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https://github.com/deepmodeling/Uni-Lab-OS
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6 Commits
e1074f06d2
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dependabot
| Author | SHA1 | Date | |
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fcea02585a | ||
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07cf690897 | ||
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cfea27460a | ||
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b7d3e980a9 |
@@ -3,7 +3,7 @@
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package:
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name: unilabos
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version: 0.10.17
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version: 0.10.18
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source:
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path: ../../unilabos
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@@ -46,13 +46,15 @@ requirements:
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- jinja2
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- requests
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- uvicorn
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- opcua # [not osx]
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- if: not osx
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then:
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- opcua
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- pyserial
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- pandas
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- pymodbus
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- matplotlib
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- pylibftdi
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- uni-lab::unilabos-env ==0.10.17
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- uni-lab::unilabos-env ==0.10.18
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about:
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repository: https://github.com/deepmodeling/Uni-Lab-OS
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@@ -2,7 +2,7 @@
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package:
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name: unilabos-env
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version: 0.10.17
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version: 0.10.18
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build:
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noarch: generic
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@@ -3,7 +3,7 @@
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package:
|
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name: unilabos-full
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version: 0.10.17
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version: 0.10.18
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build:
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noarch: generic
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@@ -11,7 +11,7 @@ build:
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requirements:
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run:
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# Base unilabos package (includes unilabos-env)
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- uni-lab::unilabos ==0.10.17
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- uni-lab::unilabos ==0.10.18
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# Documentation tools
|
||||
- sphinx
|
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- sphinx_rtd_theme
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||||
|
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2
.github/workflows/conda-pack-build.yml
vendored
2
.github/workflows/conda-pack-build.yml
vendored
@@ -312,7 +312,7 @@ jobs:
|
||||
|
||||
- name: Upload distribution package
|
||||
if: steps.should_build.outputs.should_build == 'true'
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uses: actions/upload-artifact@v6
|
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uses: actions/upload-artifact@v7
|
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with:
|
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name: unilab-pack-${{ matrix.platform }}-${{ github.event.inputs.branch }}
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path: dist-package/
|
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|
||||
2
.github/workflows/multi-platform-build.yml
vendored
2
.github/workflows/multi-platform-build.yml
vendored
@@ -149,7 +149,7 @@ jobs:
|
||||
|
||||
- name: Upload conda package artifacts
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
uses: actions/upload-artifact@v6
|
||||
uses: actions/upload-artifact@v7
|
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with:
|
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name: conda-package-${{ matrix.platform }}
|
||||
path: conda-packages-temp
|
||||
|
||||
2
.github/workflows/unilabos-conda-build.yml
vendored
2
.github/workflows/unilabos-conda-build.yml
vendored
@@ -195,7 +195,7 @@ jobs:
|
||||
|
||||
- name: Upload conda package artifacts
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
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uses: actions/upload-artifact@v6
|
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uses: actions/upload-artifact@v7
|
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with:
|
||||
name: conda-package-unilabos-${{ matrix.platform }}
|
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path: conda-packages-temp
|
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|
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@@ -1,6 +1,6 @@
|
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package:
|
||||
name: ros-humble-unilabos-msgs
|
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version: 0.10.17
|
||||
version: 0.10.18
|
||||
source:
|
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path: ../../unilabos_msgs
|
||||
target_directory: src
|
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|
||||
@@ -1,6 +1,6 @@
|
||||
package:
|
||||
name: unilabos
|
||||
version: "0.10.17"
|
||||
version: "0.10.18"
|
||||
|
||||
source:
|
||||
path: ../..
|
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|
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2
setup.py
2
setup.py
@@ -4,7 +4,7 @@ package_name = 'unilabos'
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|
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setup(
|
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name=package_name,
|
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version='0.10.17',
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version='0.10.18',
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packages=find_packages(),
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include_package_data=True,
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install_requires=['setuptools'],
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|
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@@ -1 +1 @@
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__version__ = "0.10.17"
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__version__ = "0.10.18"
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|
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@@ -1159,19 +1159,11 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
|
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Number of mix cycles. If *None* (default) no mixing occurs regardless of
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||||
mix_stage.
