更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。

unilabos/devices/liquid_handling/biomek.py

@@ -0,0 +1,173 @@
+import requests
+from typing import List, Sequence, Optional, Union, Literal
+from geometry_msgs.msg import Point
+from unilabos_msgs.msg import Resource
+
+from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker  # type: ignore
+from .liquid_handler_abstract import LiquidHandlerAbstract
+
+
+class LiquidHandlerBiomek(LiquidHandlerAbstract):
+    """
+    Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
+    该类用于处理Biomek液体处理器的特定操作。
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._status = "Idle"  # 初始状态为 Idle
+        self._success = False  # 初始成功状态为 False
+        self._status_queue = kwargs.get("status_queue", None)  # 状态队列
+        self.temp_protocol = {}
+
+    def create_protocol(
+        self,
+        protocol_name: str,
+        protocol_description: str,
+        protocol_version: str,
+        protocol_author: str,
+        protocol_date: 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,
+            },
+            "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
+        """
+        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
+        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[List(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] = []
+    ):
+        # TODO：需要对好接口，下面这个是临时的
+        self.temp_protocol["steps"].append(
+            {
+                "type": "transfer",
+                "sources": [source.to_dict() for source in sources],
+                "targets": [target.to_dict() for target in targets],
+                "tip_racks": [tip_rack.to_dict() for tip_rack in tip_racks],
+                "use_channels": use_channels,
+                "asp_vols": asp_vols,
+                "dis_vols": dis_vols,
+                "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,
+            }
+        )

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 (
+from pylabrobot.resources import Resource, TipRack, Container, Coordinate, Well
-    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],
@@ -35,8 +43,8 @@ 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,
+        top: Optional[List[float]] = None,
-        none_keys: List[str] = []
+        none_keys: List[str] = [],
     ):
         """A complete *remove* (aspirate → waste) operation."""
         trash = self.deck.get_trash_area()
@@ -48,7 +56,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                     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(
@@ -100,7 +108,7 @@ 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."""
 
@@ -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*.
 
@@ -207,8 +216,9 @@ class LiquidHandlerAbstract(LiquidHandler):
                     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 (
+                for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in zip(
-                        zip(sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates)):
+                    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,
+    async def touch_tip(self, targets: Sequence[Container]):
-                        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(
@@ -298,7 +306,7 @@ 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
             return
@@ -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/registry/devices/liquid_handler.yaml

@@ -22,8 +22,8 @@ liquid_handler:
           is_96_well: is_96_well
           top: top
           none_keys: none_keys
-        feedback: { }
+        feedback: {}
-        result: { }
+        result: {}
       add_liquid:
         type: LiquidHandlerAdd
         goal:
@@ -43,8 +43,8 @@ liquid_handler:
           mix_rate: mix_rate
           mix_liquid_height: mix_liquid_height
           none_keys: none_keys
-        feedback: { }
+        feedback: {}
-        result: { }
+        result: {}
       transfer_liquid:
         type: LiquidHandlerTransfer
         goal:
@@ -69,8 +69,8 @@ liquid_handler:
           mix_liquid_height: mix_liquid_height
           delays: delays
           none_keys: none_keys
-        feedback: { }
+        feedback: {}
-        result: { }
+        result: {}
       mix:
         type: LiquidHandlerMix
         goal:
@@ -81,16 +81,16 @@ liquid_handler:
           offsets: offsets
           mix_rate: mix_rate
           none_keys: none_keys
-        feedback: { }
+        feedback: {}
-        result: { }
+        result: {}
       move_to:
         type: LiquidHandlerMoveTo
         goal:
           well: well
           dis_to_top: dis_to_top
           channel: channel
-        feedback: { }
+        feedback: {}
-        result: { }
+        result: {}
       aspirate:
         type: LiquidHandlerAspirate
         goal:
@@ -272,3 +272,62 @@ 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:
+      status: String
+      success: Boolean
+    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: {}
+  schema:
+    type: object
+    properties: {}
+    required: []
+    additionalProperties: false

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)]

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"

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
+---
+---