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* add biomek.py demo implementation * 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。 * Test * fix biomek success type * Convert LH action to biomek. * Update biomek.py * 注册表上报handle和schema (param input) * 修复biomek缺少的字段 * delete 's' * Remove warnings * Update biomek.py * Biomek test * Update biomek.py * 新增transfer_biomek的msg * New transfer_biomek * Updated transfer_biomek * 更新transfer_biomek的msg * 更新transfer_biomek的msg * 支持Biomek创建 * new action * fix key name typo * New parameter for biomek to run. * Refine * Update * new actions * new actions * 1 * registry * fix biomek startup add action handles * fix handles not as default entry * biomek_test.py biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json * Update biomek.py * biomek_test.py * fix liquid_handler.biomek handles * host node新增resource add时间统计 create_resource新增handle bump version to 0.9.2 * 修正物料上传时间 改用biomek_test 增加ResultInfoEncoder 支持返回结果上传 * 正确发送return_info结果 * 同步执行状态信息 * 取消raiseValueError提示 * Update biomek_test.py * 0608 DONE * 同步了Biomek.py 现在应可用 * biomek switch back to non-test * temp disable initialize resource * Refine biomek * Refine copy issue * Refine --------- Co-authored-by: Junhan Chang <changjh@pku.edu.cn> Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com> Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>
363 lines
15 KiB
Python
363 lines
15 KiB
Python
from __future__ import annotations
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from typing import List, Sequence, Optional, Literal, Union, Iterator
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import asyncio
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import time
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from pylabrobot.liquid_handling import LiquidHandler
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from pylabrobot.resources import Resource, TipRack, Container, Coordinate, Well
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class LiquidHandlerAbstract(LiquidHandler):
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"""Extended LiquidHandler with additional operations."""
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# ---------------------------------------------------------------
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# REMOVE LIQUID --------------------------------------------------
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# ---------------------------------------------------------------
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async def create_protocol(
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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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sources: Sequence[Container],
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waste_liquid: Optional[Container] = None,
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*,
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use_channels: Optional[List[int]] = None,
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flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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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: Optional[Literal["wide", "tight", "custom"]] = "wide",
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delays: Optional[List[int]] = None,
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is_96_well: Optional[bool] = False,
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top: Optional[List[float]] = None,
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none_keys: List[str] = [],
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):
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"""A complete *remove* (aspirate → waste) operation."""
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trash = self.deck.get_trash_area()
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try:
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if is_96_well:
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pass # This mode is not verified
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else:
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if len(vols) != len(sources):
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raise ValueError("Length of `vols` must match `sources`.")
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for src, vol in zip(sources, vols):
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await self.move_to(src, dis_to_top=top[0] if top else 0)
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tip = next(self.current_tip)
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await self.pick_up_tips(tip)
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await self.aspirate(
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resources=[src],
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vols=[vol],
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use_channels=use_channels, # only aspirate96 used, default to None
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flow_rates=[flow_rates[0]] if flow_rates else None,
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offsets=[offsets[0]] if offsets else None,
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liquid_height=[liquid_height[0]] if liquid_height else None,
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blow_out_air_volume=blow_out_air_volume[0] if blow_out_air_volume else None,
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spread=spread,
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)
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await self.custom_delay(seconds=delays[0] if delays else 0)
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await self.dispense(
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resources=waste_liquid,
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vols=[vol],
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use_channels=use_channels,
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flow_rates=[flow_rates[1]] if flow_rates else None,
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offsets=[offsets[1]] if offsets else None,
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liquid_height=[liquid_height[1]] if liquid_height else None,
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blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
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spread=spread,
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)
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await self.discard_tips() # For now, each of tips is discarded after use
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except Exception as e:
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raise RuntimeError(f"Liquid removal failed: {e}") from e
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# ---------------------------------------------------------------
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# ADD LIQUID -----------------------------------------------------
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# ---------------------------------------------------------------
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async def add_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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reagent_sources: Sequence[Container],
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targets: Sequence[Container],
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*,
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use_channels: Optional[List[int]] = None,
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flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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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: Optional[Literal["wide", "tight", "custom"]] = "wide",
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is_96_well: bool = False,
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delays: Optional[List[int]] = None,
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mix_time: Optional[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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none_keys: List[str] = [],
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):
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"""A complete *add* (aspirate reagent → dispense into targets) operation."""
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try:
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if is_96_well:
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pass # This mode is not verified.
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else:
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if len(asp_vols) != len(targets):
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raise ValueError("Length of `vols` must match `targets`.")
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tip = next(self.current_tip)
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await self.pick_up_tips(tip)
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for _ in range(len(targets)):
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await self.aspirate(
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resources=reagent_sources,
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vols=[asp_vols[_]],
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use_channels=use_channels,
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flow_rates=[flow_rates[0]] if flow_rates else None,
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offsets=[offsets[0]] if offsets else None,
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liquid_height=[liquid_height[0]] if liquid_height else None,
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blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
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spread=spread,
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)
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if delays is not None:
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await self.custom_delay(seconds=delays[0])
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await self.dispense(
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resources=[targets[_]],
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vols=[dis_vols[_]],
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use_channels=use_channels,
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flow_rates=[flow_rates[1]] if flow_rates else None,
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offsets=[offsets[1]] if offsets else None,
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blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
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liquid_height=[liquid_height[1]] if liquid_height else None,
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spread=spread,
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)
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if delays is not None:
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await self.custom_delay(seconds=delays[1])
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await self.mix(
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targets=targets[_],
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mix_time=mix_time,
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mix_vol=mix_vol,
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offsets=offsets if offsets else None,
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height_to_bottom=mix_liquid_height if mix_liquid_height else None,
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mix_rate=mix_rate if mix_rate else None,
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)
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if delays is not None:
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await self.custom_delay(seconds=delays[1])
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await self.touch_tip(targets[_])
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await self.discard_tips()
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except Exception as e:
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raise RuntimeError(f"Liquid addition failed: {e}") from e
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# ---------------------------------------------------------------
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# TRANSFER LIQUID ------------------------------------------------
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# ---------------------------------------------------------------
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async 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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"""Transfer liquid from each *source* well/plate to the corresponding *target*.
