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Author SHA1 Message Date
Xuwznln
957fb41a6f Feat/samples (#229)
* add sample_material

* adapt to new samples sys
2026-02-05 00:42:12 +08:00
Xuwznln
26271bcab8 adapt to new samples sys 2026-02-04 18:49:08 +08:00
Xuwznln
84a8223173 adapt to new edge format 2026-02-03 23:22:38 +08:00
Xuwznln
e8d1263488 workflow upload & prcxi transfer liquid 2026-02-03 18:10:32 +08:00
Xuwznln
380b39100d lh liquid 2026-02-03 15:15:57 +08:00
14 changed files with 1342 additions and 272 deletions

View File

@@ -46,7 +46,7 @@ requirements:
- jinja2 - jinja2
- requests - requests
- uvicorn - uvicorn
- opcua - opcua # [not osx]
- pyserial - pyserial
- pandas - pandas
- pymodbus - pymodbus

View File

@@ -54,6 +54,7 @@ class JobAddReq(BaseModel):
action_type: str = Field( action_type: str = Field(
examples=["unilabos_msgs.action._str_single_input.StrSingleInput"], description="action type", default="" examples=["unilabos_msgs.action._str_single_input.StrSingleInput"], description="action type", default=""
) )
sample_material: dict = Field(examples=[{"string": "string"}], description="sample uuid to material uuid", default_factory=dict)
action_args: dict = Field(examples=[{"string": "string"}], description="action arguments", default_factory=dict) action_args: dict = Field(examples=[{"string": "string"}], description="action arguments", default_factory=dict)
task_id: str = Field(examples=["task_id"], description="task uuid (auto-generated if empty)", default="") task_id: str = Field(examples=["task_id"], description="task uuid (auto-generated if empty)", default="")
job_id: str = Field(examples=["job_id"], description="goal uuid (auto-generated if empty)", default="") job_id: str = Field(examples=["job_id"], description="goal uuid (auto-generated if empty)", default="")

View File

@@ -327,6 +327,7 @@ def job_add(req: JobAddReq) -> JobData:
queue_item, queue_item,
action_type=action_type, action_type=action_type,
action_kwargs=action_args, action_kwargs=action_args,
sample_material=req.sample_material,
server_info=server_info, server_info=server_info,
) )

View File

@@ -545,7 +545,7 @@ class MessageProcessor:
try: try:
message_str = json.dumps(msg, ensure_ascii=False) message_str = json.dumps(msg, ensure_ascii=False)
await self.websocket.send(message_str) await self.websocket.send(message_str)
logger.trace(f"[MessageProcessor] Message sent: {msg.get('action', 'unknown')}") # type: ignore # noqa: E501 # logger.trace(f"[MessageProcessor] Message sent: {msg.get('action', 'unknown')}") # type: ignore # noqa: E501
except Exception as e: except Exception as e:
logger.error(f"[MessageProcessor] Failed to send message: {str(e)}") logger.error(f"[MessageProcessor] Failed to send message: {str(e)}")
logger.error(traceback.format_exc()) logger.error(traceback.format_exc())
@@ -688,6 +688,7 @@ class MessageProcessor:
queue_item, queue_item,
action_type=req.action_type, action_type=req.action_type,
action_kwargs=req.action_args, action_kwargs=req.action_args,
sample_material=req.sample_material,
server_info=req.server_info, server_info=req.server_info,
) )
@@ -1301,7 +1302,7 @@ class WebSocketClient(BaseCommunicationClient):
}, },
} }
self.message_processor.send_message(message) self.message_processor.send_message(message)
logger.trace(f"[WebSocketClient] Device status published: {device_id}.{property_name}") # logger.trace(f"[WebSocketClient] Device status published: {device_id}.{property_name}")
def publish_job_status( def publish_job_status(
self, feedback_data: dict, item: QueueItem, status: str, return_info: Optional[dict] = None self, feedback_data: dict, item: QueueItem, status: str, return_info: Optional[dict] = None

View File

@@ -1,15 +1,11 @@
from __future__ import annotations from __future__ import annotations
import asyncio
import time import time
import traceback import traceback
from collections import Counter from collections import Counter
from typing import List, Sequence, Optional, Literal, Union, Iterator, Dict, Any, Callable, Set, cast from typing import List, Sequence, Optional, Literal, Union, Iterator, Dict, Any, Callable, Set, cast
from typing_extensions import TypedDict
from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, LiquidHandlerChatterboxBackend, Strictness from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, LiquidHandlerChatterboxBackend, Strictness
from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
from unilabos.devices.liquid_handling.laiyu.backend.laiyu_v_backend import UniLiquidHandlerLaiyuBackend
from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod
from pylabrobot.liquid_handling.standard import GripDirection from pylabrobot.liquid_handling.standard import GripDirection
from pylabrobot.resources import ( from pylabrobot.resources import (
@@ -27,26 +23,38 @@ from pylabrobot.resources import (
Trash, Trash,
Tip, Tip,
) )
from typing_extensions import TypedDict
from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
from unilabos.registry.placeholder_type import ResourceSlot from unilabos.registry.placeholder_type import ResourceSlot
from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode from unilabos.resources.resource_tracker import (
from unilabos.resources.resource_tracker import ResourceTreeSet ResourceTreeSet,
ResourceDict,
EXTRA_SAMPLE_UUID,
EXTRA_UNILABOS_SAMPLE_UUID,
)
from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, ROS2DeviceNode
class SimpleReturn(TypedDict): class SimpleReturn(TypedDict):
samples: list samples: List[List[ResourceDict]]
volumes: list volumes: List[float]
class SetLiquidReturn(TypedDict): class SetLiquidReturn(TypedDict):
wells: list wells: List[List[ResourceDict]]
volumes: list volumes: List[float]
class SetLiquidFromPlateReturn(TypedDict): class SetLiquidFromPlateReturn(TypedDict):
plate: list plate: List[List[ResourceDict]]
wells: list wells: List[List[ResourceDict]]
volumes: list volumes: List[float]
class TransferLiquidReturn(TypedDict):
sources: List[List[ResourceDict]]
targets: List[List[ResourceDict]]
class LiquidHandlerMiddleware(LiquidHandler): class LiquidHandlerMiddleware(LiquidHandler):
@@ -228,12 +236,11 @@ class LiquidHandlerMiddleware(LiquidHandler):
res_samples = [] res_samples = []
res_volumes = [] res_volumes = []
for resource, volume, channel in zip(resources, vols, use_channels): for resource, volume, channel in zip(resources, vols, use_channels):
res_samples.append( sample_uuid_value = resource.unilabos_extra.get(EXTRA_SAMPLE_UUID, None)
{"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)} res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: sample_uuid_value})
)
res_volumes.append(volume) res_volumes.append(volume)
self.pending_liquids_dict[channel] = { self.pending_liquids_dict[channel] = {
"sample_uuid": resource.unilabos_extra.get("sample_uuid", None), EXTRA_SAMPLE_UUID: sample_uuid_value,
"volume": volume, "volume": volume,
} }
return SimpleReturn(samples=res_samples, volumes=res_volumes) return SimpleReturn(samples=res_samples, volumes=res_volumes)
@@ -275,10 +282,10 @@ class LiquidHandlerMiddleware(LiquidHandler):
res_samples = [] res_samples = []
res_volumes = [] res_volumes = []
for resource, volume, channel in zip(resources, vols, use_channels): for resource, volume, channel in zip(resources, vols, use_channels):
res_uuid = self.pending_liquids_dict[channel]["sample_uuid"] res_uuid = self.pending_liquids_dict[channel][EXTRA_SAMPLE_UUID]
self.pending_liquids_dict[channel]["volume"] -= volume self.pending_liquids_dict[channel]["volume"] -= volume
resource.unilabos_extra["sample_uuid"] = res_uuid resource.unilabos_extra[EXTRA_SAMPLE_UUID] = res_uuid
res_samples.append({"name": resource.name, "sample_uuid": res_uuid}) res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: res_uuid})
res_volumes.append(volume) res_volumes.append(volume)
return SimpleReturn(samples=res_samples, volumes=res_volumes) return SimpleReturn(samples=res_samples, volumes=res_volumes)
@@ -682,14 +689,17 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), volumes=res_volumes # type: ignore wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), volumes=res_volumes # type: ignore
) )
@classmethod
def set_liquid_from_plate( def set_liquid_from_plate(
cls, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float] self, plate: List[ResourceSlot], well_names: list[str], liquid_names: list[str], volumes: list[float]
) -> SetLiquidFromPlateReturn: ) -> SetLiquidFromPlateReturn:
"""Set the liquid in wells of a plate by well names (e.g., A1, A2, B3). """Set the liquid in wells of a plate by well names (e.g., A1, A2, B3).
如果 liquid_names 和 volumes 为空,但 plate 和 well_names 不为空,直接返回 plate 和 wells。 如果 liquid_names 和 volumes 为空,但 plate 和 well_names 不为空,直接返回 plate 和 wells。
""" """
if isinstance(plate, list): # 未来移除
plate = plate[0]
assert issubclass(plate.__class__, Plate), "plate must be a Plate"
plate: Plate = cast(Plate, plate)
# 根据 well_names 获取对应的 Well 对象 # 根据 well_names 获取对应的 Well 对象
wells = [plate.get_well(name) for name in well_names] wells = [plate.get_well(name) for name in well_names]
res_volumes = [] res_volumes = []
@@ -706,6 +716,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
well.set_liquids([(liquid_name, volume)]) # type: ignore well.set_liquids([(liquid_name, volume)]) # type: ignore
res_volumes.append(volume) res_volumes.append(volume)
task = ROS2DeviceNode.run_async_func(self._ros_node.update_resource, True, **{"resources": wells})
submit_time = time.time()
while not task.done():
if time.time() - submit_time > 10:
self._ros_node.lab_logger().info(f"set_liquid_from_plate {plate} 超时")
break
time.sleep(0.01)
return SetLiquidFromPlateReturn( return SetLiquidFromPlateReturn(
plate=ResourceTreeSet.from_plr_resources([plate], known_newly_created=False).dump(), # type: ignore plate=ResourceTreeSet.from_plr_resources([plate], known_newly_created=False).dump(), # type: ignore
wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), # type: ignore wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), # type: ignore
@@ -1111,7 +1129,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
mix_liquid_height: Optional[float] = None, mix_liquid_height: Optional[float] = None,
delays: Optional[List[int]] = None, delays: Optional[List[int]] = None,
none_keys: List[str] = [], none_keys: List[str] = [],
): ) -> TransferLiquidReturn:
"""Transfer liquid with automatic mode detection. """Transfer liquid with automatic mode detection.
Supports three transfer modes: Supports three transfer modes:
@@ -1251,6 +1269,11 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
"Supported modes: 1->N, N->1, or N->N." "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_one_to_one( async def _transfer_one_to_one(
self, self,
sources: Sequence[Container], sources: Sequence[Container],

