支持Biomek创建

unilabos/devices/liquid_handling/biomek.py

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+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, backend=None, deck=None, *args, **kwargs):
+        super().__init__(backend, deck, *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':{       
+                "Solvent": "Water",
+            }
+        }
+        self.dispense_techniques = {
+            'MC P300 high':{       
+            "Span8": False,
+            "Pod": "Pod1",
+            "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,
+            "Span8Wash": False,
+            "Span8WashVolume": "2",
+            "Span8WasteVolume": "1",
+            "SplitVolume": False,
+            "SplitVolumeCleaning": False,
+            "Stop": "Destinations",
+            "UseCurrentTips": False,    
+            "UseDisposableTips": False,
+            "UseFixedTips": False,
+            "UseJIT": True,
+            "UseMandrelSelection": True,
+            "UseProbes": [True, True, True, True, True, True, True, True],
+            "WashCycles": "3",
+            "WashVolume": "110%",
+            "Wizard": 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。
+
+        """
+        
+        asp_params = self.aspirate_techniques.get(aspirate_techniques, {})
+        dis_params = self.dispense_techniques.get(dispense_techniques, {})
+
+        transfer_params = {
+            "Span8": False,
+            "Pod": "Pod1",
+            "items": {},                      
+            "Wash": False,
+            "Dynamic?": True,
+            "AutoSelectActiveWashTechnique": False,
+            "ActiveWashTechnique": "",
+            "ChangeTipsBetweenDests": False,
+            "ChangeTipsBetweenSources": True,
+            "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 = {}
+        items["Source"] = source
+        items["Destination"] = target
+        items["Volume"] = volume 
+        transfer_params["items"] = items
+        transfer_params["Solvent"] =  asp_params['Solvent']
+        transfer_params["TipLocation"] = tip_rack
+        transfer_params.update(asp_params)
+        transfer_params.update(dis_params)
+        self.temp_protocol["steps"].append(transfer_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": "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": "Tip Rack BC230 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 P7",
+            "parent": "deck",
+            "slot_on_deck": "P7",
+            "class_name": "BC230",
+            "liquid_type": [],
+            "liquid_volume": [],
+            "liquid_input_wells": [
+            ]
+        },
+        {
+            "id": "Tip Rack BC230 on P8",
+            "parent": "deck",
+            "slot_on_deck": "P8",
+            "class_name": "BC230",
+            "liquid_type": [],
+            "liquid_volume": [],
+            "liquid_input_wells": [
+            ]
+        },
+            {
+            "id": "Tip Rack BC230 P16",
+            "parent": "deck",
+            "slot_on_deck": "P16",
+            "class_name": "BC230",
+            "liquid_type": [],
+            "liquid_volume": [],
+            "liquid_input_wells": [
+            ]
+        },
+        {
+            "id": "stock plate on 4",
+            "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 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": "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']:
+        if step['operation'] != 'transfer':
+            continue
+        parameters = step['parameters']
+        tip_rack=parameters['tip_rack']
+        # 找到labwares中与tip_rack匹配的项的id
+        tip_rack_id = [lw['id'] for lw in labwares if lw['class_name'] == tip_rack][0]
+
+        handler.transfer_biomek(source=parameters['source'],
+                                target=parameters['target'],
+                                volume=parameters['volume'],
+                                tip_rack=tip_rack_id,
+                                aspirate_techniques='MC P300 high',
+                                dispense_techniques='MC P300 high'
+                                )
+    print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))
+

