Biomek test

unilabos/devices/liquid_handling/biomek.py

@@ -15,8 +15,8 @@ from .liquid_handler_abstract import LiquidHandlerAbstract
 import json
 from typing import Sequence, Optional, List, Union, Literal
 
-
 class LiquidHandlerBiomek(LiquidHandlerAbstract):
+
     """
     Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
     该类用于处理Biomek液体处理器的特定操作。
@@ -29,6 +29,28 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         self._status_queue = kwargs.get("status_queue", None)  # 状态队列
         self.temp_protocol = {}
         self.py32_path = "/opt/py32"  # Biomek的Python 3.2路径
+        self.technique = {
+            'MC P300 high':{       
+                "use_channels": "Span8",
+                "asp_vols": [50],
+                "asp_flow_rates": 50,
+                "dis_flow_rates": 50,
+                "offsets": None,
+                "touch_tip": True,
+                "liquid_height": 20,
+                "blow_out_air_volume": 20,
+                "spread": "wide",
+                "is_96_well": True,
+                "mix_stage": "none",
+                "mix_times": None,
+                "mix_vol": None,
+                "mix_rate": None,
+                "mix_liquid_height": None,
+                "delays": None,
+                "none_keys": [] 
+            }
+        }
+
 
     def create_protocol(
         self,
@@ -143,7 +165,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         targets: Sequence[Container],
         tip_racks: Sequence[TipRack],
         solvent: Optional[str] = None,
-        TipLocation: Optional[str] = None,
+        TipLocation :str = None, 
         *,
         use_channels: Optional[List[int]] = None,
         asp_vols: Union[List[float], float],
@@ -157,7 +179,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         spread: Literal["wide", "tight", "custom"] = "wide",
         is_96_well: bool = False,
         mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
-        mix_times: Optional[List(int)] = None,
+        mix_times: Optional[int] = None,
         mix_vol: Optional[int] = None,
         mix_rate: Optional[int] = None,
         mix_liquid_height: Optional[float] = None,
@@ -208,7 +230,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
             items[str(idx)] = {
                 "Source": str(src),
                 "Destination": str(dst),
-                "Volume": asp_vols[idx] 
+                "Volume": dis_vols[idx] 
             }
         transfer_params["items"] = items
         transfer_params["Solvent"] =  solvent if solvent else "Water"
@@ -223,3 +245,29 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
 
         return 
         
+    def transfer_biomek(
+            self,
+            parameters: dict,
+            technique: str,
+    ):
+        """
+        处理Biomek的液体转移操作。
+
+        """
+        sources = parameters.get("source")
+        targets = parameters.get("target")
+        tip_rack = parameters.get("tip_rack")
+        volume = parameters.get("volume")
+        liquid_type = parameters.get("liquid_type", "Well Content")
+        other_params = self.technique.get(technique, {})
+
+        self.transfer_liquid(
+            sources=[sources],
+            targets=[targets],
+            TipLocation=tip_rack,
+            tip_racks=[tip_rack],
+            solvent=liquid_type,
+            dis_vols=[volume],
+            **other_params
+        )
+        return 

unilabos/devices/liquid_handling/biomek_test.py

@@ -0,0 +1,568 @@
+import requests
+from typing import List, Sequence, Optional, Union, Literal
+# from geometry_msgs.msg import Point
+# from unilabos_msgs.msg import Resource
+from pylabrobot.resources import (
+    Resource,
+    TipRack,
+    Container,
+    Coordinate,
+    Well
+)