View File

@@ -52,6 +52,7 @@ from unilabos.devices.liquid_handling.liquid_handler_abstract import (
SimpleReturn, SimpleReturn,
SetLiquidReturn, SetLiquidReturn,
SetLiquidFromPlateReturn, SetLiquidFromPlateReturn,
TransferLiquidReturn,
) )
from unilabos.registry.placeholder_type import ResourceSlot from unilabos.registry.placeholder_type import ResourceSlot
from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
@@ -154,25 +155,29 @@ class PRCXI9300Plate(Plate):
**kwargs, **kwargs,
): ):
# 如果 ordered_items 不为 None直接使用 # 如果 ordered_items 不为 None直接使用
items = None
ordering_param = None
if ordered_items is not None: if ordered_items is not None:
items = ordered_items items = ordered_items
elif ordering is not 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) # 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 Plate 自己创建 Well 对象 # 如果是字符串,说明这是位置名称,需要让 Plate 自己创建 Well 对象
# 我们只传递位置信息(键),不传递值,使用 ordering 参数 # 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): if ordering:
values = list(ordering.values())
value = values[0]
if isinstance(value, str):
# ordering 的值是字符串,只使用键(位置信息)创建新的 OrderedDict # ordering 的值是字符串,只使用键(位置信息)创建新的 OrderedDict
# 传递 ordering 参数而不是 ordered_items让 Plate 自己创建 Well 对象 # 传递 ordering 参数而不是 ordered_items让 Plate 自己创建 Well 对象
items = None items = None
# 使用 ordering 参数,只包含位置信息(键) # 使用 ordering 参数,只包含位置信息(键)
ordering_param = collections.OrderedDict((k, None) for k in ordering.keys()) ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
elif value is None:
ordering_param = ordering
else: else:
# ordering 的值已经是对象,可以直接使用 # ordering 的值已经是对象,可以直接使用
items = ordering items = ordering
ordering_param = None ordering_param = None
else:
items = None
ordering_param = None
# 根据情况传递不同的参数 # 根据情况传递不同的参数
if items is not None: if items is not None:
@@ -590,7 +595,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
return super().set_liquid(wells, liquid_names, volumes) return super().set_liquid(wells, liquid_names, volumes)
def set_liquid_from_plate( def set_liquid_from_plate(
self, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float] self, plate: List[ResourceSlot], well_names: list[str], liquid_names: list[str], volumes: list[float]
) -> SetLiquidFromPlateReturn: ) -> SetLiquidFromPlateReturn:
return super().set_liquid_from_plate(plate, well_names, liquid_names, volumes) return super().set_liquid_from_plate(plate, well_names, liquid_names, volumes)
@@ -713,7 +718,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
mix_liquid_height: Optional[float] = None, mix_liquid_height: Optional[float] = None,
delays: Optional[List[int]] = None, delays: Optional[List[int]] = None,
none_keys: List[str] = [], none_keys: List[str] = [],
): ) -> TransferLiquidReturn:
return await super().transfer_liquid( return await super().transfer_liquid(
sources, sources,
targets, targets,

View File

@@ -638,7 +638,7 @@ liquid_handler:
placeholder_keys: {} placeholder_keys: {}
result: {} result: {}
schema: schema:
description: 吸头迭代函数。用于自动管理和切换吸头架中的吸头,实现批量实验中的吸头自动分配和追踪。该函数监控吸头使用状态,自动切换到下一个可用吸头位置,确保实验流程的连续性。适用于高通量实验、批量处理、自动化流水线等需要大量吸头管理的应用场景。 description: 吸头迭代函数。用于自动管理和切换枪头盒中的吸头,实现批量实验中的吸头自动分配和追踪。该函数监控吸头使用状态,自动切换到下一个可用吸头位置,确保实验流程的连续性。适用于高通量实验、批量处理、自动化流水线等需要大量吸头管理的应用场景。
properties: properties:
feedback: {} feedback: {}
goal: goal:
@@ -712,6 +712,43 @@ liquid_handler:
title: set_group参数 title: set_group参数
type: object type: object
type: UniLabJsonCommand type: UniLabJsonCommand
auto-set_liquid_from_plate:
feedback: {}
goal: {}
goal_default:
liquid_names: null
plate: null
volumes: null
well_names: null
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties:
liquid_names:
type: string
plate:
type: string
volumes:
type: string
well_names:
type: string
required:
- plate
- well_names
- liquid_names
- volumes
type: object
result: {}
required:
- goal
title: set_liquid_from_plate参数
type: object
type: UniLabJsonCommand
auto-set_tiprack: auto-set_tiprack:
feedback: {} feedback: {}
goal: {} goal: {}
@@ -721,7 +758,7 @@ liquid_handler:
placeholder_keys: {} placeholder_keys: {}
result: {} result: {}
schema: schema:
description: 吸头架设置函数。用于配置和初始化液体处理系统的吸头架信息,包括吸头架位置、类型、容量等参数。该函数建立吸头资源管理系统,为后续的吸头选择和使用提供基础配置。适用于系统初始化、吸头架更换、实验配置等需要吸头资源管理的操作场景。 description: 枪头盒设置函数。用于配置和初始化液体处理系统的枪头盒信息,包括枪头盒位置、类型、容量等参数。该函数建立吸头资源管理系统,为后续的吸头选择和使用提供基础配置。适用于系统初始化、枪头盒更换、实验配置等需要吸头资源管理的操作场景。
properties: properties:
feedback: {} feedback: {}
goal: goal:
@@ -4093,32 +4130,32 @@ liquid_handler:
- 0 - 0
handles: handles:
input: input:
- data_key: liquid - data_key: sources
data_source: handle data_source: handle
data_type: resource data_type: resource
handler_key: sources handler_key: sources
label: sources label: 待移动液体
- data_key: liquid - data_key: targets
data_source: executor
data_type: resource
handler_key: targets
label: targets
- data_key: liquid
data_source: executor
data_type: resource
handler_key: tip_rack
label: tip_rack
output:
- data_key: liquid
data_source: handle data_source: handle
data_type: resource data_type: resource
handler_key: targets
label: 转移目标
- data_key: tip_racks
data_source: handle
data_type: resource
handler_key: tip_rack
label: 枪头盒
output:
- data_key: sources.@flatten
data_source: executor
data_type: resource
handler_key: sources_out handler_key: sources_out
label: sources label: 移液后源孔
- data_key: liquid - data_key: targets.@flatten
data_source: executor data_source: executor
data_type: resource data_type: resource
handler_key: targets_out handler_key: targets_out
label: targets label: 移液后目标孔
placeholder_keys: placeholder_keys:
sources: unilabos_resources sources: unilabos_resources
targets: unilabos_resources targets: unilabos_resources
@@ -5114,19 +5151,34 @@ liquid_handler.biomek:
- 0 - 0
handles: handles:
input: input:
- data_key: liquid - data_key: sources
data_source: handle data_source: handle
data_type: resource data_type: resource
handler_key: liquid-input handler_key: sources
io_type: target io_type: target
label: Liquid Input label: 待移动液体
- data_key: targets
data_source: handle
data_type: resource
handler_key: targets
label: 转移目标
- data_key: tip_racks
data_source: handle
data_type: resource
handler_key: tip_rack
label: 枪头盒
output: output:
- data_key: liquid - data_key: sources.@flatten
data_source: executor data_source: executor
data_type: resource data_type: resource
handler_key: liquid-output handler_key: sources_out
io_type: source io_type: source
label: Liquid Output 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
placeholder_keys: placeholder_keys:
sources: unilabos_resources sources: unilabos_resources
targets: unilabos_resources targets: unilabos_resources
@@ -9451,6 +9503,7 @@ liquid_handler.prcxi:
type: string type: string
type: array type: array
plate: plate:
items:
properties: properties:
category: category:
type: string type: string
@@ -9523,6 +9576,8 @@ liquid_handler.prcxi:
- data - data
title: plate title: plate
type: object type: object
title: plate
type: array
volumes: volumes:
items: items:
type: number type: number
@@ -9544,8 +9599,7 @@ liquid_handler.prcxi:
title: Plate title: Plate
type: array type: array
volumes: volumes:
items: items: {}
type: number
title: Volumes title: Volumes
type: array type: array
wells: wells:
@@ -9922,18 +9976,18 @@ liquid_handler.prcxi:
data_source: handle data_source: handle
data_type: resource data_type: resource
handler_key: tip_rack_identifier handler_key: tip_rack_identifier
label: 头盒 label: 头盒
output: output:
- data_key: liquid - data_key: sources.@flatten
data_source: handle data_source: executor
data_type: resource data_type: resource
handler_key: sources_out handler_key: sources_out
label: sources label: 移液后源孔
- data_key: liquid - data_key: targets.@flatten
data_source: executor data_source: executor
data_type: resource data_type: resource
handler_key: targets_out handler_key: targets_out
label: targets label: 移液后目标孔
placeholder_keys: placeholder_keys:
sources: unilabos_resources sources: unilabos_resources
targets: unilabos_resources targets: unilabos_resources