unilabos/devices/liquid_handling/biomek_test.py

@@ -0,0 +1,747 @@
+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.aspirate_techniques = {
+            'MC P300 high':{       
+                "Solvent": "Water",
+            }
+        }
+        self.dispense_techniques = {
+            'MC P300 high':{       
+            "Span8": False,
+            "Pod": "Pod1",
+            "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,
+            "Span8Wash": False,
+            "Span8WashVolume": "2",
+            "Span8WasteVolume": "1",
+            "SplitVolume": False,
+            "SplitVolumeCleaning": False,
+            "Stop": "Destinations",
+            "UseCurrentTips": False,    
+            "UseDisposableTips": False,
+            "UseFixedTips": False,
+            "UseJIT": True,
+            "UseMandrelSelection": True,
+            "UseProbes": [True, True, True, True, True, True, True, True],
+            "WashCycles": "3",
+            "WashVolume": "110%",
+            "Wizard": False
+            }
+        }
+
+
+    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_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。
+
+        """
+        
+        asp_params = self.aspirate_techniques.get(aspirate_techniques, {})
+        dis_params = self.dispense_techniques.get(dispense_techniques, {})
+
+        transfer_params = {
+            "Span8": False,
+            "Pod": "Pod1",
+            "items": {},                      
+            "Wash": False,
+            "Dynamic?": True,
+            "AutoSelectActiveWashTechnique": False,
+            "ActiveWashTechnique": "",
+            "ChangeTipsBetweenDests": False,
+            "ChangeTipsBetweenSources": True,
+            "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 = {}
+        items["Source"] = source
+        items["Destination"] = target
+        items["Volume"] = volume 
+        transfer_params["items"] = items
+        transfer_params["Solvent"] =  asp_params['Solvent']
+        transfer_params["TipLocation"] = tip_rack
+        transfer_params.update(asp_params)
+        transfer_params.update(dis_params)
+        self.temp_protocol["steps"].append(transfer_params)
+
+        return 
+
+labware_with_liquid = '''
+[    {
+        "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": "Tip Rack BC230 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 P7",
+        "parent": "deck",
+        "slot_on_deck": "P7",
+        "class_name": "BC230",
+        "liquid_type": [],
+        "liquid_volume": [],
+        "liquid_input_wells": [
+        ]
+    },
+    {
+        "id": "Tip Rack BC230 on P8",
+        "parent": "deck",
+        "slot_on_deck": "P8",
+        "class_name": "BC230",
+        "liquid_type": [],
+        "liquid_volume": [],
+        "liquid_input_wells": [
+        ]
+    },
+        {
+        "id": "Tip Rack BC230 P16",
+        "parent": "deck",
+        "slot_on_deck": "P16",
+        "class_name": "BC230",
+        "liquid_type": [],
+        "liquid_volume": [],
+        "liquid_input_wells": [
+        ]
+    },
+    {
+        "id": "stock plate on 4",
+        "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 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": "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']:
+    if step['operation'] != 'transfer':
+        continue
+    parameters = step['parameters']
+    
+
+    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'
+                            )
+    
+print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))
+

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -6,13 +6,8 @@ import asyncio
 import time
 
 from pylabrobot.liquid_handling import LiquidHandler
-from pylabrobot.resources import (
-    Resource,
-    TipRack,
-    Container,
-    Coordinate,
-    Well
-)
+from pylabrobot.resources import Resource, TipRack, Container, Coordinate, Well
+
 
 class LiquidHandlerAbstract(LiquidHandler):
     """Extended LiquidHandler with additional operations."""
@@ -21,6 +16,19 @@ class LiquidHandlerAbstract(LiquidHandler):
     # REMOVE LIQUID --------------------------------------------------
     # ---------------------------------------------------------------
 
+    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],
@@ -35,26 +43,26 @@ class LiquidHandlerAbstract(LiquidHandler):
         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] = []
+        top: Optional[List[float]] = None,
+        none_keys: List[str] = [],
     ):
         """A complete *remove* (aspirate → waste) operation."""
         trash = self.deck.get_trash_area()
         try:
             if is_96_well:
-                pass # This mode is not verified
+                pass  # This mode is not verified
             else:
                 if len(vols) != len(sources):
                     raise ValueError("Length of `vols` must match `sources`.")
 
                 for src, vol in zip(sources, vols):
-                    self.move_to(src, dis_to_top=top[0] if top else 0)
+                    await self.move_to(src, dis_to_top=top[0] if top else 0)
                     tip = next(self.current_tip)
                     await self.pick_up_tips(tip)
                     await self.aspirate(
                         resources=[src],
                         vols=[vol],
-                        use_channels=use_channels, # only aspirate96 used, default to None
+                        use_channels=use_channels,  # only aspirate96 used, default to None
                         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,
@@ -64,15 +72,15 @@ class LiquidHandlerAbstract(LiquidHandler):
                     await self.custom_delay(seconds=delays[0] if delays else 0)
                     await self.dispense(
                         resources=waste_liquid,
-                         vols=[vol],
-                         use_channels=use_channels,
-                         flow_rates=[flow_rates[1]] if flow_rates else None,
-                         offsets=[offsets[1]] if offsets else None,
-                         liquid_height=[liquid_height[1]] if liquid_height else None,
-                         blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
-                         spread=spread,
-                     )
-                    await self.discard_tips() # For now, each of tips is discarded after use
+                        vols=[vol],
+                        use_channels=use_channels,
+                        flow_rates=[flow_rates[1]] if flow_rates else None,
+                        offsets=[offsets[1]] if offsets else None,
+                        liquid_height=[liquid_height[1]] if liquid_height else None,
+                        blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
+                        spread=spread,
+                    )
+                    await self.discard_tips()  # For now, each of tips is discarded after use
 
