open_pub/Uni-Lab-OS
1
0
Fork 0
mirror of https://github.com/deepmodeling/Uni-Lab-OS synced 2026-03-24 05:48:20 +00:00
Code Issues Packages Projects Releases Wiki Activity

merge lab_resource，并修改transfer liquid

Browse Source
This commit is contained in:
q434343
2026-02-28 16:05:29 +08:00
parent f38f3dfc89
commit 41be9e4e19
13 changed files with 11222 additions and 338 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
unilabos/app/ws_client.py
View File

@@ -1177,6 +1177,11 @@ class QueueProcessor:
logger.debug(f"[QueueProcessor] Sending busy status for {len(queued_jobs)} queued jobs")
for job_info in queued_jobs:
# 快照可能已过期：在遍历过程中 end_job() 可能已将此 job 移至 READY，
# 此时不应再发送 busy/need_more，否则会覆盖已发出的 free=True 通知
if job_info.status != JobStatus.QUEUE:
continue
message = {
"action": "report_action_state",
"data": {

384
unilabos/devices/liquid_handling/liquid_handler_abstract.py
View File

@@ -21,7 +21,7 @@ from pylabrobot.resources import (
ResourceHolder,
Lid,
Trash,
Tip,
Tip, TubeRack,
)
from typing_extensions import TypedDict
@@ -208,7 +208,8 @@ class LiquidHandlerMiddleware(LiquidHandler):
spread: Literal["wide", "tight", "custom"] = "wide",
**backend_kwargs,
):
if spread == "":
spread = "wide"
if self._simulator:
return await self._simulate_handler.aspirate(
resources,
@@ -221,6 +222,7 @@ class LiquidHandlerMiddleware(LiquidHandler):
spread,
**backend_kwargs,
)
try:
await super().aspirate(
resources,
vols,
@@ -232,6 +234,21 @@ class LiquidHandlerMiddleware(LiquidHandler):
spread,
**backend_kwargs,
)
except ValueError as e:
if "Resource is too small to space channels" in str(e) and spread != "custom":
await super().aspirate(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread="custom",
**backend_kwargs,
)
else:
raise
res_samples = []
res_volumes = []
@@ -243,7 +260,8 @@ class LiquidHandlerMiddleware(LiquidHandler):
channels_to_use = use_channels
for resource, volume, channel in zip(resources, vols, channels_to_use):
res_samples.append({"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)})
sample_uuid_value = getattr(resource, "unilabos_extra", {}).get(EXTRA_SAMPLE_UUID, None)
res_samples.append({"name": resource.name, "sample_uuid": sample_uuid_value})
res_volumes.append(volume)
self.pending_liquids_dict[channel] = {
EXTRA_SAMPLE_UUID: sample_uuid_value,
@@ -263,6 +281,8 @@ class LiquidHandlerMiddleware(LiquidHandler):
spread: Literal["wide", "tight", "custom"] = "wide",
**backend_kwargs,
) -> SimpleReturn:
if spread == "":
spread = "wide"
if self._simulator:
return await self._simulate_handler.dispense(
resources,
@@ -275,6 +295,7 @@ class LiquidHandlerMiddleware(LiquidHandler):
spread,
**backend_kwargs,
)
try:
await super().dispense(
resources,
vols,
@@ -283,8 +304,24 @@ class LiquidHandlerMiddleware(LiquidHandler):
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
except ValueError as e:
if "Resource is too small to space channels" in str(e) and spread != "custom":
await super().dispense(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
"custom",
**backend_kwargs,
)
else:
raise
res_samples = []
res_volumes = []
for resource, volume, channel in zip(resources, vols, use_channels):
@@ -702,10 +739,13 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
如果 liquid_names 和 volumes 为空，但 plate 和 well_names 不为空，直接返回 plate 和 wells。
"""
assert issubclass(plate.__class__, Plate), "plate must be a Plate"
plate: Plate = cast(Plate, cast(Resource, plate))
assert issubclass(plate.__class__, Plate) or issubclass(plate.__class__, TubeRack) , f"plate must be a Plate, now: {type(plate)}"
plate: Union[Plate, TubeRack]
# 根据 well_names 获取对应的 Well 对象
if issubclass(plate.__class__, Plate):
wells = [plate.get_well(name) for name in well_names]
elif issubclass(plate.__class__, TubeRack):
wells = [plate.get_tube(name) for name in well_names]
res_volumes = []
# 如果 liquid_names 和 volumes 都为空，直接返回
@@ -851,7 +891,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for _ in range(len(sources)):
tip = []
for __ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
await self.aspirate(
resources=[sources[_]],
@@ -891,7 +931,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for i in range(0, len(sources), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
current_targets = waste_liquid[i : i + 8]
current_reagent_sources = sources[i : i + 8]
@@ -985,7 +1025,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for _ in range(len(targets)):
tip = []
for x in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
await self.aspirate(
@@ -1037,7 +1077,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for i in range(0, len(targets), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
current_targets = targets[i : i + 8]
current_reagent_sources = reagent_sources[i : i + 8]
@@ -1162,11 +1202,19 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
Number of mix cycles. If *None* (default) no mixing occurs regardless of
mix_stage.
"""
num_sources = len(sources)
num_targets = len(targets)
len_asp_vols = len(asp_vols)