View File

@@ -151,12 +151,40 @@ def canonicalize_links_ports(links: List[Dict[str, Any]], resource_tree_set: Res
""" """
# 构建 id 到 uuid 的映射 # 构建 id 到 uuid 的映射
id_to_uuid: Dict[str, str] = {} id_to_uuid: Dict[str, str] = {}
uuid_to_id: Dict[str, str] = {}
for node in resource_tree_set.all_nodes: for node in resource_tree_set.all_nodes:
id_to_uuid[node.res_content.id] = node.res_content.uuid id_to_uuid[node.res_content.id] = node.res_content.uuid
uuid_to_id[node.res_content.uuid] = node.res_content.id
# 第三遍处理:为每个 link 添加 source_uuid 和 target_uuid
for link in links:
source_id = link.get("source")
target_id = link.get("target")
# 添加 source_uuid
if source_id and source_id in id_to_uuid:
link["source_uuid"] = id_to_uuid[source_id]
# 添加 target_uuid
if target_id and target_id in id_to_uuid:
link["target_uuid"] = id_to_uuid[target_id]
source_uuid = link.get("source_uuid")
target_uuid = link.get("target_uuid")
# 添加 source_uuid
if source_uuid and source_uuid in uuid_to_id:
link["source"] = uuid_to_id[source_uuid]
# 添加 target_uuid
if target_uuid and target_uuid in uuid_to_id:
link["target"] = uuid_to_id[target_uuid]
# 第一遍处理将字符串类型的port转换为字典格式 # 第一遍处理将字符串类型的port转换为字典格式
for link in links: for link in links:
port = link.get("port") port = link.get("port")
if port is None:
continue
if link.get("type", "physical") == "physical": if link.get("type", "physical") == "physical":
link["type"] = "fluid" link["type"] = "fluid"
if isinstance(port, int): if isinstance(port, int):
@@ -179,13 +207,15 @@ def canonicalize_links_ports(links: List[Dict[str, Any]], resource_tree_set: Res
link["port"] = {link["source"]: None, link["target"]: None} link["port"] = {link["source"]: None, link["target"]: None}
# 构建边字典,键为(source节点, target节点)值为对应的port信息 # 构建边字典,键为(source节点, target节点)值为对应的port信息
edges = {(link["source"], link["target"]): link["port"] for link in links} edges = {(link["source"], link["target"]): link["port"] for link in links if link.get("port")}
# 第二遍处理填充反向边的dest信息 # 第二遍处理填充反向边的dest信息
delete_reverses = [] delete_reverses = []
for i, link in enumerate(links): for i, link in enumerate(links):
s, t = link["source"], link["target"] s, t = link["source"], link["target"]
current_port = link["port"] current_port = link.get("port")
if current_port is None:
continue
if current_port.get(t) is None: if current_port.get(t) is None:
reverse_key = (t, s) reverse_key = (t, s)
reverse_port = edges.get(reverse_key) reverse_port = edges.get(reverse_key)
@@ -200,20 +230,6 @@ def canonicalize_links_ports(links: List[Dict[str, Any]], resource_tree_set: Res
current_port[t] = current_port[s] current_port[t] = current_port[s]
# 删除已被使用反向端口信息的反向边 # 删除已被使用反向端口信息的反向边
standardized_links = [link for i, link in enumerate(links) if i not in delete_reverses] standardized_links = [link for i, link in enumerate(links) if i not in delete_reverses]
# 第三遍处理:为每个 link 添加 source_uuid 和 target_uuid
for link in standardized_links:
source_id = link.get("source")
target_id = link.get("target")
# 添加 source_uuid
if source_id and source_id in id_to_uuid:
link["source_uuid"] = id_to_uuid[source_id]
# 添加 target_uuid
if target_id and target_id in id_to_uuid:
link["target_uuid"] = id_to_uuid[target_id]
return standardized_links return standardized_links
@@ -284,6 +300,8 @@ def modify_to_backend_format(data: list[dict[str, Any]]) -> list[dict[str, Any]]
edge["sourceHandle"] = port[source] edge["sourceHandle"] = port[source]
elif "source_port" in edge: elif "source_port" in edge:
edge["sourceHandle"] = edge.pop("source_port") edge["sourceHandle"] = edge.pop("source_port")
elif "source_handle" in edge:
edge["sourceHandle"] = edge.pop("source_handle")
else: else:
typ = edge.get("type") typ = edge.get("type")
if typ == "communication": if typ == "communication":
@@ -292,6 +310,8 @@ def modify_to_backend_format(data: list[dict[str, Any]]) -> list[dict[str, Any]]
edge["targetHandle"] = port[target] edge["targetHandle"] = port[target]
elif "target_port" in edge: elif "target_port" in edge:
edge["targetHandle"] = edge.pop("target_port") edge["targetHandle"] = edge.pop("target_port")
elif "target_handle" in edge:
edge["targetHandle"] = edge.pop("target_handle")
else: else:
typ = edge.get("type") typ = edge.get("type")
if typ == "communication": if typ == "communication":

View File

@@ -14,6 +14,20 @@ if TYPE_CHECKING:
EXTRA_CLASS = "unilabos_resource_class" EXTRA_CLASS = "unilabos_resource_class"
EXTRA_SAMPLE_UUID = "sample_uuid"
EXTRA_UNILABOS_SAMPLE_UUID = "unilabos_sample_uuid"
# 函数参数名常量 - 用于自动注入 sample_uuids 列表
PARAM_SAMPLE_UUIDS = "sample_uuids"
# JSON Command 中的系统参数字段名
JSON_UNILABOS_PARAM = "unilabos_param"
# 返回值中的 samples 字段名
RETURN_UNILABOS_SAMPLES = "unilabos_samples"
# sample_uuids 参数类型 (用于 virtual bench 等设备添加 sample_uuids 参数)
SampleUUIDsType = Dict[str, Optional["PLRResource"]]
class ResourceDictPositionSize(BaseModel): class ResourceDictPositionSize(BaseModel):
@@ -529,6 +543,7 @@ class ResourceTreeSet(object):
plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True) plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True)
from pylabrobot.resources import Coordinate from pylabrobot.resources import Coordinate
from pylabrobot.serializer import deserialize from pylabrobot.serializer import deserialize
location = cast(Coordinate, deserialize(plr_dict["location"])) location = cast(Coordinate, deserialize(plr_dict["location"]))
plr_resource.location = location plr_resource.location = location
plr_resource.load_all_state(all_states) plr_resource.load_all_state(all_states)