         except Exception as e:
             raise RuntimeError(f"Liquid removal failed: {e}") from e
@@ -100,13 +108,13 @@ class LiquidHandlerAbstract(LiquidHandler):
         mix_vol: Optional[int] = None,
         mix_rate: Optional[int] = None,
         mix_liquid_height: Optional[float] = None,
-        none_keys: List[str] = []
+        none_keys: List[str] = [],
     ):
         """A complete *add* (aspirate reagent → dispense into targets) operation."""
 
         try:
             if is_96_well:
-                pass # This mode is not verified.
+                pass  # This mode is not verified.
             else:
                 if len(asp_vols) != len(targets):
                     raise ValueError("Length of `vols` must match `targets`.")
@@ -122,7 +130,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                         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
+                        spread=spread,
                     )
                     if delays is not None:
                         await self.custom_delay(seconds=delays[0])
@@ -144,7 +152,8 @@ class LiquidHandlerAbstract(LiquidHandler):
                         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)
+                        mix_rate=mix_rate if mix_rate else None,
+                    )
                     if delays is not None:
                         await self.custom_delay(seconds=delays[1])
                     await self.touch_tip(targets[_])
@@ -158,13 +167,13 @@ class LiquidHandlerAbstract(LiquidHandler):
     # ---------------------------------------------------------------
     async def transfer_liquid(
         self,
-        asp_vols: Union[List[float], float],
-        dis_vols: Union[List[float], float],
         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,
@@ -179,7 +188,7 @@ class LiquidHandlerAbstract(LiquidHandler):
         mix_rate: Optional[int] = None,
         mix_liquid_height: Optional[float] = None,
         delays: Optional[List[int]] = None,
-        none_keys: List[str] = []
+        none_keys: List[str] = [],
     ):
         """Transfer liquid from each *source* well/plate to the corresponding *target*.
 
@@ -201,14 +210,15 @@ class LiquidHandlerAbstract(LiquidHandler):
             # 96‑channel head mode
             # ------------------------------------------------------------------
             if is_96_well:
-                pass # This mode is not verified
+                pass  # This mode is not verified
             else:
                 if not (len(asp_vols) == len(sources) and len(dis_vols) == len(targets)):
                     raise ValueError("`sources`, `targets`, and `vols` must have the same length.")
 
                 tip_iter = self.iter_tips(tip_racks)
-                for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in (
-                        zip(sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates)):
+                for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in zip(
+                    sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates
+                ):
                     tip = next(tip_iter)
                     await self.pick_up_tips(tip)
                     # Aspirate from source
@@ -247,9 +257,9 @@ class LiquidHandlerAbstract(LiquidHandler):
         except Exception as exc:
             raise RuntimeError(f"Liquid transfer failed: {exc}") from exc
 
-# ---------------------------------------------------------------
-# Helper utilities
-# ---------------------------------------------------------------
+    # ---------------------------------------------------------------
+    # Helper utilities
+    # ---------------------------------------------------------------
 
     async def custom_delay(self, seconds=0, msg=None):
         """
@@ -266,28 +276,26 @@ class LiquidHandlerAbstract(LiquidHandler):
                 print(f"Done: {msg}")
                 print(f"Current time: {time.strftime('%H:%M:%S')}")
 
-    async def touch_tip(self,
-                        targets: Sequence[Container],
-                        ):
+    async def touch_tip(self, targets: Sequence[Container]):
         """Touch the tip to the side of the well."""
         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)],
+            offsets=[Coordinate(x=-targets.get_size_x() / 2, y=0, z=0)],
             liquid_height=None,
-            blow_out_air_volume=None
+            blow_out_air_volume=None,
         )
-        #await self.custom_delay(seconds=1) # In the simulation, we do not need to wait
+        # 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)],
+            offsets=[Coordinate(x=targets.get_size_x() / 2, y=0, z=0)],
             liquid_height=None,
-            blow_out_air_volume=None
+            blow_out_air_volume=None,
         )
 
     async def mix(
@@ -298,9 +306,9 @@ class LiquidHandlerAbstract(LiquidHandler):
         height_to_bottom: Optional[float] = None,
         offsets: Optional[Coordinate] = None,
         mix_rate: Optional[float] = None,
-        none_keys: List[str] = []
+        none_keys: List[str] = [],
     ):
-        if mix_time is None: # No mixing required
+        if mix_time is None:  # No mixing required
             return
         """Mix the liquid in the target wells."""
         for _ in range(mix_time):
@@ -333,7 +341,7 @@ class LiquidHandlerAbstract(LiquidHandler):
         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):
+    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.
 
