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https://github.com/dptech-corp/Uni-Lab-OS.git
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add biomek.py demo implementation
This commit is contained in:
Junhan Chang
167
unilabos/devices/liquid_handling/biomek.py
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167
unilabos/devices/liquid_handling/biomek.py
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@@ -0,0 +1,167 @@
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import requests
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from typing import List, Sequence, Optional, Union, Literal
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from .liquid_handler_abstract import LiquidHandlerAbstract
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class LiquidHandlerBiomek(LiquidHandlerAbstract):
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"""
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Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
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该类用于处理Biomek液体处理器的特定操作。
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"""
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def __init__(self, *args, **kwargs):
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super().__init__(*args, **kwargs)
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self._status = "Idle" # 初始状态为 Idle
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self._success = False # 初始成功状态为 False
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self._status_queue = kwargs.get("status_queue", None) # 状态队列
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self.temp_protocol = {}
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def create_protocol(self,
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protocol_name: str,
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protocol_description: str,
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protocol_version: str,
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protocol_author: str,
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protocol_date: str,
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):
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"""
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创建一个新的协议。
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Args:
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protocol_name (str): 协议名称
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protocol_description (str): 协议描述
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protocol_version (str): 协议版本
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protocol_author (str): 协议作者
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protocol_date (str): 协议日期
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protocol_type (str): 协议类型
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none_keys (List[str]): 需要设置为None的键列表
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Returns:
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dict: 创建的协议字典
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"""
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self.temp_protocol = {
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"meta": {
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"name": protocol_name,
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"description": protocol_description,
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"version": protocol_version,
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"author": protocol_author,
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"date": protocol_date,
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},
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"labwares": [],
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"steps": [],
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}
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return self.temp_protocol
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def run_protocol(self):
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"""
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执行创建的实验流程。
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工作站的完整执行流程是，
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从 create_protocol 开始，创建新的 method，
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随后执行 transfer_liquid 等操作向实验流程添加步骤，
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最后 run_protocol 执行整个方法。
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Returns:
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dict: 执行结果
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"""
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if not self.temp_protocol:
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raise ValueError("No protocol created. Please create a protocol first.")
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# 模拟执行协议
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self._status = "Running"
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self._success = True
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# 在这里可以添加实际执行协议的逻辑
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response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
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def create_resource(
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self,
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device_id: str,
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res_id: str,
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class_name: str,
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parent: str,
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bind_locations: Point,
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liquid_input_slot: list[int],
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liquid_type: list[str],
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liquid_volume: list[int],
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slot_on_deck: int,
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):
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"""
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创建一个新的资源。
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Args:
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device_id (str): 设备ID
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res_id (str): 资源ID
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class_name (str): 资源类名
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parent (str): 父级ID
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bind_locations (Point): 绑定位置
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liquid_input_slot (list[int]): 液体输入槽列表
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liquid_type (list[str]): 液体类型列表
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liquid_volume (list[int]): 液体体积列表
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slot_on_deck (int): 甲板上的槽位
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Returns:
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dict: 创建的资源字典
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"""
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# TODO：需要对好接口，下面这个是临时的
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resource = {
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"id": res_id,
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"class": class_name,
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"parent": parent,
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"bind_locations": bind_locations.to_dict(),
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"liquid_input_slot": liquid_input_slot,
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"liquid_type": liquid_type,
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"liquid_volume": liquid_volume,
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"slot_on_deck": slot_on_deck,
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}
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self.temp_protocol["labwares"].append(resource)
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return resource
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def transfer_liquid(
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self,
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sources: Sequence[Container],
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targets: Sequence[Container],
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tip_racks: Sequence[TipRack],
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*,
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use_channels: Optional[List[int]] = None,
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asp_vols: Union[List[float], float],
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dis_vols: Union[List[float], float],
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asp_flow_rates: Optional[List[Optional[float]]] = None,
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dis_flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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touch_tip: bool = False,
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liquid_height: Optional[List[Optional[float]]] = None,
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blow_out_air_volume: Optional[List[Optional[float]]] = None,
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spread: Literal["wide", "tight", "custom"] = "wide",
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is_96_well: bool = False,
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mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
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mix_times: Optional[List(int)] = None,
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mix_vol: Optional[int] = None,
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mix_rate: Optional[int] = None,
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mix_liquid_height: Optional[float] = None,
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delays: Optional[List[int]] = None,
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none_keys: List[str] = []
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):
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# TODO：需要对好接口，下面这个是临时的
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self.temp_protocol["steps"].append({
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"type": "transfer",
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"sources": [source.to_dict() for source in sources],
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"targets": [target.to_dict() for target in targets],
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"tip_racks": [tip_rack.to_dict() for tip_rack in tip_racks],
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"use_channels": use_channels,
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"asp_vols": asp_vols,
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"dis_vols": dis_vols,
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"asp_flow_rates": asp_flow_rates,
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"dis_flow_rates": dis_flow_rates,
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"offsets": offsets,
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"touch_tip": touch_tip,
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"liquid_height": liquid_height,
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"blow_out_air_volume": blow_out_air_volume,
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"spread": spread,
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"is_96_well": is_96_well,
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"mix_stage": mix_stage,
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"mix_times": mix_times,
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"mix_vol": mix_vol,
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"mix_rate": mix_rate,
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"mix_liquid_height": mix_liquid_height,
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"delays": delays,
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})
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@@ -21,6 +21,18 @@ class LiquidHandlerAbstract(LiquidHandler):
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# REMOVE LIQUID --------------------------------------------------
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# ---------------------------------------------------------------
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async def create_protocol(self,
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protocol_name: str,
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protocol_description: str,
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protocol_version: str,
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protocol_author: str,
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protocol_date: str,
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protocol_type: str,
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none_keys: List[str] = []
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):
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"""Create a new protocol with the given metadata."""
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pass
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async def remove_liquid(
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self,
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vols: List[float],
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@@ -158,13 +170,13 @@ class LiquidHandlerAbstract(LiquidHandler):
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# ---------------------------------------------------------------
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async def transfer_liquid(
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self,
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asp_vols: Union[List[float], float],
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dis_vols: Union[List[float], float],
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sources: Sequence[Container],
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targets: Sequence[Container],
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tip_racks: Sequence[TipRack],
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*,
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use_channels: Optional[List[int]] = None,
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asp_vols: Union[List[float], float],
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dis_vols: Union[List[float], float],
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asp_flow_rates: Optional[List[Optional[float]]] = None,
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dis_flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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@@ -266,9 +278,7 @@ class LiquidHandlerAbstract(LiquidHandler):
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print(f"Done: {msg}")
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print(f"Current time: {time.strftime('%H:%M:%S')}")
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async def touch_tip(self,
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targets: Sequence[Container],
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):
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async def touch_tip(self, targets: Sequence[Container]):
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"""Touch the tip to the side of the well."""
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await self.aspirate(
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resources=[targets],
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