View File

@@ -4,8 +4,20 @@ import json
import threading import threading
import time import time
import traceback import traceback
from typing import get_type_hints, TypeVar, Generic, Dict, Any, Type, TypedDict, Optional, List, TYPE_CHECKING, Union, \ from typing import (
Tuple get_type_hints,
TypeVar,
Generic,
Dict,
Any,
Type,
TypedDict,
Optional,
List,
TYPE_CHECKING,
Union,
Tuple,
)
from concurrent.futures import ThreadPoolExecutor from concurrent.futures import ThreadPoolExecutor
import asyncio import asyncio
@@ -48,6 +60,9 @@ from unilabos.resources.resource_tracker import (
ResourceTreeSet, ResourceTreeSet,
ResourceTreeInstance, ResourceTreeInstance,
ResourceDictInstance, ResourceDictInstance,
EXTRA_SAMPLE_UUID,
PARAM_SAMPLE_UUIDS,
JSON_UNILABOS_PARAM,
) )
from unilabos.ros.utils.driver_creator import WorkstationNodeCreator, PyLabRobotCreator, DeviceClassCreator from unilabos.ros.utils.driver_creator import WorkstationNodeCreator, PyLabRobotCreator, DeviceClassCreator
from rclpy.task import Task, Future from rclpy.task import Task, Future
@@ -216,14 +231,15 @@ class PropertyPublisher:
def publish_property(self): def publish_property(self):
try: try:
self.node.lab_logger().trace(f"【.publish_property】开始发布属性: {self.name}") # self.node.lab_logger().trace(f"【.publish_property】开始发布属性: {self.name}")
value = self.get_property() value = self.get_property()
if self.print_publish: if self.print_publish:
self.node.lab_logger().trace(f"【.publish_property】发布 {self.msg_type}: {value}") pass
# self.node.lab_logger().trace(f"【.publish_property】发布 {self.msg_type}: {value}")
if value is not None: if value is not None:
msg = convert_to_ros_msg(self.msg_type, value) msg = convert_to_ros_msg(self.msg_type, value)
self.publisher_.publish(msg) self.publisher_.publish(msg)
self.node.lab_logger().trace(f"【.publish_property】属性 {self.name} 发布成功") # self.node.lab_logger().trace(f"【.publish_property】属性 {self.name} 发布成功")
except Exception as e: except Exception as e:
self.node.lab_logger().error( self.node.lab_logger().error(
f"【.publish_property】发布属性 {self.publisher_.topic} 出错: {str(e)}\n{traceback.format_exc()}" f"【.publish_property】发布属性 {self.publisher_.topic} 出错: {str(e)}\n{traceback.format_exc()}"
@@ -361,6 +377,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
from pylabrobot.resources.deck import Deck from pylabrobot.resources.deck import Deck
from pylabrobot.resources import Coordinate from pylabrobot.resources import Coordinate
from pylabrobot.resources import Plate from pylabrobot.resources import Plate
# 物料传输到对应的node节点 # 物料传输到对应的node节点
client = self._resource_clients["c2s_update_resource_tree"] client = self._resource_clients["c2s_update_resource_tree"]
request = SerialCommand.Request() request = SerialCommand.Request()
@@ -388,9 +405,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
rts: ResourceTreeSet = ResourceTreeSet.from_raw_dict_list(input_resources) rts: ResourceTreeSet = ResourceTreeSet.from_raw_dict_list(input_resources)
parent_resource = None parent_resource = None
if bind_parent_id != self.node_name: if bind_parent_id != self.node_name:
parent_resource = self.resource_tracker.figure_resource( parent_resource = self.resource_tracker.figure_resource({"name": bind_parent_id})
{"name": bind_parent_id}
)
for r in rts.root_nodes: for r in rts.root_nodes:
# noinspection PyUnresolvedReferences # noinspection PyUnresolvedReferences
r.res_content.parent_uuid = parent_resource.unilabos_uuid r.res_content.parent_uuid = parent_resource.unilabos_uuid
@@ -398,19 +413,20 @@ class BaseROS2DeviceNode(Node, Generic[T]):
for r in rts.root_nodes: for r in rts.root_nodes:
r.res_content.parent_uuid = self.uuid r.res_content.parent_uuid = self.uuid
if len(LIQUID_INPUT_SLOT) and LIQUID_INPUT_SLOT[0] == -1 and len(rts.root_nodes) == 1 and isinstance(rts.root_nodes[0], RegularContainer): if (
len(LIQUID_INPUT_SLOT)
and LIQUID_INPUT_SLOT[0] == -1
and len(rts.root_nodes) == 1
and isinstance(rts.root_nodes[0], RegularContainer)
):
# noinspection PyTypeChecker # noinspection PyTypeChecker
container_instance: RegularContainer = rts.root_nodes[0] container_instance: RegularContainer = rts.root_nodes[0]
found_resources = self.resource_tracker.figure_resource( found_resources = self.resource_tracker.figure_resource({"id": container_instance.name}, try_mode=True)
{"id": container_instance.name}, try_mode=True
)
if not len(found_resources): if not len(found_resources):
self.resource_tracker.add_resource(container_instance) self.resource_tracker.add_resource(container_instance)
logger.info(f"添加物料{container_instance.name}到资源跟踪器") logger.info(f"添加物料{container_instance.name}到资源跟踪器")
else: else:
assert ( assert len(found_resources) == 1, f"找到多个同名物料: {container_instance.name}, 请检查物料系统"
len(found_resources) == 1
), f"找到多个同名物料: {container_instance.name}, 请检查物料系统"
found_resource = found_resources[0] found_resource = found_resources[0]
if isinstance(found_resource, RegularContainer): if isinstance(found_resource, RegularContainer):
logger.info(f"更新物料{container_instance.name}的数据{found_resource.state}") logger.info(f"更新物料{container_instance.name}的数据{found_resource.state}")
@@ -422,14 +438,16 @@ class BaseROS2DeviceNode(Node, Generic[T]):
f"更新物料{container_instance.name}出现不支持的数据类型{type(found_resource)} {found_resource}" f"更新物料{container_instance.name}出现不支持的数据类型{type(found_resource)} {found_resource}"
) )
# noinspection PyUnresolvedReferences # noinspection PyUnresolvedReferences
request.command = json.dumps({ request.command = json.dumps(
{
"action": "add", "action": "add",
"data": { "data": {
"data": rts.dump(), "data": rts.dump(),
"mount_uuid": parent_resource.unilabos_uuid if parent_resource is not None else "", "mount_uuid": parent_resource.unilabos_uuid if parent_resource is not None else "",
"first_add": False, "first_add": False,
}, },
}) }
)
tree_response: SerialCommand.Response = await client.call_async(request) tree_response: SerialCommand.Response = await client.call_async(request)
uuid_maps = json.loads(tree_response.response) uuid_maps = json.loads(tree_response.response)
plr_instances = rts.to_plr_resources() plr_instances = rts.to_plr_resources()
@@ -471,7 +489,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
if len(ADD_LIQUID_TYPE) == 1 and len(LIQUID_VOLUME) == 1 and len(LIQUID_INPUT_SLOT) > 1: if len(ADD_LIQUID_TYPE) == 1 and len(LIQUID_VOLUME) == 1 and len(LIQUID_INPUT_SLOT) > 1:
ADD_LIQUID_TYPE = ADD_LIQUID_TYPE * len(LIQUID_INPUT_SLOT) ADD_LIQUID_TYPE = ADD_LIQUID_TYPE * len(LIQUID_INPUT_SLOT)
LIQUID_VOLUME = LIQUID_VOLUME * len(LIQUID_INPUT_SLOT) LIQUID_VOLUME = LIQUID_VOLUME * len(LIQUID_INPUT_SLOT)
self.lab_logger().warning(f"增加液体资源时数量为1自动补全为 {len(LIQUID_INPUT_SLOT)}") self.lab_logger().warning(
f"增加液体资源时数量为1自动补全为 {len(LIQUID_INPUT_SLOT)}"
)
for liquid_type, liquid_volume, liquid_input_slot in zip( for liquid_type, liquid_volume, liquid_input_slot in zip(
ADD_LIQUID_TYPE, LIQUID_VOLUME, LIQUID_INPUT_SLOT ADD_LIQUID_TYPE, LIQUID_VOLUME, LIQUID_INPUT_SLOT
): ):
@@ -490,9 +510,15 @@ class BaseROS2DeviceNode(Node, Generic[T]):
input_wells = [] input_wells = []
for r in LIQUID_INPUT_SLOT: for r in LIQUID_INPUT_SLOT:
input_wells.append(plr_instance.children[r]) input_wells.append(plr_instance.children[r])
final_response["liquid_input_resource_tree"] = ResourceTreeSet.from_plr_resources(input_wells).dump() final_response["liquid_input_resource_tree"] = ResourceTreeSet.from_plr_resources(
input_wells
).dump()
res.response = json.dumps(final_response) res.response = json.dumps(final_response)
if issubclass(parent_resource.__class__, Deck) and hasattr(parent_resource, "assign_child_at_slot") and "slot" in other_calling_param: if (
issubclass(parent_resource.__class__, Deck)
and hasattr(parent_resource, "assign_child_at_slot")
and "slot" in other_calling_param
):
other_calling_param["slot"] = int(other_calling_param["slot"]) other_calling_param["slot"] = int(other_calling_param["slot"])
parent_resource.assign_child_at_slot(plr_instance, **other_calling_param) parent_resource.assign_child_at_slot(plr_instance, **other_calling_param)