len_dis_vols = len(dis_vols)
# 确保 use_channels 有默认值
if use_channels is None:
# 默认使用设备所有通道（例如 8 通道移液站默认就是 0-7）
use_channels = list(range(self.channel_num)) if self.channel_num > 0 else [0]
use_channels = list(range(self.channel_num)) if self.channel_num == 8 else [0]
elif len(use_channels) == 8:
if self.channel_num != 8:
raise ValueError(f"if channel_num is 8, use_channels length must be 8, but got {len(use_channels)}")
if num_sources%8 != 0 or num_targets%8 != 0 or len_asp_vols%8 != 0 or len_dis_vols%8 != 0:
raise ValueError(f"if channel_num is 8, sources, targets, asp_vols, and dis_vols length must be divisible by 8, but got {num_sources}, {num_targets}, {len_asp_vols}, and {len_dis_vols}")
if is_96_well:
pass # This mode is not verified.
@@ -1200,86 +1248,227 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
# 识别传输模式（mix_times 为 None 也应该能正常移液，只是不做 mix）
num_sources = len(sources)
num_targets = len(targets)
len_asp_vols = len(asp_vols)
len_dis_vols = len(dis_vols)
if num_sources == 1 and num_targets > 1:
# 模式1: 一对多 (1 source -> N targets)
await self._transfer_one_to_many(
sources[0],
targets,
tip_racks,
use_channels,
asp_vols,
dis_vols,
asp_flow_rates,
dis_flow_rates,
offsets,
touch_tip,
liquid_height,
blow_out_air_volume,
spread,
mix_stage,
mix_times,
mix_vol,
mix_rate,
mix_liquid_height,
delays,
)
elif num_sources > 1 and num_targets == 1:
# 模式2: 多对一 (N sources -> 1 target)
await self._transfer_many_to_one(
sources,
targets[0],
tip_racks,
use_channels,
asp_vols,
dis_vols,
asp_flow_rates,
dis_flow_rates,
offsets,
touch_tip,
liquid_height,
blow_out_air_volume,
spread,
mix_stage,
mix_times,
mix_vol,
mix_rate,
mix_liquid_height,
delays,
)
elif num_sources == num_targets:
# 模式3: 一对一 (N sources -> N targets)
await self._transfer_one_to_one(
sources,
targets,
tip_racks,
use_channels,
asp_vols,
dis_vols,
asp_flow_rates,
dis_flow_rates,
offsets,
touch_tip,
liquid_height,
blow_out_air_volume,
spread,
mix_stage,
mix_times,
mix_vol,
mix_rate,
mix_liquid_height,
delays,
)
else:
raise ValueError(
f"Unsupported transfer mode: {num_sources} sources -> {num_targets} targets. "
"Supported modes: 1->N, N->1, or N->N."
)
# if num_targets != 1 and num_sources != 1:
# if len_asp_vols != num_sources and len_asp_vols != num_targets:
# raise ValueError(f"asp_vols length must be equal to sources or targets length, but got {len_asp_vols} and {num_sources} and {num_targets}")
# if len_dis_vols != num_sources and len_dis_vols != num_targets:
# raise ValueError(f"dis_vols length must be equal to sources or targets length, but got {len_dis_vols} and {num_sources} and {num_targets}")
if len(use_channels) != 8:
max_len = max(num_sources, num_targets)
for i in range(max_len):
# 辅助函数：安全地从列表中获取元素，如果列表为空则返回None
def safe_get(lst, idx, default=None):
return [lst[idx]] if lst else default
# 动态构建参数字典，只传递实际提供的参数
kwargs = {
'sources': [sources[i%num_sources]],
'targets': [targets[i%num_targets]],
'tip_racks': tip_racks,
'use_channels': use_channels,
'asp_vols': [asp_vols[i%len_asp_vols]],
'dis_vols': [dis_vols[i%len_dis_vols]],
}
# 条件性添加可选参数
if asp_flow_rates is not None:
kwargs['asp_flow_rates'] = [asp_flow_rates[i%len_asp_vols]]
if dis_flow_rates is not None:
kwargs['dis_flow_rates'] = [dis_flow_rates[i%len_dis_vols]]
if offsets is not None:
kwargs['offsets'] = safe_get(offsets, i)
if touch_tip is not None:
kwargs['touch_tip'] = touch_tip if touch_tip else False
if liquid_height is not None:
kwargs['liquid_height'] = safe_get(liquid_height, i)
if blow_out_air_volume is not None:
kwargs['blow_out_air_volume'] = safe_get(blow_out_air_volume, i)
if spread is not None:
kwargs['spread'] = spread
if mix_stage is not None:
kwargs['mix_stage'] = safe_get(mix_stage, i)
if mix_times is not None:
kwargs['mix_times'] = safe_get(mix_times, i)
if mix_vol is not None:
kwargs['mix_vol'] = safe_get(mix_vol, i)
if mix_rate is not None:
kwargs['mix_rate'] = safe_get(mix_rate, i)
if mix_liquid_height is not None:
kwargs['mix_liquid_height'] = safe_get(mix_liquid_height, i)
if delays is not None:
kwargs['delays'] = safe_get(delays, i)
await self._transfer_base_method(**kwargs)
# if num_sources == 1 and num_targets > 1:
# # 模式1: 一对多 (1 source -> N targets)
# await self._transfer_one_to_many(
# sources,
# targets,
# tip_racks,
# use_channels,
# asp_vols,
# dis_vols,
# asp_flow_rates,
# dis_flow_rates,
# offsets,
# touch_tip,
# liquid_height,
# blow_out_air_volume,
# spread,
# mix_stage,
# mix_times,
# mix_vol,
# mix_rate,
# mix_liquid_height,
# delays,
# )
# elif num_sources > 1 and num_targets == 1:
# # 模式2: 多对一 (N sources -> 1 target)
# await self._transfer_many_to_one(
# sources,
# targets[0],
# tip_racks,
# use_channels,
# asp_vols,
# dis_vols,
# asp_flow_rates,
# dis_flow_rates,
# offsets,
# touch_tip,
# liquid_height,
# blow_out_air_volume,
# spread,
# mix_stage,
# mix_times,
# mix_vol,
# mix_rate,
# mix_liquid_height,
# delays,
# )
# elif num_sources == num_targets:
# # 模式3: 一对一 (N sources -> N targets)
# await self._transfer_one_to_one(
# sources,
# targets,
# tip_racks,
# use_channels,
# asp_vols,
# dis_vols,
# asp_flow_rates,
# dis_flow_rates,
# offsets,
# touch_tip,
# liquid_height,
# blow_out_air_volume,
# spread,
# mix_stage,
# mix_times,
# mix_vol,
# mix_rate,
# mix_liquid_height,
# delays,
# )
# else:
# raise ValueError(
# f"Unsupported transfer mode: {num_sources} sources -> {num_targets} targets. "
# "Supported modes: 1->N, N->1, or N->N."
# )
return TransferLiquidReturn(