+# from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker  # type: ignore
+# from .liquid_handler_abstract import LiquidHandlerAbstract
+
+import json
+from typing import Sequence, Optional, List, Union, Literal
+
+steps_info = ''' 
+{
+  "steps": [
+    {
+      "step_number": 1,
+      "operation": "transfer",
+      "description": "转移PCR产物或酶促反应液至0.05ml 96孔板中",
+      "parameters": {
+        "source": "P1",
+        "target": "P11",
+        "tip_rack": "BC230",
+        "volume": 50
+      }
+    },
+    {
+      "step_number": 2,
+      "operation": "transfer",
+      "description": "加入2倍体积Bind Beads BC至产物中",
+      "parameters": {
+        "source": "P2",
+        "target": "P11",
+        "tip_rack": "BC230",
+        "volume": 100
+      }
+    },
+    {
+      "step_number": 3,
+      "operation": "move_labware",
+      "description": "移动P11至Orbital1用于振荡混匀",
+      "parameters": {
+        "source": "P11",
+        "target": "Orbital1"
+      }
+    },
+    {
+      "step_number": 4,
+      "operation": "oscillation",
+      "description": "在Orbital1上振荡混匀Bind Beads BC与PCR产物（700-900rpm，300秒）",
+      "parameters": {
+        "rpm": 800,
+        "time": 300
+      }
+    },
+    {
+      "step_number": 5,
+      "operation": "move_labware",
+      "description": "移动混匀后的板回P11",
+      "parameters": {
+        "source": "Orbital1",
+        "target": "P11"
+      }
+    },
+    {
+      "step_number": 6,
+      "operation": "move_labware",
+      "description": "将P11移动到磁力架（P12）吸附3分钟",
+      "parameters": {
+        "source": "P11",
+        "target": "P12"
+      }
+    },
+    {
+      "step_number": 7,
+      "operation": "incubation",
+      "description": "磁力架上室温静置3分钟完成吸附",
+      "parameters": {
+        "time": 180
+      }
+    },
+    {
+      "step_number": 8,
+      "operation": "transfer",
+      "description": "去除上清液至废液槽",
+      "parameters": {
+        "source": "P12",
+        "target": "P22",
+        "tip_rack": "BC230",
+        "volume": 150
+      }
+    },
+    {
+      "step_number": 9,
+      "operation": "transfer",
+      "description": "加入300-500μl 75%乙醇清洗",
+      "parameters": {
+        "source": "P3",
+        "target": "P12",
+        "tip_rack": "BC230",
+        "volume": 400
+      }
+    },
+    {
+      "step_number": 10,
+      "operation": "move_labware",
+      "description": "移动清洗板到Orbital1进行振荡",
+      "parameters": {
+        "source": "P12",
+        "target": "Orbital1"
+      }
+    },
+    {
+      "step_number": 11,
+      "operation": "oscillation",
+      "description": "乙醇清洗液振荡混匀（700-900rpm, 45秒）",
+      "parameters": {
+        "rpm": 800,
+        "time": 45
+      }
+    },
+    {
+      "step_number": 12,
+      "operation": "move_labware",
+      "description": "振荡后将板移回磁力架P12吸附",
+      "parameters": {
+        "source": "Orbital1",
+        "target": "P12"
+      }
+    },
+    {
+      "step_number": 13,
+      "operation": "incubation",
+      "description": "吸附3分钟",
+      "parameters": {
+        "time": 180
+      }
+    },
+    {
+      "step_number": 14,
+      "operation": "transfer",
+      "description": "去除乙醇上清液至废液槽",
+      "parameters": {
+        "source": "P12",
+        "target": "P22",
+        "tip_rack": "BC230",
+        "volume": 400
+      }
+    },
+    {
+      "step_number": 15,
+      "operation": "transfer",
+      "description": "第二次加入300-500μl 75%乙醇清洗",
+      "parameters": {
+        "source": "P3",
+        "target": "P12",
+        "tip_rack": "BC230",
+        "volume": 400
+      }
+    },
+    {
+      "step_number": 16,
+      "operation": "move_labware",
+      "description": "再次移动清洗板到Orbital1振荡",
+      "parameters": {
+        "source": "P12",
+        "target": "Orbital1"
+      }
+    },
+    {
+      "step_number": 17,
+      "operation": "oscillation",