else: else:
@@ -507,14 +533,16 @@ class BaseROS2DeviceNode(Node, Generic[T]):
rts_with_parent = ResourceTreeSet.from_plr_resources([parent_resource]) rts_with_parent = ResourceTreeSet.from_plr_resources([parent_resource])
if rts_with_parent.root_nodes[0].res_content.uuid_parent is None: if rts_with_parent.root_nodes[0].res_content.uuid_parent is None:
rts_with_parent.root_nodes[0].res_content.parent_uuid = self.uuid rts_with_parent.root_nodes[0].res_content.parent_uuid = self.uuid
request.command = json.dumps({ request.command = json.dumps(
{
"action": "add", "action": "add",
"data": { "data": {
"data": rts_with_parent.dump(), "data": rts_with_parent.dump(),
"mount_uuid": rts_with_parent.root_nodes[0].res_content.uuid_parent, "mount_uuid": rts_with_parent.root_nodes[0].res_content.uuid_parent,
"first_add": False, "first_add": False,
}, },
}) }
)
tree_response: SerialCommand.Response = await client.call_async(request) tree_response: SerialCommand.Response = await client.call_async(request)
uuid_maps = json.loads(tree_response.response) uuid_maps = json.loads(tree_response.response)
self.resource_tracker.loop_update_uuid(input_resources, uuid_maps) self.resource_tracker.loop_update_uuid(input_resources, uuid_maps)
@@ -811,7 +839,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
} }
def _handle_update( def _handle_update(
plr_resources: List[Union[ResourcePLR, ResourceDictInstance]], tree_set: ResourceTreeSet, additional_add_params: Dict[str, Any] plr_resources: List[Union[ResourcePLR, ResourceDictInstance]],
tree_set: ResourceTreeSet,
additional_add_params: Dict[str, Any],
) -> Tuple[Dict[str, Any], List[ResourcePLR]]: ) -> Tuple[Dict[str, Any], List[ResourcePLR]]:
""" """
处理资源更新操作的内部函数 处理资源更新操作的内部函数
@@ -836,7 +866,10 @@ class BaseROS2DeviceNode(Node, Generic[T]):
original_parent_resource = original_instance.parent original_parent_resource = original_instance.parent
original_parent_resource_uuid = getattr(original_parent_resource, "unilabos_uuid", None) original_parent_resource_uuid = getattr(original_parent_resource, "unilabos_uuid", None)
target_parent_resource_uuid = tree.root_node.res_content.uuid_parent target_parent_resource_uuid = tree.root_node.res_content.uuid_parent
not_same_parent = original_parent_resource_uuid != target_parent_resource_uuid and original_parent_resource is not None not_same_parent = (
original_parent_resource_uuid != target_parent_resource_uuid
and original_parent_resource is not None
)
old_name = original_instance.name old_name = original_instance.name
new_name = plr_resource.name new_name = plr_resource.name
parent_appended = False parent_appended = False
@@ -872,8 +905,16 @@ class BaseROS2DeviceNode(Node, Generic[T]):
else: else:
# 判断是否变更了resource_site重新登记 # 判断是否变更了resource_site重新登记
target_site = original_instance.unilabos_extra.get("update_resource_site") target_site = original_instance.unilabos_extra.get("update_resource_site")
sites = original_instance.parent.sites if original_instance.parent is not None and hasattr(original_instance.parent, "sites") else None sites = (
site_names = list(original_instance.parent._ordering.keys()) if original_instance.parent is not None and hasattr(original_instance.parent, "sites") else [] original_instance.parent.sites
if original_instance.parent is not None and hasattr(original_instance.parent, "sites")
else None
)
site_names = (
list(original_instance.parent._ordering.keys())
if original_instance.parent is not None and hasattr(original_instance.parent, "sites")
else []
)
if target_site is not None and sites is not None and site_names is not None: if target_site is not None and sites is not None and site_names is not None:
site_index = sites.index(original_instance) site_index = sites.index(original_instance)
site_name = site_names[site_index] site_name = site_names[site_index]
@@ -910,9 +951,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
action = i.get("action") # remove, add, update action = i.get("action") # remove, add, update
resources_uuid: List[str] = i.get("data") # 资源数据 resources_uuid: List[str] = i.get("data") # 资源数据
additional_add_params = i.get("additional_add_params", {}) # 额外参数 additional_add_params = i.get("additional_add_params", {}) # 额外参数
self.lab_logger().trace( self.lab_logger().trace(f"[资源同步] 处理 {action}, " f"resources count: {len(resources_uuid)}")
f"[资源同步] 处理 {action}, " f"resources count: {len(resources_uuid)}"
)
tree_set = None tree_set = None
if action in ["add", "update"]: if action in ["add", "update"]:
tree_set = await self.get_resource( tree_set = await self.get_resource(
@@ -939,9 +978,13 @@ class BaseROS2DeviceNode(Node, Generic[T]):
tree.root_node.res_content.parent_uuid = self.uuid tree.root_node.res_content.parent_uuid = self.uuid
r = SerialCommand.Request() r = SerialCommand.Request()
r.command = json.dumps( r.command = json.dumps(
{"data": {"data": new_tree_set.dump()}, "action": "update"}) # 和Update Resource一致 {"data": {"data": new_tree_set.dump()}, "action": "update"}
) # 和Update Resource一致
response: SerialCommand_Response = await self._resource_clients[ response: SerialCommand_Response = await self._resource_clients[
"c2s_update_resource_tree"].call_async(r) # type: ignore "c2s_update_resource_tree"
].call_async(
r
) # type: ignore
self.lab_logger().info(f"确认资源云端 Add 结果: {response.response}") self.lab_logger().info(f"确认资源云端 Add 结果: {response.response}")
results.append(result) results.append(result)
elif action == "update": elif action == "update":
@@ -961,9 +1004,13 @@ class BaseROS2DeviceNode(Node, Generic[T]):
tree.root_node.res_content.parent_uuid = self.uuid tree.root_node.res_content.parent_uuid = self.uuid
r = SerialCommand.Request() r = SerialCommand.Request()
r.command = json.dumps( r.command = json.dumps(
{"data": {"data": new_tree_set.dump()}, "action": "update"}) # 和Update Resource一致 {"data": {"data": new_tree_set.dump()}, "action": "update"}
) # 和Update Resource一致
response: SerialCommand_Response = await self._resource_clients[ response: SerialCommand_Response = await self._resource_clients[
"c2s_update_resource_tree"].call_async(r) # type: ignore "c2s_update_resource_tree"
].call_async(
r
) # type: ignore
self.lab_logger().info(f"确认资源云端 Update 结果: {response.response}") self.lab_logger().info(f"确认资源云端 Update 结果: {response.response}")
results.append(result) results.append(result)
elif action == "remove": elif action == "remove":
@@ -1333,7 +1380,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
resource_id=resource_data["id"], with_children=True resource_id=resource_data["id"], with_children=True
) )
if "sample_id" in resource_data: if "sample_id" in resource_data:
plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"] plr_resource.unilabos_extra[EXTRA_SAMPLE_UUID] = resource_data["sample_id"]
queried_resources[idx] = plr_resource queried_resources[idx] = plr_resource
else: else:
uuid_indices.append((idx, unilabos_uuid, resource_data)) uuid_indices.append((idx, unilabos_uuid, resource_data))
@@ -1346,7 +1393,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
for i, (idx, _, resource_data) in enumerate(uuid_indices): for i, (idx, _, resource_data) in enumerate(uuid_indices):
plr_resource = plr_resources[i] plr_resource = plr_resources[i]
if "sample_id" in resource_data: if "sample_id" in resource_data:
plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"] plr_resource.unilabos_extra[EXTRA_SAMPLE_UUID] = resource_data["sample_id"]
queried_resources[idx] = plr_resource queried_resources[idx] = plr_resource
self.lab_logger().debug(f"资源查询结果: 共 {len(queried_resources)} 个资源") self.lab_logger().debug(f"资源查询结果: 共 {len(queried_resources)} 个资源")
@@ -1354,7 +1401,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
# 通过资源跟踪器获取本地实例 # 通过资源跟踪器获取本地实例
final_resources = queried_resources if is_sequence else queried_resources[0] final_resources = queried_resources if is_sequence else queried_resources[0]
if not is_sequence: if not is_sequence:
plr = self.resource_tracker.figure_resource({"name": final_resources.name}, try_mode=False) plr = self.resource_tracker.figure_resource(
{"name": final_resources.name}, try_mode=False
)
# 保留unilabos_extra # 保留unilabos_extra
if hasattr(final_resources, "unilabos_extra") and hasattr(plr, "unilabos_extra"): if hasattr(final_resources, "unilabos_extra") and hasattr(plr, "unilabos_extra"):
plr.unilabos_extra = getattr(final_resources, "unilabos_extra", {}).copy() plr.unilabos_extra = getattr(final_resources, "unilabos_extra", {}).copy()
@@ -1393,8 +1442,12 @@ class BaseROS2DeviceNode(Node, Generic[T]):
execution_success = True execution_success = True
except Exception as _: except Exception as _:
execution_error = traceback.format_exc() execution_error = traceback.format_exc()
error(f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{str(action_kwargs)[:1000]}") error(
trace(f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{action_kwargs}") f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{str(action_kwargs)[:1000]}"
)
trace(
f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{action_kwargs}"
)
future = ROS2DeviceNode.run_async_func(ACTION, trace_error=False, **action_kwargs) future = ROS2DeviceNode.run_async_func(ACTION, trace_error=False, **action_kwargs)
future.add_done_callback(_handle_future_exception) future.add_done_callback(_handle_future_exception)
@@ -1414,9 +1467,11 @@ class BaseROS2DeviceNode(Node, Generic[T]):
except Exception as _: except Exception as _:
execution_error = traceback.format_exc() execution_error = traceback.format_exc()
error( error(
f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{str(action_kwargs)[:1000]}") f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{str(action_kwargs)[:1000]}"
)
trace( trace(
f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{action_kwargs}") f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{action_kwargs}"
)
future.add_done_callback(_handle_future_exception) future.add_done_callback(_handle_future_exception)
@@ -1539,20 +1594,39 @@ class BaseROS2DeviceNode(Node, Generic[T]):
try: try:
function_name = target["function_name"] function_name = target["function_name"]
function_args = target["function_args"] function_args = target["function_args"]
# 获取 unilabos 系统参数
unilabos_param: Dict[str, Any] = target[JSON_UNILABOS_PARAM]
assert isinstance(function_args, dict), "执行动作时JSON必须为dict类型\n原JSON: {string}" assert isinstance(function_args, dict), "执行动作时JSON必须为dict类型\n原JSON: {string}"
function = getattr(self.driver_instance, function_name) function = getattr(self.driver_instance, function_name)
assert callable( assert callable(
function function
), f"执行动作时JSON中的function_name对应的函数不可调用: {function_name}\n原JSON: {string}" ), f"执行动作时JSON中的function_name对应的函数不可调用: {function_name}\n原JSON: {string}"
# 处理 ResourceSlot 类型参数 # 处理参数(包含 unilabos 系统参数如 sample_uuids
args_list = default_manager._analyze_method_signature(function)["args"] args_list = default_manager._analyze_method_signature(function, skip_unilabos_params=False)["args"]
for arg in args_list: for arg in args_list:
arg_name = arg["name"] arg_name = arg["name"]
arg_type = arg["type"] arg_type = arg["type"]
# 跳过不在 function_args 中的参数 # 跳过不在 function_args 中的参数
if arg_name not in function_args: if arg_name not in function_args:
# 处理 sample_uuids 参数注入
if arg_name == PARAM_SAMPLE_UUIDS:
raw_sample_uuids = unilabos_param.get(PARAM_SAMPLE_UUIDS, {})
# 将 material uuid 转换为 resource 实例
# key: sample_uuid, value: material_uuid -> resource 实例
resolved_sample_uuids: Dict[str, Any] = {}
for sample_uuid, material_uuid in raw_sample_uuids.items():
if material_uuid and self.resource_tracker:
resource = self.resource_tracker.uuid_to_resources.get(material_uuid)
resolved_sample_uuids[sample_uuid] = resource if resource else material_uuid
else:
resolved_sample_uuids[sample_uuid] = material_uuid
function_args[PARAM_SAMPLE_UUIDS] = resolved_sample_uuids
self.lab_logger().debug(
f"[JsonCommand] 注入 {PARAM_SAMPLE_UUIDS}: {resolved_sample_uuids}"
)
continue continue
# 处理单个 ResourceSlot # 处理单个 ResourceSlot
@@ -1582,6 +1656,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
) )
raise JsonCommandInitError(f"ResourceSlot列表参数转换失败: {arg_name}") raise JsonCommandInitError(f"ResourceSlot列表参数转换失败: {arg_name}")
# todo: 默认反报送
return function(**function_args) return function(**function_args)
except KeyError as ex: except KeyError as ex:
raise JsonCommandInitError( raise JsonCommandInitError(
@@ -1601,21 +1676,23 @@ class BaseROS2DeviceNode(Node, Generic[T]):
raise ValueError("至少需要提供一个 UUID") raise ValueError("至少需要提供一个 UUID")
uuids_list = list(uuids) uuids_list = list(uuids)
future = self._resource_clients["c2s_update_resource_tree"].call_async(SerialCommand.Request( future = self._resource_clients["c2s_update_resource_tree"].call_async(
SerialCommand.Request(
command=json.dumps( command=json.dumps(
{ {
"data": {"data": uuids_list, "with_children": True}, "data": {"data": uuids_list, "with_children": True},
"action": "get", "action": "get",
} }
) )
)) )
)
# 等待结果使用while循环每次sleep 0.05秒最多等待30秒 # 等待结果使用while循环每次sleep 0.05秒最多等待30秒
timeout = 30.0 timeout = 30.0
elapsed = 0.0 elapsed = 0.0
while not future.done() and elapsed < timeout: while not future.done() and elapsed < timeout:
time.sleep(0.05) time.sleep(0.02)
elapsed += 0.05 elapsed += 0.02
if not future.done(): if not future.done():
raise Exception(f"资源查询超时: {uuids_list}") raise Exception(f"资源查询超时: {uuids_list}")
@@ -1666,6 +1743,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
try: try:
function_name = target["function_name"] function_name = target["function_name"]
function_args = target["function_args"] function_args = target["function_args"]
# 获取 unilabos 系统参数
unilabos_param: Dict[str, Any] = target.get(JSON_UNILABOS_PARAM, {})
assert isinstance(function_args, dict), "执行动作时JSON必须为dict类型\n原JSON: {string}" assert isinstance(function_args, dict), "执行动作时JSON必须为dict类型\n原JSON: {string}"
function = getattr(self.driver_instance, function_name) function = getattr(self.driver_instance, function_name)
assert callable( assert callable(
@@ -1675,14 +1755,30 @@ class BaseROS2DeviceNode(Node, Generic[T]):
function function
), f"执行动作时JSON中的function并非异步: {function_name}\n原JSON: {string}" ), f"执行动作时JSON中的function并非异步: {function_name}\n原JSON: {string}"
# 处理 ResourceSlot 类型参数 # 处理参数(包含 unilabos 系统参数如 sample_uuids
args_list = default_manager._analyze_method_signature(function)["args"] args_list = default_manager._analyze_method_signature(function, skip_unilabos_params=False)["args"]
for arg in args_list: for arg in args_list:
arg_name = arg["name"] arg_name = arg["name"]
arg_type = arg["type"] arg_type = arg["type"]
# 跳过不在 function_args 中的参数 # 跳过不在 function_args 中的参数
if arg_name not in function_args: if arg_name not in function_args:
# 处理 sample_uuids 参数注入
if arg_name == PARAM_SAMPLE_UUIDS:
raw_sample_uuids = unilabos_param.get(PARAM_SAMPLE_UUIDS, {})
# 将 material uuid 转换为 resource 实例
# key: sample_uuid, value: material_uuid -> resource 实例
resolved_sample_uuids: Dict[str, Any] = {}
for sample_uuid, material_uuid in raw_sample_uuids.items():
if material_uuid and self.resource_tracker:
resource = self.resource_tracker.uuid_to_resources.get(material_uuid)
resolved_sample_uuids[sample_uuid] = resource if resource else material_uuid
else:
resolved_sample_uuids[sample_uuid] = material_uuid
function_args[PARAM_SAMPLE_UUIDS] = resolved_sample_uuids
self.lab_logger().debug(
f"[JsonCommandAsync] 注入 {PARAM_SAMPLE_UUIDS}: {resolved_sample_uuids}"
)
continue continue
# 处理单个 ResourceSlot # 处理单个 ResourceSlot
@@ -1960,7 +2056,9 @@ class ROS2DeviceNode:
asyncio.set_event_loop(loop) asyncio.set_event_loop(loop)
loop.run_forever() loop.run_forever()
ROS2DeviceNode._asyncio_loop_thread = threading.Thread(target=run_event_loop, daemon=True, name="ROS2DeviceNode") ROS2DeviceNode._asyncio_loop_thread = threading.Thread(
target=run_event_loop, daemon=True, name="ROS2DeviceNode"
)
ROS2DeviceNode._asyncio_loop_thread.start() ROS2DeviceNode._asyncio_loop_thread.start()
logger.info(f"循环线程已启动") logger.info(f"循环线程已启动")