sources=ResourceTreeSet.from_plr_resources(list(sources), known_newly_created=False).dump(), # type: ignore
targets=ResourceTreeSet.from_plr_resources(list(targets), known_newly_created=False).dump(), # type: ignore
)
async def _transfer_base_method(
self,
sources: Sequence[Container],
targets: Sequence[Container],
tip_racks: Sequence[TipRack],
use_channels: List[int],
asp_vols: List[float],
dis_vols: List[float],
**kwargs
):
# 从kwargs中提取参数，提供默认值
asp_flow_rates = kwargs.get('asp_flow_rates')
dis_flow_rates = kwargs.get('dis_flow_rates')
offsets = kwargs.get('offsets')
touch_tip = kwargs.get('touch_tip', False)
liquid_height = kwargs.get('liquid_height')
blow_out_air_volume = kwargs.get('blow_out_air_volume')
spread = kwargs.get('spread', 'wide')
mix_stage = kwargs.get('mix_stage')
mix_times = kwargs.get('mix_times')
mix_vol = kwargs.get('mix_vol')
mix_rate = kwargs.get('mix_rate')
mix_liquid_height = kwargs.get('mix_liquid_height')
delays = kwargs.get('delays')
tip = []
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=[targets[0]],
mix_time=mix_times,
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,
use_channels=use_channels,
)
await self.aspirate(
resources=[sources[0]],
vols=[asp_vols[0]],
use_channels=use_channels,
flow_rates=[asp_flow_rates[0]] if asp_flow_rates and len(asp_flow_rates) > 0 else None,
offsets=[offsets[0]] if offsets and len(offsets) > 0 else None,
liquid_height=[liquid_height[0]] if liquid_height and len(liquid_height) > 0 else None,
blow_out_air_volume=(
[blow_out_air_volume[0]] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None
),
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
await self.dispense(
resources=[targets[0]],
vols=[dis_vols[0]],
use_channels=use_channels,
flow_rates=[dis_flow_rates[0]] if dis_flow_rates and len(dis_flow_rates) > 0 else None,
offsets=[offsets[0]] if offsets and len(offsets) > 0 else None,
blow_out_air_volume=(
[blow_out_air_volume[0]] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None
),
liquid_height=[liquid_height[0]] if liquid_height and len(liquid_height) > 0 else None,
spread=spread,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[1])
if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0:
await self.mix(
targets=[targets[0]],
mix_time=mix_times,
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,
use_channels=use_channels,
)
if delays is not None and len(delays) > 1:
await self.custom_delay(seconds=delays[0])
await self.touch_tip(targets[0])
await self.discard_tips(use_channels=use_channels)
async def _transfer_one_to_one(
self,
@@ -1322,7 +1511,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for _ in range(len(targets)):
tip = []
for ___ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0:
@@ -1386,7 +1575,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for i in range(0, len(targets), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
current_targets = targets[i : i + 8]
current_reagent_sources = sources[i : i + 8]
@@ -1491,7 +1680,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
# 单通道模式：一次吸液，多次分液
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0:
@@ -1563,7 +1752,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for i in range(0, len(targets), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
current_targets = targets[i : i + 8]
@@ -1702,7 +1891,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0:
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
await self.mix(
@@ -1721,7 +1910,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for idx, source in enumerate(sources):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
await self.aspirate(
@@ -1804,7 +1993,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0:
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
await self.mix(
@@ -1822,7 +2011,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for i in range(0, len(sources), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(next(self.current_tip))
tip.extend(self._get_next_tip())
await self.pick_up_tips(tip)
current_sources = sources[i : i + 8]
@@ -2022,7 +2211,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for rack in tip_racks:
for tip in rack:
yield tip
raise RuntimeError("Out of tips!")
# raise RuntimeError("Out of tips!")
def _get_next_tip(self):
"""从 current_tip 迭代器获取下一个 tip，耗尽时抛出明确错误而非 StopIteration"""
try:
return next(self.current_tip)
except StopIteration as e:
raise RuntimeError("Tip rack exhausted: no more tips available for transfer") from e
def set_tiprack(self, tip_racks: Sequence[TipRack]):
"""Set the tip racks for the liquid handler."""

