Merge branch '37-biomek-i5i7' of https://github.com/dptech-corp/Uni-Lab-OS into 37-biomek-i5i7

unilabos/devices/liquid_handling/biomek.py

@@ -1,6 +1,9 @@
 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
 
 
@@ -20,12 +23,14 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         self.temp_protocol = {}
         self.py32_path = "/opt/py32"  # Biomek的Python 3.2路径
 
-    def create_protocol(self,
+    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。
@@ -79,11 +84,10 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
 
     def create_resource(
         self,
-        device_id: str,
+        resource_tracker: DeviceNodeResourceTracker,
-        res_id: str,
+        resources: list[Resource],
-        class_name: str,
+        bind_parent_id: str,
-        parent: str,
+        bind_location: dict[str, float],
-        bind_locations: Point,
         liquid_input_slot: list[int],
         liquid_type: list[str],
         liquid_volume: list[int],
@@ -205,4 +209,4 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         self.temp_protocol["steps"].append(transfer_params)
         
         return 
-    s
+    s

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."""
@@ -21,14 +16,15 @@ class LiquidHandlerAbstract(LiquidHandler):
     # REMOVE LIQUID --------------------------------------------------
     # ---------------------------------------------------------------
 
-    async def create_protocol(self,
+    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] = []
+        none_keys: List[str] = [],
     ):
         """Create a new protocol with the given metadata."""
         pass
@@ -47,26 +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,
+        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()
         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,
@@ -76,15 +72,15 @@ class LiquidHandlerAbstract(LiquidHandler):
                     await self.custom_delay(seconds=delays[0] if delays else 0)
                     await self.dispense(
                         resources=waste_liquid,
-                         vols=[vol],
+                        vols=[vol],
-                         use_channels=use_channels,
+                        use_channels=use_channels,
-                         flow_rates=[flow_rates[1]] if flow_rates else None,
+                        flow_rates=[flow_rates[1]] if flow_rates else None,
-                         offsets=[offsets[1]] if offsets else None,
+                        offsets=[offsets[1]] if offsets else None,
-                         liquid_height=[liquid_height[1]] if liquid_height 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,
+                        blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
-                         spread=spread,
+                        spread=spread,
-                     )
+                    )
-                    await self.discard_tips() # For now, each of tips is discarded after use
+                    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
@@ -112,13 +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`.")
@@ -134,7 +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])
@@ -156,7 +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[_])
@@ -191,7 +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*.
 
@@ -213,14 +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 (
+                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
@@ -259,9 +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):
         """
@@ -285,19 +283,19 @@ class LiquidHandlerAbstract(LiquidHandler):
             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(
@@ -308,9 +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):
@@ -343,7 +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.
 
@@ -362,4 +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 +272,60 @@ 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: {}
+  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
+---
+---