+      "description": "再次乙醇清洗液振荡混匀（700-900rpm, 45秒）",
+      "parameters": {
+        "rpm": 800,
+        "time": 45
+      }
+    },
+    {
+      "step_number": 18,
+      "operation": "move_labware",
+      "description": "振荡后板送回磁力架P12吸附",
+      "parameters": {
+        "source": "Orbital1",
+        "target": "P12"
+      }
+    },
+    {
+      "step_number": 19,
+      "operation": "incubation",
+      "description": "再次吸附3分钟",
+      "parameters": {
+        "time": 180
+      }
+    },
+    {
+      "step_number": 20,
+      "operation": "transfer",
+      "description": "去除乙醇上清液至废液槽",
+      "parameters": {
+        "source": "P12",
+        "target": "P22",
+        "tip_rack": "BC230",
+        "volume": 400
+      }
+    },
+    {
+      "step_number": 21,
+      "operation": "incubation",
+      "description": "空气干燥15分钟",
+      "parameters": {
+        "time": 900
+      }
+    },
+    {
+      "step_number": 22,
+      "operation": "transfer",
+      "description": "加30-50μl Elution Buffer洗脱",
+      "parameters": {
+        "source": "P4",
+        "target": "P12",
+        "tip_rack": "BC230",
+        "volume": 40
+      }
+    },
+    {
+      "step_number": 23,
+      "operation": "move_labware",
+      "description": "移动到Orbital1振荡混匀（60秒）",
+      "parameters": {
+        "source": "P12",
+        "target": "Orbital1"
+      }
+    },
+    {
+      "step_number": 24,
+      "operation": "oscillation",
+      "description": "Elution Buffer振荡混匀（700-900rpm, 60秒）",
+      "parameters": {
+        "rpm": 800,
+        "time": 60
+      }
+    },
+    {
+      "step_number": 25,
+      "operation": "move_labware",
+      "description": "振荡后送回磁力架P12",
+      "parameters": {
+        "source": "Orbital1",
+        "target": "P12"
+      }
+    },
+    {
+      "step_number": 26,
+      "operation": "incubation",
+      "description": "室温静置3分钟（洗脱反应）",
+      "parameters": {
+        "time": 180
+      }
+    },
+    {
+      "step_number": 27,
+      "operation": "transfer",
+      "description": "将上清液（DNA）转移到新板（P13）",
+      "parameters": {
+        "source": "P12",
+        "target": "P13",
+        "tip_rack": "BC230",
+        "volume": 40
+      }
+    }
+  ]
+}
+'''
+
+
+
+#class LiquidHandlerBiomek(LiquidHandlerAbstract):
+
+
+class LiquidHandlerBiomek:
+    """
+    Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
+    该类用于处理Biomek液体处理器的特定操作。
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._status = "Idle"  # 初始状态为 Idle
+        self._success = False  # 初始成功状态为 False
+        self._status_queue = kwargs.get("status_queue", None)  # 状态队列
+        self.temp_protocol = {}
+        self.py32_path = "/opt/py32"  # Biomek的Python 3.2路径
+        self.technique = {
+            'MC P300 high':{       
+                "use_channels": "Span8",
+                "asp_vols": [50],
+                "asp_flow_rates": 50,
+                "dis_flow_rates": 50,
+                "offsets": None,
+                "touch_tip": True,
+                "liquid_height": 20,
+                "blow_out_air_volume": 20,
+                "spread": "wide",
+                "is_96_well": True,
+                "mix_stage": "none",
+                "mix_times": None,
+                "mix_vol": None,
+                "mix_rate": None,
+                "mix_liquid_height": None,
+                "delays": None,
+                "none_keys": [] 
+            }
+        }
+
+
+    def create_protocol(
+        self,
+        protocol_name: str,
+        protocol_description: str,
+        protocol_version: str,
+        protocol_author: str,
+        protocol_date: str,
+        protocol_type: str,
+        none_keys: List[str] = [],
+    ):
+        """
+        创建一个新的协议。
+
+        Args:
+            protocol_name (str): 协议名称