62
unilabos/devices/liquid_handling/prcxi/prcxi.py
View File

@@ -928,7 +928,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
none_keys: List[str] = [],
) -> TransferLiquidReturn:
if self.step_mode:
self._unilabos_backend.create_protocol(f"step_mode_protocol_{time.time()}")
await self.create_protocol(f"step_mode_protocol_{time.time()}")
res =await super().transfer_liquid(
sources,
@@ -953,32 +953,10 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
delays=delays,
none_keys=none_keys,
)
self._unilabos_backend.run_protocol()
if self.step_mode:
await self.run_protocol()
return res
else:
return await super().transfer_liquid(
sources,
targets,
tip_racks,
use_channels=use_channels,
asp_vols=asp_vols,
dis_vols=dis_vols,
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,
)
async def custom_delay(self, seconds=0, msg=None):
return await super().custom_delay(seconds, msg)
@@ -1028,7 +1006,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
spread: Literal["wide", "tight", "custom"] = "wide",
**backend_kwargs,
):
try:
return await super().aspirate(
resources,
vols,
@@ -1040,6 +1018,20 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
spread,
**backend_kwargs,
)
except ValueError as e:
if "Resource is too small to space channels" in str(e) and spread != "custom":
return await super().aspirate(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread="custom",
**backend_kwargs,
)
raise
async def drop_tips(
self,
@@ -1063,6 +1055,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
spread: Literal["wide", "tight", "custom"] = "wide",
**backend_kwargs,
):
try:
return await super().dispense(
resources,
vols,
@@ -1074,6 +1067,21 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
spread,
**backend_kwargs,
)
except ValueError as e:
if "Resource is too small to space channels" in str(e) and spread != "custom":
# 目标资源过小无法分布多通道时，退化为 custom（所有通道对准中心）
return await super().dispense(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
"custom",
**backend_kwargs,
)
raise
async def discard_tips(
self,