View File

@@ -1,17 +1,17 @@
import collections import collections
from dataclasses import dataclass, field
import json import json
import threading import threading
import time import time
import traceback import traceback
import uuid import uuid
from dataclasses import dataclass, field
from typing import TYPE_CHECKING, Optional, Dict, Any, List, ClassVar, Set, Union from typing import TYPE_CHECKING, Optional, Dict, Any, List, ClassVar, Set, Union
from typing_extensions import TypedDict
from action_msgs.msg import GoalStatus from action_msgs.msg import GoalStatus
from geometry_msgs.msg import Point from geometry_msgs.msg import Point
from rclpy.action import ActionClient, get_action_server_names_and_types_by_node from rclpy.action import ActionClient, get_action_server_names_and_types_by_node
from rclpy.service import Service from rclpy.service import Service
from typing_extensions import TypedDict
from unilabos_msgs.msg import Resource # type: ignore from unilabos_msgs.msg import Resource # type: ignore
from unilabos_msgs.srv import ( from unilabos_msgs.srv import (
ResourceAdd, ResourceAdd,
@@ -23,10 +23,20 @@ from unilabos_msgs.srv import (
from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response
from unique_identifier_msgs.msg import UUID from unique_identifier_msgs.msg import UUID
from unilabos.registry.placeholder_type import ResourceSlot, DeviceSlot
from unilabos.registry.registry import lab_registry from unilabos.registry.registry import lab_registry
from unilabos.resources.container import RegularContainer from unilabos.resources.container import RegularContainer
from unilabos.resources.graphio import initialize_resource from unilabos.resources.graphio import initialize_resource
from unilabos.resources.registry import add_schema from unilabos.resources.registry import add_schema
from unilabos.resources.resource_tracker import (
ResourceDict,
ResourceDictInstance,
ResourceTreeSet,
ResourceTreeInstance,
RETURN_UNILABOS_SAMPLES,
JSON_UNILABOS_PARAM,
PARAM_SAMPLE_UUIDS,
)
from unilabos.ros.initialize_device import initialize_device_from_dict from unilabos.ros.initialize_device import initialize_device_from_dict
from unilabos.ros.msgs.message_converter import ( from unilabos.ros.msgs.message_converter import (
get_msg_type, get_msg_type,
@@ -37,17 +47,10 @@ from unilabos.ros.msgs.message_converter import (
) )
from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, ROS2DeviceNode, DeviceNodeResourceTracker from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, ROS2DeviceNode, DeviceNodeResourceTracker
from unilabos.ros.nodes.presets.controller_node import ControllerNode from unilabos.ros.nodes.presets.controller_node import ControllerNode
from unilabos.resources.resource_tracker import (
ResourceDict,
ResourceDictInstance,
ResourceTreeSet,
ResourceTreeInstance,
)
from unilabos.utils import logger from unilabos.utils import logger
from unilabos.utils.exception import DeviceClassInvalid from unilabos.utils.exception import DeviceClassInvalid
from unilabos.utils.log import warning from unilabos.utils.log import warning
from unilabos.utils.type_check import serialize_result_info from unilabos.utils.type_check import serialize_result_info
from unilabos.registry.placeholder_type import ResourceSlot, DeviceSlot
if TYPE_CHECKING: if TYPE_CHECKING:
from unilabos.app.ws_client import QueueItem from unilabos.app.ws_client import QueueItem
@@ -755,6 +758,7 @@ class HostNode(BaseROS2DeviceNode):
item: "QueueItem", item: "QueueItem",
action_type: str, action_type: str,
action_kwargs: Dict[str, Any], action_kwargs: Dict[str, Any],
sample_material: Dict[str, str],
server_info: Optional[Dict[str, Any]] = None, server_info: Optional[Dict[str, Any]] = None,
) -> None: ) -> None:
""" """
@@ -772,14 +776,14 @@ class HostNode(BaseROS2DeviceNode):
if action_name.startswith("auto-"): if action_name.startswith("auto-"):
action_name = action_name[5:] action_name = action_name[5:]
action_id = f"/devices/{device_id}/_execute_driver_command" action_id = f"/devices/{device_id}/_execute_driver_command"
action_kwargs = { json_command: Dict[str, Any] = {
"string": json.dumps(
{
"function_name": action_name, "function_name": action_name,
"function_args": action_kwargs, "function_args": action_kwargs,
JSON_UNILABOS_PARAM: {
PARAM_SAMPLE_UUIDS: sample_material,
},
} }
) action_kwargs = {"string": json.dumps(json_command)}
}
if action_type.startswith("UniLabJsonCommandAsync"): if action_type.startswith("UniLabJsonCommandAsync"):
action_id = f"/devices/{device_id}/_execute_driver_command_async" action_id = f"/devices/{device_id}/_execute_driver_command_async"
else: else:
@@ -790,24 +794,9 @@ class HostNode(BaseROS2DeviceNode):
raise ValueError(f"ActionClient {action_id} not found.") raise ValueError(f"ActionClient {action_id} not found.")
action_client: ActionClient = self._action_clients[action_id] action_client: ActionClient = self._action_clients[action_id]
# 遍历action_kwargs下的所有子dict将"sample_uuid"的值赋给"sample_id"
def assign_sample_id(obj):
if isinstance(obj, dict):
if "sample_uuid" in obj:
obj["sample_id"] = obj["sample_uuid"]
obj.pop("sample_uuid")
for k, v in obj.items():
if k != "unilabos_extra":
assign_sample_id(v)
elif isinstance(obj, list):
for item in obj:
assign_sample_id(item)
assign_sample_id(action_kwargs)
goal_msg = convert_to_ros_msg(action_client._action_type.Goal(), action_kwargs) goal_msg = convert_to_ros_msg(action_client._action_type.Goal(), action_kwargs)
self.lab_logger().info(f"[Host Node] Sending goal for {action_id}: {str(goal_msg)[:1000]}") # self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {str(goal_msg)[:1000]}")
self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {action_kwargs}") self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {action_kwargs}")
self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {goal_msg}") self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {goal_msg}")
action_client.wait_for_server() action_client.wait_for_server()
@@ -867,14 +856,14 @@ class HostNode(BaseROS2DeviceNode):
# 适配后端的一些额外处理 # 适配后端的一些额外处理
return_value = return_info.get("return_value") return_value = return_info.get("return_value")
if isinstance(return_value, dict): if isinstance(return_value, dict):
unilabos_samples = return_value.pop("unilabos_samples", None) unilabos_samples = return_value.pop(RETURN_UNILABOS_SAMPLES, None)
if isinstance(unilabos_samples, list) and unilabos_samples: if isinstance(unilabos_samples, list) and unilabos_samples:
self.lab_logger().info( self.lab_logger().info(
f"[Host Node] Job {job_id[:8]} returned {len(unilabos_samples)} sample(s): " f"[Host Node] Job {job_id[:8]} returned {len(unilabos_samples)} sample(s): "
f"{[s.get('name', s.get('id', 'unknown')) if isinstance(s, dict) else str(s)[:20] for s in unilabos_samples[:5]]}" f"{[s.get('name', s.get('id', 'unknown')) if isinstance(s, dict) else str(s)[:20] for s in unilabos_samples[:5]]}"
f"{'...' if len(unilabos_samples) > 5 else ''}" f"{'...' if len(unilabos_samples) > 5 else ''}"
) )
return_info["unilabos_samples"] = unilabos_samples return_info[RETURN_UNILABOS_SAMPLES] = unilabos_samples
suc = return_info.get("suc", False) suc = return_info.get("suc", False)
if not suc: if not suc:
status = "failed" status = "failed"
@@ -1180,7 +1169,7 @@ class HostNode(BaseROS2DeviceNode):
""" """
更新节点信息回调 更新节点信息回调
""" """
# self.lab_logger().info(f"[Host Node] Node info update request received: {request}") self.lab_logger().trace(f"[Host Node] Node info update request received: {request}")
try: try:
from unilabos.app.communication import get_communication_client from unilabos.app.communication import get_communication_client
from unilabos.app.web.client import HTTPClient, http_client from unilabos.app.web.client import HTTPClient, http_client

View File

@@ -0,0 +1,795 @@
{
"nodes": [
{
"id": "PRCXI",
"name": "PRCXI",
"type": "device",
"class": "liquid_handler.prcxi",
"parent": "",
"pose": {
"size": {
"width": 562,
"height": 394,
"depth": 0
}
},
"config": {
"axis": "Left",
"deck": {
"_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck",
"_resource_child_name": "PRCXI_Deck"
},
"host": "10.20.30.184",
"port": 9999,
"debug": true,
"setup": true,
"is_9320": true,
"timeout": 10,
"matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb",
"simulator": true,
"channel_num": 2
},
"data": {
"reset_ok": true
},
"schema": {},
"description": "",
"model": null,
"position": {
"x": 0,
"y": 240,
"z": 0
}
},
{
"id": "PRCXI_Deck",
"name": "PRCXI_Deck",
"children": [],
"parent": "PRCXI",
"type": "deck",
"class": "",
"position": {
"x": 10,
"y": 10,
"z": 0
},
"config": {
"type": "PRCXI9300Deck",
"size_x": 542,
"size_y": 374,
"size_z": 0,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "deck",
"barcode": null
},
"data": {}
},
{
"id": "T1",
"name": "T1",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 0,
"y": 288,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T1",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T2",
"name": "T2",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 138,
"y": 288,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T2",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T3",
"name": "T3",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 276,
"y": 288,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T3",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T4",
"name": "T4",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 414,
"y": 288,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T4",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T5",
"name": "T5",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 0,
"y": 192,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T5",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T6",
"name": "T6",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 138,
"y": 192,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T6",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T7",
"name": "T7",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 276,
"y": 192,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T7",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T8",
"name": "T8",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 414,
"y": 192,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T8",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T9",
"name": "T9",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 0,
"y": 96,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T9",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T10",
"name": "T10",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 138,
"y": 96,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T10",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T11",
"name": "T11",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 276,
"y": 96,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T11",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T12",
"name": "T12",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 414,
"y": 96,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T12",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T13",
"name": "T13",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 0,
"y": 0,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T13",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T14",
"name": "T14",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 138,
"y": 0,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T14",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T15",
"name": "T15",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 276,
"y": 0,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T15",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
},
{
"id": "T16",
"name": "T16",
"children": [],
"parent": "PRCXI_Deck",
"type": "plate",
"class": "",
"position": {
"x": 414,
"y": 0,
"z": 0
},
"config": {
"type": "PRCXI9300Container",
"size_x": 127,
"size_y": 85.5,
"size_z": 10,
"rotation": {
"x": 0,
"y": 0,
"z": 0,
"type": "Rotation"
},
"category": "plate",
"model": null,
"barcode": null,
"ordering": {},
"sites": [
{
"label": "T16",
"visible": true,
"position": { "x": 0, "y": 0, "z": 0 },
"size": { "width": 128.0, "height": 86, "depth": 0 },
"content_type": [
"plate",
"tip_rack",
"plates",
"tip_racks",
"tube_rack"
]
}
]
},
"data": {}
}
],
"edges": []
}