+            protocol_description (str): 协议描述
+            protocol_version (str): 协议版本
+            protocol_author (str): 协议作者
+            protocol_date (str): 协议日期
+            protocol_type (str): 协议类型
+            none_keys (List[str]): 需要设置为None的键列表
+
+        Returns:
+            dict: 创建的协议字典
+        """
+        self.temp_protocol = {
+            "meta": {
+                "name": protocol_name,
+                "description": protocol_description,
+                "version": protocol_version,
+                "author": protocol_author,
+                "date": protocol_date,
+                "type": protocol_type,
+            },
+            "labwares": [],
+            "steps": [],
+        }
+        return self.temp_protocol
+
+#     def run_protocol(self):
+#         """
+#         执行创建的实验流程。
+#         工作站的完整执行流程是，
+#         从 create_protocol 开始，创建新的 method，
+#         随后执行 transfer_liquid 等操作向实验流程添加步骤，
+#         最后 run_protocol 执行整个方法。
+
+#         Returns:
+#             dict: 执行结果
+#         """
+#         #use popen or subprocess to create py32 process and communicate send the temp protocol to it
+#         if not self.temp_protocol:
+#             raise ValueError("No protocol created. Please create a protocol first.")
+
+#         # 模拟执行协议
+#         self._status = "Running"
+#         self._success = True
+#         # 在这里可以添加实际执行协议的逻辑
+
+#         response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
+
+#     def create_resource(
+#         self,
+#         resource_tracker: DeviceNodeResourceTracker,
+#         resources: list[Resource],
+#         bind_parent_id: str,
+#         bind_location: dict[str, float],
+#         liquid_input_slot: list[int],
+#         liquid_type: list[str],
+#         liquid_volume: list[int],
+#         slot_on_deck: int,
+#         res_id,
+#         class_name,
+#         bind_locations,
+#         parent
+#     ):
+#         """
+#         创建一个新的资源。
+
+#         Args:
+#             device_id (str): 设备ID
+#             res_id (str): 资源ID
+#             class_name (str): 资源类名
+#             parent (str): 父级ID
+#             bind_locations (Point): 绑定位置
+#             liquid_input_slot (list[int]): 液体输入槽列表
+#             liquid_type (list[str]): 液体类型列表
+#             liquid_volume (list[int]): 液体体积列表
+#             slot_on_deck (int): 甲板上的槽位
+
+#         Returns:
+#             dict: 创建的资源字典
+#         """
+#         # TODO：需要对好接口，下面这个是临时的
+#         resource = {
+#             "id": res_id,
+#             "class": class_name,
+#             "parent": parent,
+#             "bind_locations": bind_locations.to_dict(),
+#             "liquid_input_slot": liquid_input_slot,
+#             "liquid_type": liquid_type,
+#             "liquid_volume": liquid_volume,
+#             "slot_on_deck": slot_on_deck,
+#         }
+#         self.temp_protocol["labwares"].append(resource)
+#         return resource
+
+    def transfer_liquid(
+        self,
+        sources: Sequence[Container],
+        targets: Sequence[Container],
+        tip_racks: Sequence[TipRack],
+        solvent: Optional[str] = None,
+        TipLocation :str = None, 
+        *,
+        use_channels: Optional[List[int]] = None,
+        asp_vols: Union[List[float], float],
+        dis_vols: Union[List[float], float],
+        asp_flow_rates: Optional[List[Optional[float]]] = None,
+        dis_flow_rates: Optional[List[Optional[float]]] = None,
+        offsets: Optional[List[Coordinate]] = None,
+        touch_tip: bool = False,
+        liquid_height: Optional[List[Optional[float]]] = None,
+        blow_out_air_volume: Optional[List[Optional[float]]] = None,
+        spread: Literal["wide", "tight", "custom"] = "wide",
+        is_96_well: bool = False,
+        mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