153
unilabos/registry/devices/liquid_handler.yaml
View File

@@ -4134,19 +4134,8 @@ liquid_handler:
data_source: handle
data_type: resource
handler_key: sources
label: sources
label: 待移动液体
- data_key: targets
data_source: handle
data_type: resource
handler_key: targets
label: targets
- data_key: tip_racks
data_source: handle
data_type: resource
handler_key: tip_racks
label: tip_racks
output:
- data_key: sources
data_source: handle
data_type: resource
handler_key: targets
@@ -4161,9 +4150,9 @@ liquid_handler:
data_source: executor
data_type: resource
handler_key: sources_out
label: sources
- data_key: targets
data_source: handle
label: 移液后源孔
- data_key: targets.@flatten
data_source: executor
data_type: resource
handler_key: targets_out
label: 移液后目标孔
@@ -4812,13 +4801,13 @@ liquid_handler.biomek:
targets: ''
handles:
input:
- data_key: sources
- data_key: liquid
data_source: handle
data_type: resource
handler_key: sources
label: sources
output:
- data_key: targets
- data_key: liquid
data_source: handle
data_type: resource
handler_key: targets
@@ -4971,21 +4960,21 @@ liquid_handler.biomek:
volume: 0.0
handles:
input:
- data_key: sources
- data_key: liquid
data_source: handle
data_type: resource
handler_key: sources
label: sources
- data_key: targets
data_source: handle
- data_key: liquid
data_source: executor
data_type: resource
handler_key: targets
label: targets
- data_key: tip_racks
data_source: handle
- data_key: liquid
data_source: executor
data_type: resource
handler_key: tip_racks
label: tip_racks
handler_key: tip_rack
label: tip_rack
output:
- data_key: sources
data_source: handle
@@ -5166,28 +5155,30 @@ liquid_handler.biomek:
data_source: handle
data_type: resource
handler_key: sources
label: sources
io_type: target
label: 待移动液体
- data_key: targets
data_source: handle
data_type: resource
handler_key: targets
label: targets
label: 转移目标
- data_key: tip_racks
data_source: handle
data_type: resource
handler_key: tip_racks
label: tip_racks
handler_key: tip_rack
label: 枪头盒
output:
- data_key: sources
data_source: handle
- data_key: sources.@flatten
data_source: executor
data_type: resource
handler_key: sources_out
label: sources
- data_key: targets
data_source: handle
io_type: source
label: 移液后源孔
- data_key: targets.@flatten
data_source: executor
data_type: resource
handler_key: targets_out
label: targets
label: 移液后目标孔
placeholder_keys:
sources: unilabos_resources
targets: unilabos_resources
@@ -7735,31 +7726,6 @@ liquid_handler.prcxi:
title: move_to参数
type: object
type: UniLabJsonCommandAsync
auto-plr_pos_to_prcxi:
feedback: {}
goal: {}
goal_default:
resource: null
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties:
resource:
type: object
required:
- resource
type: object
result: {}
required:
- goal
title: plr_pos_to_prcxi参数
type: object
type: UniLabJsonCommand
auto-post_init:
feedback: {}
goal: {}
@@ -8655,19 +8621,7 @@ liquid_handler.prcxi:
z: 0.0
sample_id: ''
type: ''
handles:
input:
- data_key: plate
data_source: handle
data_type: resource
handler_key: plate
label: plate
output:
- data_key: plate
data_source: handle
data_type: resource
handler_key: plate
label: plate
handles: {}
placeholder_keys:
plate: unilabos_resources
to: unilabos_resources
@@ -10276,26 +10230,26 @@ liquid_handler.prcxi:
- data_key: sources
data_source: handle
data_type: resource
handler_key: sources
label: sources
handler_key: sources_identifier
label: 待移动液体
- data_key: targets
data_source: handle
data_type: resource
handler_key: targets
label: targets
handler_key: targets_identifier
label: 转移目标
- data_key: tip_racks
data_source: handle
data_type: resource
handler_key: tip_racks
label: tip_racks
handler_key: tip_rack_identifier
label: 枪头盒
output:
- data_key: sources
data_source: handle
- data_key: sources.@flatten
data_source: executor
data_type: resource
handler_key: sources_out
label: sources
- data_key: targets
data_source: handle
label: 移液后源孔
- data_key: targets.@flatten
data_source: executor
data_type: resource
handler_key: targets_out
label: 移液后目标孔
@@ -10679,12 +10633,6 @@ liquid_handler.prcxi:
type: string
deck:
type: object
deck_y:
default: 400
type: string
deck_z:
default: 300
type: string
host:
type: string
is_9320:
@@ -10695,44 +10643,17 @@ liquid_handler.prcxi:
type: string
port:
type: integer
rail_interval:
default: 0
type: string
rail_nums:
default: 4
type: string
rail_width:
default: 27.5
type: string
setup:
default: true
type: string
simulator:
default: false
type: string
start_rail:
default: 2
type: string
step_mode:
default: false
type: string
timeout:
type: number
x_increase:
default: -0.003636
type: string
x_offset:
default: -0.8
type: string
xy_coupling:
default: -0.0045
type: string
y_increase:
default: -0.003636
type: string
y_offset:
default: -37.98
type: string
required:
- deck
- host

2
unilabos/registry/registry.py
View File

@@ -92,7 +92,7 @@ class Registry:
test_resource_method_info = host_node_enhanced_info.get("action_methods", {}).get("test_resource", {})
test_resource_schema = self._generate_unilab_json_command_schema(
test_resource_method_info.get("args", []),
"auto-test_resource",
"test_resource",
test_resource_method_info.get("return_annotation"),
)
test_resource_schema["description"] = "用于测试物料、设备和样本。"