@@ -352,4 +360,3 @@ class LiquidHandlerAbstract(LiquidHandler):
         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)
-

unilabos/devices/liquid_handling/test liquid handler/convert_biomek.py

@@ -0,0 +1,154 @@
+
+import json
+from typing import Sequence, Optional, List, Union, Literal
+json_path = "/Users/guangxinzhang/Documents/Deep Potential/opentrons/convert/protocols/enriched_steps/sci-lucif-assay4.json"
+
+with open(json_path, "r") as f:
+    data = json.load(f)
+
+transfer_example = data[0]
+#print(transfer_example)
+
+
+temp_protocol = []
+TipLocation = "BC1025F"  # Assuming this is a fixed tip location for the transfer
+sources = transfer_example["sources"]  # Assuming sources is a list of Container objects
+targets = transfer_example["targets"]  # Assuming targets is a list of Container objects
+tip_racks = transfer_example["tip_racks"]  # Assuming tip_racks is a list of TipRack objects
+asp_vols = transfer_example["asp_vols"]  # Assuming asp_vols is a list of volumes
+solvent = "PBS"
+
+def transfer_liquid(
+        #self,
+        sources,#: Sequence[Container],
+        targets,#: Sequence[Container],
+        tip_racks,#: Sequence[TipRack],
+        TipLocation,
+        # *,
+        # use_channels: Optional[List[int]] = None,
+        asp_vols: Union[List[float], float],
+        solvent: Optional[str] = None,
+        # 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[]] = 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[list() = 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] = []
+    ):
+        # -------- Build Biomek transfer step --------
+        # 1) Construct default parameter scaffold (values mirror Biomek “Transfer” block).
+
+        transfer_params = {
+            "Span8": False,
+            "Pod": "Pod1",
+            "items": {},                       # to be filled below
+            "Wash": False,
+            "Dynamic?": True,
+            "AutoSelectActiveWashTechnique": False,
+            "ActiveWashTechnique": "",
+            "ChangeTipsBetweenDests": False,
+            "ChangeTipsBetweenSources": False,
+            "DefaultCaption": "",              # filled after we know first pair/vol
+            "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": asp_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
+
+        return transfer_params
+
+action = transfer_liquid(sources=sources,targets=targets,tip_racks=tip_racks, asp_vols=asp_vols,solvent = solvent, TipLocation=TipLocation)
+print(json.dumps(action,indent=2))  
+# print(action)
+
+
+
+
+"""
+      "transfer": {
+
+        "items": {},
+        "Wash": false,
+        "Dynamic?": true,
+        "AutoSelectActiveWashTechnique": false,
+        "ActiveWashTechnique": "",
+        "ChangeTipsBetweenDests": true,
+        "ChangeTipsBetweenSources": false,
+        "DefaultCaption": "Transfer 100 µL from P13 to P3",
+        "UseExpression": false,
+        "LeaveTipsOn": false,
+        "MandrelExpression": "",
+        "Repeats": "1",
+        "RepeatsByVolume": false,
+        "Replicates": "1",
+        "ShowTipHandlingDetails": true,
+        "ShowTransferDetails": true,
+        
+        "Span8Wash": false,
+        "Span8WashVolume": "2",
+        "Span8WasteVolume": "1",
+        "SplitVolume": false,
+        "SplitVolumeCleaning": false,
+        "Stop": "Destinations",
+        "TipLocation": "BC1025F",
+        "UseCurrentTips": false,
+        "UseDisposableTips": false,
+        "UseFixedTips": false,
+        "UseJIT": true,
+        "UseMandrelSelection": true,
+        "UseProbes": [true, true, true, true, true, true, true, true],
+        "WashCycles": "3",
+        "WashVolume": "110%",
+        "Wizard": false
+"""
+
+
+
+

