mirror of
https://github.com/deepmodeling/Uni-Lab-OS
synced 2026-03-24 19:49:19 +00:00
Compare commits
9 Commits
dependabot
...
e1074f06d2
| Author | SHA1 | Date | |
|---|---|---|---|
|
|
e1074f06d2 | ||
|
|
0dc273f366 | ||
|
|
2e5fac26b3 | ||
|
|
5c2da9b793 | ||
|
|
45efbfcd12 | ||
|
|
8da6fdfd0b | ||
|
|
29ea9909a5 | ||
|
|
ee6307a568 | ||
|
|
8a0116c852 |
@@ -1184,6 +1184,11 @@ 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": {
|
||||
|
||||
@@ -21,7 +21,7 @@ from pylabrobot.resources import (
|
||||
ResourceHolder,
|
||||
Lid,
|
||||
Trash,
|
||||
Tip,
|
||||
Tip, TubeRack,
|
||||
)
|
||||
from typing_extensions import TypedDict
|
||||
|
||||
@@ -696,10 +696,13 @@ 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
|
||||
wells = [plate.get_well(name) for name in well_names]
|
||||
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
|
||||
@@ -1156,11 +1159,19 @@ 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.
|
||||
@@ -1188,90 +1199,234 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
|
||||
if mix_times is not None:
|
||||
mix_times = int(mix_times)
|
||||
|
||||
# 设置tip racks
|
||||
self.set_tiprack(tip_racks)
|
||||
|
||||
# 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) == 1:
|
||||
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(next(self.current_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,
|
||||
sources: Sequence[Container],
|
||||
|
||||
@@ -91,7 +91,7 @@ class PRCXI9300Deck(Deck):
|
||||
"""
|
||||
|
||||
def __init__(self, name: str, size_x: float, size_y: float, size_z: float, **kwargs):
|
||||
super().__init__(name, size_x, size_y, size_z)
|
||||
super().__init__(size_x, size_y, size_z, name)
|
||||
self.slots = [None] * 16 # PRCXI 9300/9320 最大有 16 个槽位
|
||||
self.slot_locations = [Coordinate(0, 0, 0)] * 16
|
||||
|
||||
@@ -248,14 +248,15 @@ class PRCXI9300TipRack(TipRack):
|
||||
if ordered_items is not None:
|
||||
items = ordered_items
|
||||
elif ordering is not None:
|
||||
# 检查 ordering 中的值是否是字符串(从 JSON 反序列化时的情况)
|
||||
# 如果是字符串,说明这是位置名称,需要让 TipRack 自己创建 Tip 对象
|
||||
# 我们只传递位置信息(键),不传递值,使用 ordering 参数
|
||||
if ordering and isinstance(next(iter(ordering.values()), None), str):
|
||||
# ordering 的值是字符串,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 检查 ordering 中的值类型来决定如何处理:
|
||||
# - 字符串值(从 JSON 反序列化): 只用键创建 ordering_param
|
||||
# - None 值(从第二次往返序列化): 同样只用键创建 ordering_param
|
||||
# - 对象值(已经是实际的 Resource 对象): 直接作为 ordered_items 使用
|
||||
first_val = next(iter(ordering.values()), None) if ordering else None
|
||||
if not ordering or first_val is None or isinstance(first_val, str):
|
||||
# ordering 的值是字符串或 None,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 传递 ordering 参数而不是 ordered_items,让 TipRack 自己创建 Tip 对象
|
||||
items = None
|
||||
# 使用 ordering 参数,只包含位置信息(键)
|
||||
ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
|
||||
else:
|
||||
# ordering 的值已经是对象,可以直接使用
|
||||
@@ -397,14 +398,15 @@ class PRCXI9300TubeRack(TubeRack):
|
||||
items_to_pass = ordered_items
|
||||
ordering_param = None
|
||||
elif ordering is not None:
|
||||
# 检查 ordering 中的值是否是字符串(从 JSON 反序列化时的情况)
|
||||
# 如果是字符串,说明这是位置名称,需要让 TubeRack 自己创建 Tube 对象
|
||||
# 我们只传递位置信息(键),不传递值,使用 ordering 参数
|
||||
if ordering and isinstance(next(iter(ordering.values()), None), str):
|
||||
# ordering 的值是字符串,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 检查 ordering 中的值类型来决定如何处理:
|
||||
# - 字符串值(从 JSON 反序列化): 只用键创建 ordering_param
|
||||
# - None 值(从第二次往返序列化): 同样只用键创建 ordering_param
|
||||
# - 对象值(已经是实际的 Resource 对象): 直接作为 ordered_items 使用
|
||||
first_val = next(iter(ordering.values()), None) if ordering else None
|
||||
if not ordering or first_val is None or isinstance(first_val, str):
|
||||
# ordering 的值是字符串或 None,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 传递 ordering 参数而不是 ordered_items,让 TubeRack 自己创建 Tube 对象
|
||||
items_to_pass = None
|
||||
# 使用 ordering 参数,只包含位置信息(键)
|
||||
ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
|
||||
else:
|
||||
# ordering 的值已经是对象,可以直接使用
|
||||
@@ -719,7 +721,9 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
|
||||
delays: Optional[List[int]] = None,
|
||||
none_keys: List[str] = [],
|
||||
) -> TransferLiquidReturn:
|
||||
return await super().transfer_liquid(
|
||||
if self.step_mode:
|
||||
await self.create_protocol(f"transfer_liquid{time.time()}")
|
||||
res = await super().transfer_liquid(
|
||||
sources,
|
||||
targets,
|
||||
tip_racks,
|
||||
@@ -742,6 +746,9 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
|
||||
delays=delays,
|
||||
none_keys=none_keys,
|
||||
)
|
||||
if self.step_mode:
|
||||
await self.run_protocol()
|
||||
return res
|
||||
|
||||
async def custom_delay(self, seconds=0, msg=None):
|
||||
return await super().custom_delay(seconds, msg)
|
||||
|
||||
6884
unilabos/registry/resources/opentrons/lab.yaml
Normal file
6884
unilabos/registry/resources/opentrons/lab.yaml
Normal file
File diff suppressed because it is too large
Load Diff
3681
unilabos/resources/lab_resources.py
Normal file
3681
unilabos/resources/lab_resources.py
Normal file
File diff suppressed because it is too large
Load Diff
1
unilabos/resources/opentrons_custom_labware_defs.json
Normal file
1
unilabos/resources/opentrons_custom_labware_defs.json
Normal file
File diff suppressed because one or more lines are too long
@@ -572,6 +572,71 @@ 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()
|
||||
|
||||
@@ -591,9 +656,7 @@ 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
|
||||
|
||||
@@ -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(
|
||||
|
||||
@@ -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 = {
|
||||
|
||||
Reference in New Issue
Block a user