6884
unilabos/registry/resources/opentrons/lab.yaml Normal file
View File

File diff suppressed because it is too large Load Diff

3681
unilabos/resources/lab_resources.py Normal file
View File

File diff suppressed because it is too large Load Diff

1
unilabos/resources/opentrons_custom_labware_defs.json Normal file
View File

File diff suppressed because one or more lines are too long

136
unilabos/resources/resource_tracker.py
View File

@@ -38,24 +38,52 @@ class LabSample(TypedDict):
extra: Dict[str, Any]
class ResourceDictPositionSizeType(TypedDict):
depth: float
width: float
height: float
class ResourceDictPositionSize(BaseModel):
depth: float = Field(description="Depth", default=0.0) # z
width: float = Field(description="Width", default=0.0) # x
height: float = Field(description="Height", default=0.0) # y
class ResourceDictPositionScaleType(TypedDict):
x: float
y: float
z: float
class ResourceDictPositionScale(BaseModel):
x: float = Field(description="x scale", default=0.0)
y: float = Field(description="y scale", default=0.0)
z: float = Field(description="z scale", default=0.0)
class ResourceDictPositionObjectType(TypedDict):
x: float
y: float
z: float
class ResourceDictPositionObject(BaseModel):
x: float = Field(description="X coordinate", default=0.0)
y: float = Field(description="Y coordinate", default=0.0)
z: float = Field(description="Z coordinate", default=0.0)
class ResourceDictPositionType(TypedDict):
size: ResourceDictPositionSizeType
scale: ResourceDictPositionScaleType
layout: Literal["2d", "x-y", "z-y", "x-z"]
position: ResourceDictPositionObjectType
position3d: ResourceDictPositionObjectType
rotation: ResourceDictPositionObjectType
cross_section_type: Literal["rectangle", "circle", "rounded_rectangle"]
class ResourceDictPosition(BaseModel):
size: ResourceDictPositionSize = Field(description="Resource size", default_factory=ResourceDictPositionSize)
scale: ResourceDictPositionScale = Field(description="Resource scale", default_factory=ResourceDictPositionScale)
@@ -74,6 +102,24 @@ class ResourceDictPosition(BaseModel):
)
class ResourceDictType(TypedDict):
id: str
uuid: str
name: str
description: str
resource_schema: Dict[str, Any]
model: Dict[str, Any]
icon: str
parent_uuid: Optional[str]
parent: Optional["ResourceDictType"]
type: Union[Literal["device"], str]
klass: str
pose: ResourceDictPositionType
config: Dict[str, Any]
data: Dict[str, Any]
extra: Dict[str, Any]
# 统一的资源字典模型，parent 自动序列化为 parent_uuid，children 不序列化
class ResourceDict(BaseModel):
id: str = Field(description="Resource ID")
@@ -468,10 +514,17 @@ class ResourceTreeSet(object):
trees.append(tree_instance)
return cls(trees)
def to_plr_resources(self, skip_devices=True) -> List["PLRResource"]:
def to_plr_resources(
self, skip_devices: bool = True, requested_uuids: Optional[List[str]] = None
) -> List["PLRResource"]:
"""
将 ResourceTreeSet 转换为 PLR 资源列表
Args:
skip_devices: 是否跳过 device 类型节点
requested_uuids: 若指定，则按此 UUID 顺序返回对应资源（用于批量查询时一一对应），
否则返回各树的根节点列表
Returns:
List[PLRResource]: PLR 资源实例列表
"""
@@ -526,6 +579,71 @@ class ResourceTreeSet(object):
d["model"] = res.config.get("model", None)
return d
# deserialize 会单独处理的元数据 key，不传给构造函数
_META_KEYS = {"type", "parent_name", "location", "children", "rotation", "barcode"}
# deserialize 自定义逻辑使用的 key（如 TipSpot 用 prototype_tip 构建 make_tip），需保留
_DESERIALIZE_PRESERVED_KEYS = {"prototype_tip"}
def remove_incompatible_params(plr_d: dict) -> None:
"""递归移除 PLR 类不接受的参数，避免 deserialize 报错。
- 移除构造函数不接受的参数（如 compute_height_from_volume、ordering、category）
- 对 TubeRack：将 ordering 转为 ordered_items
- 保留 deserialize 自定义逻辑需要的 key（如 prototype_tip）
"""
if "type" in plr_d:
sub_cls = find_subclass(plr_d["type"], PLRResource)
if sub_cls is not None:
spec = inspect.signature(sub_cls)
valid_params = set(spec.parameters.keys())
# TubeRack 特殊处理：先转换 ordering，再参与后续过滤
if "ordering" not in valid_params and "ordering" in plr_d:
ordering = plr_d.pop("ordering", None)
if sub_cls.__name__ == "TubeRack":
plr_d["ordered_items"] = (
_ordering_to_ordered_items(plr_d, ordering)
if ordering
else {}
)
# 移除构造函数不接受的参数（保留 META 和 deserialize 自定义逻辑需要的 key）
for key in list(plr_d.keys()):
if (
key not in _META_KEYS
and key not in _DESERIALIZE_PRESERVED_KEYS
and key not in valid_params
):
plr_d.pop(key, None)
for child in plr_d.get("children", []):
remove_incompatible_params(child)
def _ordering_to_ordered_items(plr_d: dict, ordering: dict) -> dict:
"""将 ordering 转为 ordered_items，从 children 构建 Tube 对象"""
from pylabrobot.resources import Tube, Coordinate
from pylabrobot.serializer import deserialize as plr_deserialize
children = plr_d.get("children", [])
ordered_items = {}
for idx, (ident, child_name) in enumerate(ordering.items()):
child_data = children[idx] if idx < len(children) else None
if child_data is None:
continue
loc_data = child_data.get("location")
loc = (
plr_deserialize(loc_data)
if loc_data
else Coordinate(0, 0, 0)
)
tube = Tube(
name=child_data.get("name", child_name or ident),
size_x=child_data.get("size_x", 10),
size_y=child_data.get("size_y", 10),
size_z=child_data.get("size_z", 50),
max_volume=child_data.get("max_volume", 1000),
)
tube.location = loc
ordered_items[ident] = tube
plr_d["children"] = [] # 已并入 ordered_items，避免重复反序列化
return ordered_items
plr_resources = []
tracker = DeviceNodeResourceTracker()
@@ -545,9 +663,7 @@ class ResourceTreeSet(object):
raise ValueError(
f"无法找到类型 {plr_dict['type']} 对应的 PLR 资源类。原始信息：{tree.root_node.res_content}"
)
spec = inspect.signature(sub_cls)
if "category" not in spec.parameters:
plr_dict.pop("category", None)
remove_incompatible_params(plr_dict)
plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True)
from pylabrobot.resources import Coordinate
from pylabrobot.serializer import deserialize
@@ -567,6 +683,18 @@ class ResourceTreeSet(object):
logger.error(f"堆栈: {traceback.format_exc()}")
raise
if requested_uuids:
# 按请求的 UUID 顺序返回对应资源（从整棵树中按 uuid 提取）
result = []
for uid in requested_uuids:
if uid in tracker.uuid_to_resources:
result.append(tracker.uuid_to_resources[uid])
else:
raise ValueError(
f"请求的 UUID {uid} 在资源树中未找到。"
f"可用 UUID 数量: {len(tracker.uuid_to_resources)}"
)
return result
return plr_resources
@classmethod