|
||||
"""
|
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num_sources = len(sources)
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num_targets = len(targets)
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len_asp_vols = len(asp_vols)
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len_dis_vols = len(dis_vols)
|
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|
||||
# 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 == 8 else [0]
|
||||
elif len(use_channels) == 8:
|
||||
if self.channel_num != 8:
|
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raise ValueError(f"if channel_num is 8, use_channels length must be 8, but got {len(use_channels)}")
|
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if num_sources%8 != 0 or num_targets%8 != 0 or len_asp_vols%8 != 0 or len_dis_vols%8 != 0:
|
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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}")
|
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use_channels = list(range(self.channel_num)) if self.channel_num > 0 else [0]
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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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@@ -1199,234 +1191,90 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
|
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if mix_times is not None:
|
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mix_times = int(mix_times)
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|
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# 设置tip racks
|
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self.set_tiprack(tip_racks)
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|
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# 识别传输模式(mix_times 为 None 也应该能正常移液,只是不做 mix)
|
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num_sources = len(sources)
|
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num_targets = len(targets)
|
||||
len_asp_vols = len(asp_vols)
|
||||
len_dis_vols = len(dis_vols)
|
||||
|
||||
# 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."
|
||||
# )
|
||||
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."
|
||||
)
|
||||
|
||||
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],
|
||||
|
||||
@@ -721,9 +721,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
|
||||
delays: Optional[List[int]] = None,
|
||||
none_keys: List[str] = [],
|
||||
) -> TransferLiquidReturn:
|
||||
if self.step_mode:
|
||||
await self.create_protocol(f"transfer_liquid{time.time()}")
|
||||
res = await super().transfer_liquid(
|
||||
return await super().transfer_liquid(
|
||||
sources,
|
||||
targets,
|
||||
tip_racks,
|
||||
@@ -746,9 +744,6 @@ 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)
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because one or more lines are too long
@@ -572,71 +572,6 @@ 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()
|
||||
|
||||
@@ -656,7 +591,9 @@ 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}"
|
||||
)
|
||||
remove_incompatible_params(plr_dict)
|
||||
spec = inspect.signature(sub_cls)
|
||||
if "category" not in spec.parameters:
|
||||
plr_dict.pop("category", None)
|
||||
plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True)
|
||||
from pylabrobot.resources import Coordinate
|
||||
from pylabrobot.serializer import deserialize
|
||||
|
||||
@@ -119,14 +119,11 @@ 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)
|
||||
@@ -370,10 +367,11 @@ 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: labware 信息字典,格式为 {name: {slot, well, labware, ...}, ...}
|
||||
labware_info: reagent 信息字典,格式为 {name: {slot, well}, ...},用于 set_liquid 和 well 查找
|
||||
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"
|
||||
@@ -381,19 +379,7 @@ def build_protocol_graph(
|
||||
|
||||
protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
|
||||
|
||||
# ==================== 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,
|
||||
}
|
||||
|
||||
# ==================== 第一步:按 slot 创建 create_resource 节点 ====================
|
||||
# 创建 Group 节点,包含所有 create_resource 节点
|
||||
group_node_id = str(uuid.uuid4())
|
||||
G.add_node(
|
||||
@@ -409,38 +395,41 @@ def build_protocol_graph(
|
||||
param=None,
|
||||
)
|
||||
|
||||
# 为每个唯一的 slot 创建 create_resource 节点
|
||||
for slot, info in slots_info.items():
|
||||
# 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
|
||||
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=f"{res_type_name}_slot{slot}",
|
||||
description=f"Create plate on slot {slot}",
|
||||
name=lw_name,
|
||||
description=f"Create {lw_name}",
|
||||
lab_node_type="Labware",
|
||||
footer="create_resource-host_node",
|
||||
device_name=DEVICE_NAME_HOST,
|
||||
type=NODE_TYPE_DEFAULT,
|
||||
parent_uuid=group_node_id, # 指向 Group 节点
|
||||
minimized=True, # 折叠显示
|
||||
parent_uuid=group_node_id,
|
||||
minimized=True,
|
||||
param={
|
||||
"res_id": res_id,
|
||||
"device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
|
||||
"class_name": res_type_name,
|
||||
"class_name": lw_type,
|
||||
"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
|
||||
@@ -522,7 +511,6 @@ def build_protocol_graph(
|
||||
"reagent": "reagent",
|
||||
"solvent": "solvent",
|
||||
"compound": "compound",
|
||||
"tip_racks": "tip_rack_identifier",
|
||||
}
|
||||
|
||||
OUTPUT_PORT_MAPPING = {
|
||||
|
||||
@@ -2,7 +2,7 @@
|
||||
<?xml-model href="http://download.ros.org/schema/package_format3.xsd" schematypens="http://www.w3.org/2001/XMLSchema"?>
|
||||
<package format="3">
|
||||
<name>unilabos_msgs</name>
|
||||
<version>0.10.17</version>
|
||||
<version>0.10.18</version>
|
||||
<description>ROS2 Messages package for unilabos devices</description>
|
||||
<maintainer email="changjh@pku.edu.cn">Junhan Chang</maintainer>
|
||||
<maintainer email="18435084+Xuwznln@users.noreply.github.com">Xuwznln</maintainer>
|
||||
|
||||
Reference in New Issue
Block a user