unilabos/registry/devices/liquid_handler.yaml

@@ -1,5 +1,6 @@
 liquid_handler:
   description: Liquid handler device controlled by pylabrobot
+  icon: icon_yiyezhan.webp
   class:
     module: unilabos.devices.liquid_handling.liquid_handler_abstract:LiquidHandlerAbstract
     type: python
@@ -22,8 +23,8 @@ liquid_handler:
           is_96_well: is_96_well
           top: top
           none_keys: none_keys
-        feedback: { }
-        result: { }
+        feedback: {}
+        result: {}
       add_liquid:
         type: LiquidHandlerAdd
         goal:
@@ -43,8 +44,8 @@ liquid_handler:
           mix_rate: mix_rate
           mix_liquid_height: mix_liquid_height
           none_keys: none_keys
-        feedback: { }
-        result: { }
+        feedback: {}
+        result: {}
       transfer_liquid:
         type: LiquidHandlerTransfer
         goal:
@@ -69,8 +70,8 @@ liquid_handler:
           mix_liquid_height: mix_liquid_height
           delays: delays
           none_keys: none_keys
-        feedback: { }
-        result: { }
+        feedback: {}
+        result: {}
       mix:
         type: LiquidHandlerMix
         goal:
@@ -81,16 +82,16 @@ liquid_handler:
           offsets: offsets
           mix_rate: mix_rate
           none_keys: none_keys
-        feedback: { }
-        result: { }
+        feedback: {}
+        result: {}
       move_to:
         type: LiquidHandlerMoveTo
         goal:
           well: well
           dis_to_top: dis_to_top
           channel: channel
-        feedback: { }
-        result: { }
+        feedback: {}
+        result: {}
       aspirate:
         type: LiquidHandlerAspirate
         goal:
@@ -245,6 +246,21 @@ liquid_handler:
           target_vols: target_vols
           aspiration_flow_rate: aspiration_flow_rate
           dispense_flow_rates: dispense_flow_rates
+  handles:
+    input:
+    - handler_key: liquid-input
+      label: Liquid Input
+      data_type: resource
+      io_type: target
+      data_source: handle
+      data_key: liquid
+    output:
+    - handler_key: liquid-output
+      label: Liquid Output
+      data_type: resource
+      io_type: source
+      data_source: executor
+      data_key: liquid
   schema:
     type: object
     properties:
@@ -272,3 +288,71 @@ liquid_handler.revvity:
           status: status
         result:
           success: success
+
+liquid_handler.biomek:
+  description: Biomek液体处理器设备，基于pylabrobot控制
+  icon: icon_yiyezhan.webp
+  class:
+    module: unilabos.devices.liquid_handling.biomek:LiquidHandlerBiomek
+    type: python
+    status_types: {}
+    action_value_mappings:
+      create_protocol:
+        type: LiquidHandlerProtocolCreation
+        goal:
+          protocol_name: protocol_name
+          protocol_description: protocol_description
+          protocol_version: protocol_version
+          protocol_author: protocol_author
+          protocol_date: protocol_date
+          protocol_type: protocol_type
+          none_keys: none_keys
+        feedback: {}
+        result: {}
+      run_protocol:
+        type: EmptyIn
+        goal: {}
+        feedback: {}
+        result: {}
+      transfer_liquid:
+        type: LiquidHandlerTransfer
+        goal:
+          asp_vols: asp_vols
+          dis_vols: dis_vols
+          sources: sources
+          targets: targets
+          tip_racks: tip_racks
+          use_channels: use_channels
+          asp_flow_rates: asp_flow_rates
+          dis_flow_rates: dis_flow_rates
+          offsets: offsets
+          touch_tip: touch_tip
+          liquid_height: liquid_height
+          blow_out_air_volume: blow_out_air_volume
+          spread: spread
+          is_96_well: is_96_well
+          mix_stage: mix_stage
+          mix_times: mix_times
+          mix_vol: mix_vol
+          mix_rate: mix_rate
+          mix_liquid_height: mix_liquid_height
+          delays: delays
+          none_keys: none_keys
+        feedback: {}
+        result: {}
+      transfer_biomek:
+        type: LiquidHandlerTransferBiomek
+        goal:
+          source: source,
+          target: target,
+          tip_rack: tip_rack,
+          volume: volume,
+          aspirate_techniques: aspirate_techniques,
+          dispense_techniques: dispense_techniques,
+        feedback: {}
+        result: {}
+  schema:
+    type: object
+    properties: {}
+    required: []
+    additionalProperties: false

unilabos/registry/devices/pump_and_valve.yaml

@@ -23,17 +23,48 @@ syringe_pump_with_valve.runze:
         type: string
         description: The position of the valve
     required:
-      - status
-      - position
-      - valve_position
+    - status
+    - position
+    - valve_position
     additionalProperties: false
 