8
unilabos/ros/nodes/base_device_node.py
View File

@@ -460,7 +460,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
}
res.response = json.dumps(final_response)
# 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"):
if hasattr(self.driver_instance, "create_resource") and self.node_name != "host_node":
create_resource_func = getattr(self.driver_instance, "create_resource")
try:
ret = create_resource_func(
@@ -1389,9 +1389,13 @@ class BaseROS2DeviceNode(Node, Generic[T]):
if uuid_indices:
uuids = [item[1] for item in uuid_indices]
resource_tree = await self.get_resource(uuids)
plr_resources = resource_tree.to_plr_resources()
plr_resources = resource_tree.to_plr_resources(requested_uuids=uuids)
for i, (idx, _, resource_data) in enumerate(uuid_indices):
try:
plr_resource = plr_resources[i]
except Exception as e:
self.lab_logger().error(f"资源查询结果: 共 {len(queried_resources)} 个资源，但查询结果只有 {len(plr_resources)} 个资源，索引为 {i} 的资源不存在")
raise e
if "sample_id" in resource_data:
plr_resource.unilabos_extra[EXTRA_SAMPLE_UUID] = resource_data["sample_id"]
queried_resources[idx] = plr_resource

5
unilabos/ros/nodes/presets/host_node.py
View File

@@ -35,7 +35,7 @@ from unilabos.resources.resource_tracker import (
ResourceTreeInstance,
RETURN_UNILABOS_SAMPLES,
JSON_UNILABOS_PARAM,
PARAM_SAMPLE_UUIDS,
PARAM_SAMPLE_UUIDS, SampleUUIDsType, LabSample,
)
from unilabos.ros.initialize_device import initialize_device_from_dict
from unilabos.ros.msgs.message_converter import (
@@ -65,6 +65,7 @@ class DeviceActionStatus:
class TestResourceReturn(TypedDict):
resources: List[List[ResourceDict]]
devices: List[Dict[str, Any]]
unilabos_samples: List[LabSample]
class TestLatencyReturn(TypedDict):
@@ -1582,6 +1583,7 @@ class HostNode(BaseROS2DeviceNode):
def test_resource(
self,
sample_uuids: SampleUUIDsType,
resource: ResourceSlot = None,
resources: List[ResourceSlot] = None,
device: DeviceSlot = None,
@@ -1596,6 +1598,7 @@ class HostNode(BaseROS2DeviceNode):
return {
"resources": ResourceTreeSet.from_plr_resources([resource, *resources], known_newly_created=True).dump(),
"devices": [device, *devices],
"unilabos_samples": [LabSample(sample_uuid=sample_uuid, oss_path="", extra={"material_uuid": content} if isinstance(content, str) else content.serialize()) for sample_uuid, content in sample_uuids.items()]
}
def handle_pong_response(self, pong_data: dict):

47
unilabos/test/experiments/prcxi_9320_slim.json
View File

@@ -21,12 +21,12 @@
},
"host": "10.20.30.184",
"port": 9999,
"debug": true,
"setup": true,
"debug": false,
"setup": false,
"is_9320": true,
"timeout": 10,
"matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb",
"simulator": true,
"simulator": false,
"channel_num": 2
},
"data": {
@@ -789,6 +789,47 @@
]
},
"data": {}
},
{
"id": "trash",
"name": "trash",
"children": [],
"parent": "T16",
"type": "trash",
"class": "",
"position": {
"x": 0,
"y": 0,
"z": 0
},
"config": {
"type": "PRCXI9300Trash",
"size_x": 127.5,
"size_y": 86,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "trash",
"model": null,
"barcode": null,
"max_volume": "Infinity",
"material_z_thickness": 0,
"compute_volume_from_height": null,
"compute_height_from_volume": null
},
"data": {
"liquids": [],
"pending_liquids": [],
"liquid_history": [],
"Material": {
"uuid": "730067cf07ae43849ddf4034299030e9"
}
}
}
],
"edges": []