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Parameters
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----------
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asp_vols, dis_vols
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Single volume (µL) or list matching the number of transfers.
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sources, targets
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Same‑length sequences of containers (wells or plates). In 96‑well mode
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each must contain exactly one plate.
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tip_racks
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One or more TipRacks providing fresh tips.
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is_96_well
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Set *True* to use the 96‑channel head.
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"""
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try:
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# ------------------------------------------------------------------
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# 96‑channel head mode
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# ------------------------------------------------------------------
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if is_96_well:
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pass # This mode is not verified
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else:
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if not (len(asp_vols) == len(sources) and len(dis_vols) == len(targets)):
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raise ValueError("`sources`, `targets`, and `vols` must have the same length.")
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tip_iter = self.iter_tips(tip_racks)
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for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in zip(
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sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates
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):
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tip = next(tip_iter)
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await self.pick_up_tips(tip)
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# Aspirate from source
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await self.aspirate(
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resources=[src],
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vols=[asp_vol],
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use_channels=use_channels,
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flow_rates=[asp_flow_rate],
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offsets=offsets,
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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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)
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self.custom_delay(seconds=delays[0] if delays else 0)
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# Dispense into target
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await self.dispense(
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resources=[tgt],
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vols=[dis_vol],
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use_channels=use_channels,
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flow_rates=[dis_flow_rate],
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offsets=offsets,
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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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)
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await self.mix(
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targets=[tgt],
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mix_time=mix_times[0] if mix_times else None,
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mix_vol=mix_vol[0] if mix_vol else None,
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mix_rate=mix_rate[0] if mix_rate else None,
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)
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if touch_tip:
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await self.touch_tip(tgt)
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await self.discard_tips()
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except Exception as exc:
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raise RuntimeError(f"Liquid transfer failed: {exc}") from exc
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# ---------------------------------------------------------------
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# Helper utilities
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# ---------------------------------------------------------------
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async def custom_delay(self, seconds=0, msg=None):
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"""
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seconds: seconds to wait
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msg: information to be printed
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"""
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if seconds != None and seconds > 0:
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if msg:
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print(f"Waiting time: {msg}")
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print(f"Current time: {time.strftime('%H:%M:%S')}")
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print(f"Time to finish: {time.strftime('%H:%M:%S', time.localtime(time.time() + seconds))}")
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await asyncio.sleep(seconds)
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if msg:
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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, 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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vols=[0],
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use_channels=None,
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flow_rates=None,
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offsets=[Coordinate(x=-targets.get_size_x() / 2, y=0, z=0)],
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liquid_height=None,
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blow_out_air_volume=None,
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)
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# await self.custom_delay(seconds=1) # In the simulation, we do not need to wait
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await self.aspirate(
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resources=[targets],
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vols=[0],
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use_channels=None,
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flow_rates=None,
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offsets=[Coordinate(x=targets.get_size_x() / 2, y=0, z=0)],
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liquid_height=None,
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blow_out_air_volume=None,
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)
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async def mix(
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self,
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targets: Sequence[Container],
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mix_time: int = None,
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mix_vol: Optional[int] = None,
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height_to_bottom: Optional[float] = None,
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offsets: Optional[Coordinate] = None,
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mix_rate: Optional[float] = None,
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none_keys: List[str] = [],
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):
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if mix_time is None: # No mixing required
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return
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"""Mix the liquid in the target wells."""
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for _ in range(mix_time):
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await self.aspirate(
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resources=[targets],
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vols=[mix_vol],
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flow_rates=[mix_rate] if mix_rate else None,
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offsets=[offsets] if offsets else None,
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liquid_height=[height_to_bottom] if height_to_bottom else None,
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)
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await self.custom_delay(seconds=1)
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await self.dispense(
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resources=[targets],
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vols=[mix_vol],
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flow_rates=[mix_rate] if mix_rate else None,
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offsets=[offsets] if offsets else None,
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liquid_height=[height_to_bottom] if height_to_bottom else None,
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)
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def iter_tips(self, tip_racks: Sequence[TipRack]) -> Iterator[Resource]:
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"""Yield tips from a list of TipRacks one-by-one until depleted."""
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for rack in tip_racks:
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for tip in rack:
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yield tip
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raise RuntimeError("Out of tips!")
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def set_tiprack(self, tip_racks: Sequence[TipRack]):
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"""Set the tip racks for the liquid handler."""
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self.tip_racks = tip_racks
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tip_iter = self.iter_tips(tip_racks)
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self.current_tip = tip_iter
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async def move_to(self, well: Well, dis_to_top: float = 0, channel: int = 0):
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"""
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Move a single channel to a specific well with a given z-height.
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Parameters
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----------
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well : Well
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The target well.
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dis_to_top : float
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Height in mm to move to relative to the well top.
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channel : int
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Pipetting channel to move (default: 0).
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"""
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await self.prepare_for_manual_channel_operation(channel=channel)
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abs_loc = well.get_absolute_location()
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well_height = well.get_absolute_size_z()
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await self.move_channel_x(channel, abs_loc.x)
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await self.move_channel_y(channel, abs_loc.y)
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await self.move_channel_z(channel, abs_loc.z + well_height + dis_to_top)
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