, ): """ 处理Biomek的液体转移操作。 """ items = [] asp_params = self.aspirate_techniques.get(aspirate_techniques, {}) dis_params = self.dispense_techniques.get(dispense_techniques, {}) asp_params['Position'] = source dis_params['Position'] = target asp_params['Volume'] = str(volume) dis_params['Volume'] = str(volume) items.append(asp_params) items.append(dis_params) transfer_params = { "Span8": False, "Pod": "Pod1", "items": [], "Wash": False, "Dynamic?": True, "AutoSelectActiveWashTechnique": False, "ActiveWashTechnique": "", "ChangeTipsBetweenDests": True, "ChangeTipsBetweenSources": False, "DefaultCaption": "", "UseExpression": False, "LeaveTipsOn": False, "MandrelExpression": "", "Repeats": "1", "RepeatsByVolume": False, "Replicates": "1", "ShowTipHandlingDetails": False, "ShowTransferDetails": True, "Solvent": "Water", "Span8Wash": False, "Span8WashVolume": "2", "Span8WasteVolume": "1", "SplitVolume": False, "SplitVolumeCleaning": False, "Stop": "Destinations", "TipLocation": "BC230", "UseCurrentTips": False, "UseDisposableTips": False, "UseFixedTips": False, "UseJIT": True, "UseMandrelSelection": True, "UseProbes": [True, True, True, True, True, True, True, True], "WashCycles": "4", "WashVolume": "110%", "Wizard": False } transfer_params["items"] = items transfer_params["Solvent"] = 'Water' transfer_params["TipLocation"] = tip_rack self.temp_protocol["steps"].append(transfer_params) return def move_biomek( self, source: str, target: str, ): """ 处理Biomek移动板子的操作。 """ move_params = { "Pod": "Pod1", "GripSide": "A1 near", "Source": source, "Target": target, "LeaveBottomLabware": False, } self.temp_protocol["steps"].append(move_params) return def incubation_biomek( self, time: int, ): """ 处理Biomek的孵育操作。 """ incubation_params = { "Message": "Paused", "Location": "the whole system", "Time": time, "Mode": "TimedResource" } self.temp_protocol["steps"].append(incubation_params) return def oscillation_biomek( self, rpm: int, time: int, ): """ 处理Biomek的振荡操作。 """ oscillation_params = { 'Device': 'OrbitalShaker0', 'Parameters': (str(rpm), '2', str(time), 'CounterClockwise'), 'Command': 'Timed Shake' } self.temp_protocol["steps"].append(oscillation_params) return if __name__ == "__main__": steps_info = ''' { "steps": [ { "step_number": 1, "operation": "transfer", "description": "转移PCR产物或酶促反应液至0.05ml 96孔板中", "parameters": { "source": "P1", "target": "P11", "tip_rack": "BC230", "volume": 50 } }, { "step_number": 2, "operation": "transfer", "description": "加入2倍体积Bind Beads BC至产物中", "parameters": { "source": "P2", "target": "P11", "tip_rack": "BC230", "volume": 100 } }, { "step_number": 3, "operation": "move_labware", "description": "移动P11至Orbital1用于振荡混匀", "parameters": { "source": "P11", "target": "Orbital1" } }, { "step_number": 4, "operation": "oscillation", "description": "在Orbital1上振荡混匀Bind Beads BC与PCR产物（700-900rpm，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 } } ] } ''' labware_with_liquid = ''' [ { "id": "Tip Rack BC230 on TL1", "parent": "deck", "slot_on_deck": "TL1", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on TL2", "parent": "deck", "slot_on_deck": "TL2", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on TL3", "parent": "deck", "slot_on_deck": "TL3", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on TL4", "parent": "deck", "slot_on_deck": "TL4", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on TL5", "parent": "deck", "slot_on_deck": "TL5", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on P5", "parent": "deck", "slot_on_deck": "P5", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on P6", "parent": "deck", "slot_on_deck": "P6", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on P15", "parent": "deck", "slot_on_deck": "P15", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "Tip Rack BC230 on P16", "parent": "deck", "slot_on_deck": "P16", "class_name": "BC230", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "stock plate on P1", "parent": "deck", "slot_on_deck": "P1", "class_name": "nest_12_reservoir_15ml", "liquid_type": [ "master_mix" ], "liquid_volume": [10000], "liquid_input_wells": [ "A1" ] }, { "id": "stock plate on P2", "parent": "deck", "slot_on_deck": "P2", "class_name": "nest_12_reservoir_15ml", "liquid_type": [ "bind beads" ], "liquid_volume": [10000], "liquid_input_wells": [ "A1" ] }, { "id": "stock plate on P3", "parent": "deck", "slot_on_deck": "P3", "class_name": "nest_12_reservoir_15ml", "liquid_type": [ "ethyl alcohol" ], "liquid_volume": [10000], "liquid_input_wells": [ "A1" ] }, { "id": "elution buffer on P4", "parent": "deck", "slot_on_deck": "P4", "class_name": "nest_12_reservoir_15ml", "liquid_type": [ "elution buffer" ], "liquid_volume": [5000], "liquid_input_wells": [ "A1" ] }, { "id": "oscillation", "parent": "deck", "slot_on_deck": "Orbital1", "class_name": "Orbital", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "working plate on P11", "parent": "deck", "slot_on_deck": "P11", "class_name": "NEST 2ml Deep Well Plate", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "magnetics module on P12", "parent": "deck", "slot_on_deck": "P12", "class_name": "magnetics module", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "working plate on P13", "parent": "deck", "slot_on_deck": "P13", "class_name": "NEST 2ml Deep Well Plate", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] }, { "id": "waste on P22", "parent": "deck", "slot_on_deck": "P22", "class_name": "nest_1_reservoir_195ml", "liquid_type": [], "liquid_volume": [], "liquid_input_wells": [] } ] ''' handler = LiquidHandlerBiomek() handler.temp_protocol = { "meta": {}, "labwares": [], "steps": [] } input_steps = json.loads(steps_info) labwares = json.loads(labware_with_liquid) for step in input_steps['steps']: operation = step['operation'] parameters = step['parameters'] if operation == 'transfer': handler.transfer_biomek(source=parameters['source'], target=parameters['target'], volume=parameters['volume'], tip_rack=parameters['tip_rack'], aspirate_techniques='MC P300 high', dispense_techniques='MC P300 high') elif operation == 'move_labware': handler.move_biomek(source=parameters['source'], target=parameters['target']) elif operation == 'oscillation': handler.oscillation_biomek(rpm=parameters['rpm'], time=parameters['time']) elif operation == 'incubation': handler.incubation_biomek(time=parameters['time']) print(json.dumps(handler.temp_protocol, indent=4))