54
unilabos/workflow/common.py
View File

@@ -119,11 +119,14 @@ DEVICE_NAME_DEFAULT = "PRCXI" # transfer_liquid, set_liquid_from_plate 等动
# 节点类型
NODE_TYPE_DEFAULT = "ILab" # 所有节点的默认类型
CLASS_NAMES_MAPPING = {
"plate": "PRCXI_BioER_96_wellplate",
"tip_rack": "PRCXI_300ul_Tips",
}
# create_resource 节点默认参数
CREATE_RESOURCE_DEFAULTS = {
"device_id": "/PRCXI",
"parent_template": "/PRCXI/PRCXI_Deck/T{slot}", # {slot} 会被替换为实际的 slot 值
"class_name": "PRCXI_BioER_96_wellplate",
}
# 默认液体体积 (uL)
@@ -367,11 +370,10 @@ def build_protocol_graph(
"""统一的协议图构建函数，根据设备类型自动选择构建逻辑
Args:
labware_info: reagent 信息字典，格式为 {name: {slot, well}, ...}，用于 set_liquid 和 well 查找
labware_info: labware 信息字典，格式为 {name: {slot, well, labware, ...}, ...}
protocol_steps: 协议步骤列表
workstation_name: 工作站名称
action_resource_mapping: action 到 resource_name 的映射字典，可选
labware_defs: labware 定义列表，格式为 [{"name": "...", "slot": "1", "type": "lab_xxx"}, ...]
"""
G = WorkflowGraph()
resource_last_writer = {} # reagent_name -> "node_id:port"
@@ -379,7 +381,19 @@ def build_protocol_graph(
protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
# ==================== 第一步：按 slot 创建 create_resource 节点 ====================
# ==================== 第一步：按 slot 去重创建 create_resource 节点 ====================
# 收集所有唯一的 slot
slots_info = {} # slot -> {labware, res_id}
for labware_id, item in labware_info.items():
slot = str(item.get("slot", ""))
if slot and slot not in slots_info:
res_id = f"plate_slot_{slot}"
slots_info[slot] = {
"labware": item.get("labware", ""),
"res_id": res_id,
"labware_id": labware_id,
}
# 创建 Group 节点，包含所有 create_resource 节点
group_node_id = str(uuid.uuid4())
G.add_node(
@@ -395,41 +409,38 @@ def build_protocol_graph(
param=None,
)
# 直接使用 JSON 中的 labware 定义，每个 slot 一条记录，type 即 class_name
res_index = 0
for lw in (labware_defs or []):
slot = str(lw.get("slot", ""))
if not slot or slot in slot_to_create_resource:
continue # 跳过空 slot 或已处理的 slot
lw_name = lw.get("name", f"slot {slot}")
lw_type = lw.get("type", CREATE_RESOURCE_DEFAULTS["class_name"])
res_id = f"plate_slot_{slot}"
res_index += 1
# 为每个唯一的 slot 创建 create_resource 节点
for slot, info in slots_info.items():
node_id = str(uuid.uuid4())
res_id = info["res_id"]
res_type_name = info["labware"].lower().replace(".", "point")
res_type_name = f"lab_{res_type_name}"
G.add_node(
node_id,
template_name="create_resource",
resource_name="host_node",
name=lw_name,
description=f"Create {lw_name}",
name=f"{res_type_name}_slot{slot}",
description=f"Create plate on slot {slot}",
lab_node_type="Labware",
footer="create_resource-host_node",
device_name=DEVICE_NAME_HOST,
type=NODE_TYPE_DEFAULT,
parent_uuid=group_node_id,
minimized=True,
parent_uuid=group_node_id, # 指向 Group 节点
minimized=True, # 折叠显示
param={
"res_id": res_id,
"device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
"class_name": lw_type,
"class_name": res_type_name,
"parent": CREATE_RESOURCE_DEFAULTS["parent_template"].format(slot=slot),
"bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
"slot_on_deck": slot,
},
)
slot_to_create_resource[slot] = node_id
if "tip" in res_type_name and "rack" in res_type_name:
resource_last_writer[info["labware_id"]] = f"{node_id}:labware"
# create_resource 之间不需要 ready 连接
# ==================== 第二步：为每个 reagent 创建 set_liquid_from_plate 节点 ====================
# 创建 Group 节点，包含所有 set_liquid_from_plate 节点
@@ -511,6 +522,7 @@ def build_protocol_graph(
"reagent": "reagent",
"solvent": "solvent",
"compound": "compound",
"tip_racks": "tip_rack_identifier",
}
OUTPUT_PORT_MAPPING = {