-
 solenoid_valve.mock:
   description: Mock solenoid valve
   class:
     module: unilabos.devices.pump_and_valve.solenoid_valve_mock:SolenoidValveMock
     type: python
+    status_types:
+      status: String
+      valve_position: String
+    action_value_mappings:
+      open:
+        type: EmptyIn
+        goal: {}
+        feedback: {}
+        result: {}
+      close:
+        type: EmptyIn
+        goal: {}
+        feedback: {}
+        result: {}
+  handles:
+    input:
+    - handler_key: fluid-input
+      label: Fluid Input
+      data_type: fluid
+    output:
+    - handler_key: fluid-output
+      label: Fluid Output
+      data_type: fluid
+  init_param_schema:
+    type: object
+    properties:
+      port:
+        type: string
+        description: "通信端口"
+        default: "COM6"
+    required:
+    - port
 
 solenoid_valve:
   description: Solenoid valve

unilabos/registry/devices/vacuum_and_purge.yaml

@@ -22,9 +22,76 @@ vacuum_pump.mock:
           string: string
         feedback: {}
         result: {}
+  handles:
+    input:
+    - handler_key: fluid-input
+      label: Fluid Input
+      data_type: fluid
+      io_type: target
+      data_source: handle
+      data_key: fluid_in
+    output:
+    - handler_key: fluid-output
+      label: Fluid Output
+      data_type: fluid
+      io_type: source
+      data_source: executor
+      data_key: fluid_out
+  init_param_schema:
+    type: object
+    properties:
+      port:
+        type: string
+        description: "通信端口"
+        default: "COM6"
+    required:
+    - port
 
 gas_source.mock:
   description: Mock gas source
   class:
     module: unilabos.devices.pump_and_valve.vacuum_pump_mock:VacuumPumpMock
     type: python
+    status_types:
+      status: String
+    action_value_mappings:
+      open:
+        type: EmptyIn
+        goal: {}
+        feedback: {}
+        result: {}
+      close:
+        type: EmptyIn
+        goal: {}
+        feedback: {}
+        result: {}
+      set_status:
+        type: StrSingleInput
+        goal:
+          string: string
+        feedback: {}
+        result: {}
+  handles:
+    input:
+    - handler_key: fluid-input
+      label: Fluid Input
+      data_type: fluid
+      io_type: target
+      data_source: handle
+      data_key: fluid_in
+    output:
+    - handler_key: fluid-output
+      label: Fluid Output
+      data_type: fluid
+      io_type: source
+      data_source: executor
+      data_key: fluid_out
+  init_param_schema:
+    type: object
+    properties:
+      port:
+        type: string
+        description: "通信端口"
+        default: "COM6"
+    required:
+    - port

unilabos/registry/registry.py

@@ -25,9 +25,7 @@ class Registry:
         self.ResourceCreateFromOuterEasy = self._replace_type_with_class(
             "ResourceCreateFromOuterEasy", "host_node", f"动作 create_resource"
         )
-        self.EmptyIn = self._replace_type_with_class(
-            "EmptyIn", "host_node", f""
-        )
+        self.EmptyIn = self._replace_type_with_class("EmptyIn", "host_node", f"")
         self.device_type_registry = {}
         self.resource_type_registry = {}
         self._setup_called = False  # 跟踪setup是否已调用
@@ -99,6 +97,8 @@ class Registry:
                     },
                     "icon": "icon_device.webp",
                     "registry_type": "device",
+                    "handles": [],
+                    "init_param_schema": {},
                     "schema": {"properties": {}, "additionalProperties": False, "type": "object"},
                     "file_path": "/",
                 }
@@ -132,6 +132,10 @@ class Registry:
                         resource_info["description"] = ""
                     if "icon" not in resource_info:
                         resource_info["icon"] = ""
+                    if "handles" not in resource_info:
+                        resource_info["handles"] = []
+                    if "init_param_schema" not in resource_info:
+                        resource_info["init_param_schema"] = {}
                     resource_info["registry_type"] = "resource"
                 self.resource_type_registry.update(data)
                 logger.debug(
@@ -194,6 +198,10 @@ class Registry:
                         device_config["description"] = ""
                     if "icon" not in device_config:
                         device_config["icon"] = ""
+                    if "handles" not in device_config:
+                        device_config["handles"] = []
+                    if "init_param_schema" not in device_config:
+                        device_config["init_param_schema"] = {}
                     device_config["registry_type"] = "device"
                     if "class" in device_config:
                         # 处理状态类型

