diff --git a/unilabos/devices/liquid_handling/biomek.py b/unilabos/devices/liquid_handling/biomek.py index 7692905e..ccca72d1 100644 --- a/unilabos/devices/liquid_handling/biomek.py +++ b/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, - res_id: str, - class_name: str, - parent: str, - bind_locations: Point, + 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], @@ -205,4 +209,4 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract): self.temp_protocol["steps"].append(transfer_params) return - s \ No newline at end of file + s diff --git a/unilabos/devices/liquid_handling/liquid_handler_abstract.py b/unilabos/devices/liquid_handling/liquid_handler_abstract.py index 2596e843..4faa0427 100644 --- a/unilabos/devices/liquid_handling/liquid_handler_abstract.py +++ b/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.""" @@ -21,14 +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, - 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, @@ -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], - 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 @@ -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 ( - 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 @@ -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) - diff --git a/unilabos/registry/devices/liquid_handler.yaml b/unilabos/registry/devices/liquid_handler.yaml index bcddae55..313a8b80 100644 --- a/unilabos/registry/devices/liquid_handler.yaml +++ b/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: { } - result: { } + feedback: {} + 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: { } - result: { } + feedback: {} + 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: { } - result: { } + feedback: {} + result: {} mix: type: LiquidHandlerMix goal: @@ -81,16 +81,16 @@ 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: @@ -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 diff --git a/unilabos/ros/nodes/base_device_node.py b/unilabos/ros/nodes/base_device_node.py index 28b67aa4..daf52300 100644 --- a/unilabos/ros/nodes/base_device_node.py +++ b/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)] diff --git a/unilabos_msgs/CMakeLists.txt b/unilabos_msgs/CMakeLists.txt index 0cd6a1e3..135e5738 100644 --- a/unilabos_msgs/CMakeLists.txt +++ b/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" diff --git a/unilabos_msgs/action/LiquidHandlerProtocolCreation.action b/unilabos_msgs/action/LiquidHandlerProtocolCreation.action new file mode 100644 index 00000000..de8c605a --- /dev/null +++ b/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 +--- +---