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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。

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This commit is contained in:
Junhan Chang
2025-05-30 13:33:10 +08:00
committed by Xuwznln
parent 6f69df440c
commit 055d120ba8
6 changed files with 320 additions and 56 deletions
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99
unilabos/devices/liquid_handling/liquid_handler_abstract.py
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@@ -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."""
@@ -21,6 +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],
@@ -35,26 +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,
@@ -64,15 +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
@@ -100,13 +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`.")
@@ -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*.
@@ -201,14 +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
@@ -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,
targets: Sequence[Container],
):
async def touch_tip(self, 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(
@@ -298,9 +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):
@@ -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)