unilabos/ros/msgs/message_converter.py

@@ -131,7 +131,7 @@ _msg_converter: Dict[Type, Any] = {
     Bool: lambda x: Bool(data=bool(x)),
     str: str,
     String: lambda x: String(data=str(x)),
-    Point: lambda x: Point(x=x.x, y=x.y, z=x.z),
+    Point: lambda x: Point(x=x.x, y=x.y, z=x.z) if not isinstance(x, dict) else Point(x=x.get("x", 0), y=x.get("y", 0), z=x.get("z", 0)),
     Resource: lambda x: Resource(
         id=x.get("id", ""),
         name=x.get("name", ""),

unilabos/ros/nodes/base_device_node.py

@@ -349,6 +349,20 @@ class BaseROS2DeviceNode(Node, Generic[T]):
             response = rclient.call(request)
             # 应该先add_resource了
             res.response = "OK"
+            # 如果driver自己就有assign的方法，那就使用driver自己的assign方法
+            if hasattr(self.driver_instance, "create_resource"):
+                create_resource_func = getattr(self.driver_instance, "create_resource")
+                create_resource_func(
+                    resource_tracker=self.resource_tracker,
+                    resources=request.resources,
+                    bind_parent_id=bind_parent_id,
+                    bind_location=location,
+                    liquid_input_slot=LIQUID_INPUT_SLOT,
+                    liquid_type=ADD_LIQUID_TYPE,
+                    liquid_volume=LIQUID_VOLUME,
+                    slot_on_deck=slot,
+                )
+                return res
             # 接下来该根据bind_parent_id进行assign了，目前只有plr可以进行assign，不然没有办法输入到物料系统中
             resource = self.resource_tracker.figure_resource({"name": bind_parent_id})
             # request.resources = [convert_to_ros_msg(Resource, resources)]
@@ -791,7 +805,9 @@ class ROS2DeviceNode:
         self.resource_tracker = DeviceNodeResourceTracker()
 
         # use_pylabrobot_creator 使用 cls的包路径检测
-        use_pylabrobot_creator = driver_class.__module__.startswith("pylabrobot") or driver_class.__name__ == "LiquidHandlerAbstract"
+        use_pylabrobot_creator = (driver_class.__module__.startswith("pylabrobot")
+                                  or driver_class.__name__ == "LiquidHandlerAbstract"
+                                  or driver_class.__name__ == "LiquidHandlerBiomek")
 
         # TODO: 要在创建之前预先请求服务器是否有当前id的物料，放到resource_tracker中，让pylabrobot进行创建
         # 创建设备类实例

unilabos_msgs/CMakeLists.txt

@@ -29,6 +29,8 @@ set(action_files
   "action/HeatChillStart.action"
   "action/HeatChillStop.action"
 
+  "action/LiquidHandlerProtocolCreation.action"
+
   "action/LiquidHandlerAspirate.action"
   "action/LiquidHandlerDiscardTips.action"
   "action/LiquidHandlerDispense.action"
@@ -43,6 +45,7 @@ set(action_files
   "action/LiquidHandlerReturnTips96.action"
   "action/LiquidHandlerStamp.action"
   "action/LiquidHandlerTransfer.action"
+  "action/LiquidHandlerTransferBiomek.action"
 
   "action/LiquidHandlerAdd.action"
   "action/LiquidHandlerMix.action"

unilabos_msgs/action/LiquidHandlerProtocolCreation.action

@@ -0,0 +1,9 @@
+string protocol_name
+string protocol_description
+string protocol_version
+string protocol_author
+string protocol_date
+string protocol_type
+string[] none_keys
+---
+---

unilabos_msgs/action/LiquidHandlerTransferBiomek.action

@@ -0,0 +1,10 @@
+string source
+string target
+string tip_rack
+float64 volume
+string aspirate_technique
+string dispense_technique
+
+---
+
+---