+        mix_times: Optional[int] = None,
+        mix_vol: Optional[int] = None,
+        mix_rate: Optional[int] = None,
+        mix_liquid_height: Optional[float] = None,
+        delays: Optional[List[int]] = None,
+        none_keys: List[str] = []
+    ):
+
+        transfer_params = {
+            "Span8": False,
+            "Pod": "Pod1",
+            "items": {},                      
+            "Wash": False,
+            "Dynamic?": True,
+            "AutoSelectActiveWashTechnique": False,
+            "ActiveWashTechnique": "",
+            "ChangeTipsBetweenDests": False,
+            "ChangeTipsBetweenSources": False,
+            "DefaultCaption": "",             
+            "UseExpression": False,
+            "LeaveTipsOn": False,
+            "MandrelExpression": "",
+            "Repeats": "1",
+            "RepeatsByVolume": False,
+            "Replicates": "1",
+            "ShowTipHandlingDetails": False,
+            "ShowTransferDetails": True,
+            "Solvent": "Water",
+            "Span8Wash": False,
+            "Span8WashVolume": "2",
+            "Span8WasteVolume": "1",
+            "SplitVolume": False,
+            "SplitVolumeCleaning": False,
+            "Stop": "Destinations",
+            "TipLocation": "BC1025F",
+            "UseCurrentTips": False,    
+            "UseDisposableTips": True,
+            "UseFixedTips": False,
+            "UseJIT": True,
+            "UseMandrelSelection": True,
+            "UseProbes": [True, True, True, True, True, True, True, True],
+            "WashCycles": "1",
+            "WashVolume": "110%",
+            "Wizard": False
+        }
+
+        items: dict = {}
+        for idx, (src, dst) in enumerate(zip(sources, targets)):
+            items[str(idx)] = {
+                "Source": str(src),
+                "Destination": str(dst),
+                "Volume": dis_vols[idx] 
+            }
+        transfer_params["items"] = items
+        transfer_params["Solvent"] =  solvent if solvent else "Water"
+        transfer_params["TipLocation"] = TipLocation
+
+        if len(tip_racks) == 1:
+                transfer_params['UseCurrentTips'] = True
+        elif len(tip_racks) > 1:
+            transfer_params["ChangeTipsBetweenDests"] = True
+
+        self.temp_protocol["steps"].append(transfer_params)
+
+        return 
+        
+    def transfer_biomek(
+            self,
+            parameters: dict,
+            technique: str,
+    ):
+        """
+        创建一个Biomek液体处理器的转移步骤。
+
+        Args:
+            step_number (int): 步骤编号
+            operation (str): 操作类型
+            description (str): 步骤描述
+            parameters (dict): 步骤参数
+
+        Returns:
+            dict: 创建的转移步骤字典
+        """
+        
+        sources = parameters.get("source")
+        targets = parameters.get("target")
+        tip_rack = parameters.get("tip_rack")
+        volume = parameters.get("volume")
+        liquid_type = parameters.get("liquid_type", "Well Content")
+        other_params = self.technique.get(technique, {})
+
+        self.transfer_liquid(
+            sources=[sources],
+            targets=[targets],
+            TipLocation=tip_rack,
+            tip_racks=[tip_rack],
+            solvent=liquid_type,
+            dis_vols=[volume],
+            **other_params
+        )
+
+        return 
+
+handler = LiquidHandlerBiomek()
+
+handler.temp_protocol = {
+    "meta": {},
+    "labwares": [],
+    "steps": []
+}
+input_steps = json.loads(steps_info)
+
+for step in input_steps['steps']:
+    if step['operation'] != 'transfer':
+        continue
+    parameters = step['parameters']
+    handler.transfer_biomek(parameters, technique='MC P300 high')
+
+print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))
+