View File

@@ -27,6 +27,7 @@ __all__ = [
from ast import Constant from ast import Constant
from unilabos.resources.resource_tracker import PARAM_SAMPLE_UUIDS
from unilabos.utils import logger from unilabos.utils import logger
from unilabos.utils.decorator import is_not_action from unilabos.utils.decorator import is_not_action
@@ -341,13 +342,18 @@ class ImportManager:
result["action_methods"][method_name] = method_info result["action_methods"][method_name] = method_info
return result return result
def _analyze_method_signature(self, method) -> Dict[str, Any]: def _analyze_method_signature(self, method, skip_unilabos_params: bool = True) -> Dict[str, Any]:
""" """
分析方法签名,提取具体的命名参数信息 分析方法签名,提取具体的命名参数信息
注意:此方法会跳过*args和**kwargs只提取具体的命名参数 注意:此方法会跳过*args和**kwargs只提取具体的命名参数
这样可以确保通过**dict方式传参时的准确性 这样可以确保通过**dict方式传参时的准确性
Args:
method: 要分析的方法
skip_unilabos_params: 是否跳过 unilabos 系统参数(如 sample_uuids
registry 补全时为 TrueJsonCommand 执行时为 False
示例用法: 示例用法:
method_info = self._analyze_method_signature(some_method) method_info = self._analyze_method_signature(some_method)
params = {"param1": "value1", "param2": "value2"} params = {"param1": "value1", "param2": "value2"}
@@ -368,6 +374,10 @@ class ImportManager:
if param.kind == param.VAR_KEYWORD: # **kwargs if param.kind == param.VAR_KEYWORD: # **kwargs
continue continue
# 跳过 sample_uuids 参数由系统自动注入registry 补全时跳过)
if skip_unilabos_params and param_name == PARAM_SAMPLE_UUIDS:
continue
is_required = param.default == inspect.Parameter.empty is_required = param.default == inspect.Parameter.empty
if is_required: if is_required:
num_required += 1 num_required += 1
@@ -563,6 +573,9 @@ class ImportManager:
for i, arg in enumerate(node.args.args): for i, arg in enumerate(node.args.args):
if arg.arg == "self": if arg.arg == "self":
continue continue
# 跳过 sample_uuids 参数(由系统自动注入)
if arg.arg == PARAM_SAMPLE_UUIDS:
continue
arg_info = { arg_info = {
"name": arg.arg, "name": arg.arg,
"type": None, "type": None,

View File

@@ -19,7 +19,9 @@
第一步: 按 slot 去重创建 create_resource 节点(创建板子) 第一步: 按 slot 去重创建 create_resource 节点(创建板子)
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
- 首先创建一个 Group 节点type="Group", minimized=true用于包含所有 create_resource 节点
- 遍历所有 reagent按 slot 去重,为每个唯一的 slot 创建一个板子 - 遍历所有 reagent按 slot 去重,为每个唯一的 slot 创建一个板子
- 所有 create_resource 节点的 parent_uuid 指向 Group 节点minimized=true
- 生成参数: - 生成参数:
res_id: plate_slot_{slot} res_id: plate_slot_{slot}
device_id: /PRCXI device_id: /PRCXI
@@ -29,11 +31,13 @@
- 输出端口: labware用于连接 set_liquid_from_plate - 输出端口: labware用于连接 set_liquid_from_plate
- 控制流: create_resource 之间通过 ready 端口串联 - 控制流: create_resource 之间通过 ready 端口串联
示例: slot=1, slot=4 -> 创建 2 个 create_resource 节点 示例: slot=1, slot=4 -> 创建 1 个 Group + 2 个 create_resource 节点
第二步: 为每个 reagent 创建 set_liquid_from_plate 节点(设置液体) 第二步: 为每个 reagent 创建 set_liquid_from_plate 节点(设置液体)
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
- 首先创建一个 Group 节点type="Group", minimized=true用于包含所有 set_liquid_from_plate 节点
- 遍历所有 reagent为每个试剂创建 set_liquid_from_plate 节点 - 遍历所有 reagent为每个试剂创建 set_liquid_from_plate 节点
- 所有 set_liquid_from_plate 节点的 parent_uuid 指向 Group 节点minimized=true
- 生成参数: - 生成参数:
plate: [](通过连接传递,来自 create_resource 的 labware plate: [](通过连接传递,来自 create_resource 的 labware
well_names: ["A1", "A3", "A5"](来自 reagent 的 well 数组) well_names: ["A1", "A3", "A5"](来自 reagent 的 well 数组)
@@ -56,7 +60,11 @@
==================== 连接关系图 ==================== ==================== 连接关系图 ====================
控制流 (ready 端口串联): 控制流 (ready 端口串联):
create_resource_1 -> create_resource_2 -> ... -> set_liquid_1 -> set_liquid_2 -> ... -> transfer_liquid_1 -> transfer_liquid_2 -> ... - create_resource 之间: 无 ready 连接
- set_liquid_from_plate 之间: 无 ready 连接
- create_resource 与 set_liquid_from_plate 之间: 无 ready 连接
- transfer_liquid 之间: 通过 ready 端口串联
transfer_liquid_1 -> transfer_liquid_2 -> transfer_liquid_3 -> ...
物料流: 物料流:
[create_resource] --labware--> [set_liquid_from_plate] --output_wells--> [transfer_liquid] --sources_out/targets_out--> [下一个 transfer_liquid] [create_resource] --labware--> [set_liquid_from_plate] --output_wells--> [transfer_liquid] --sources_out/targets_out--> [下一个 transfer_liquid]
@@ -76,6 +84,13 @@ transfer_liquid:
输入: sources -> sources_identifier, targets -> targets_identifier 输入: sources -> sources_identifier, targets -> targets_identifier
输出: sources -> sources_out, targets -> targets_out 输出: sources -> sources_out, targets -> targets_out
==================== 设备名配置 (device_name) ====================
每个节点都有 device_name 字段,指定在哪个设备上执行:
- create_resource: device_name = "host_node"(固定)
- set_liquid_from_plate: device_name = "PRCXI"(可配置,见 DEVICE_NAME_DEFAULT
- transfer_liquid 等动作: device_name = "PRCXI"(可配置,见 DEVICE_NAME_DEFAULT
==================== 校验规则 ==================== ==================== 校验规则 ====================
- 检查 sources/targets 是否在 reagent 中定义 - 检查 sources/targets 是否在 reagent 中定义
@@ -97,6 +112,13 @@ Json = Dict[str, Any]
# ==================== 默认配置 ==================== # ==================== 默认配置 ====================
# 设备名配置
DEVICE_NAME_HOST = "host_node" # create_resource 固定在 host_node 上执行
DEVICE_NAME_DEFAULT = "PRCXI" # transfer_liquid, set_liquid_from_plate 等动作的默认设备名
# 节点类型
NODE_TYPE_DEFAULT = "ILab" # 所有节点的默认类型
# create_resource 节点默认参数 # create_resource 节点默认参数
CREATE_RESOURCE_DEFAULTS = { CREATE_RESOURCE_DEFAULTS = {
"device_id": "/PRCXI", "device_id": "/PRCXI",
@@ -367,9 +389,23 @@ def build_protocol_graph(
"res_id": res_id, "res_id": res_id,
} }
# 创建 Group 节点,包含所有 create_resource 节点
group_node_id = str(uuid.uuid4())
G.add_node(
group_node_id,
name="Resources Group",
type="Group",
parent_uuid="",
lab_node_type="Device",
template_name="",
resource_name="",
footer="",
minimized=True,
param=None,
)
# 为每个唯一的 slot 创建 create_resource 节点 # 为每个唯一的 slot 创建 create_resource 节点
res_index = 0 res_index = 0
last_create_resource_id = None
for slot, info in slots_info.items(): for slot, info in slots_info.items():
node_id = str(uuid.uuid4()) node_id = str(uuid.uuid4())
res_id = info["res_id"] res_id = info["res_id"]
@@ -383,6 +419,10 @@ def build_protocol_graph(
description=f"Create plate on slot {slot}", description=f"Create plate on slot {slot}",
lab_node_type="Labware", lab_node_type="Labware",
footer="create_resource-host_node", 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
param={ param={
"res_id": res_id, "res_id": res_id,
"device_id": CREATE_RESOURCE_DEFAULTS["device_id"], "device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
@@ -394,14 +434,25 @@ def build_protocol_graph(
) )
slot_to_create_resource[slot] = node_id slot_to_create_resource[slot] = node_id
# create_resource 之间通过 ready 串联 # create_resource 之间不需要 ready 连接
if last_create_resource_id is not None:
G.add_edge(last_create_resource_id, node_id, source_port="ready", target_port="ready")
last_create_resource_id = node_id
# ==================== 第二步:为每个 reagent 创建 set_liquid_from_plate 节点 ==================== # ==================== 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
set_liquid_group_id = str(uuid.uuid4())
G.add_node(
set_liquid_group_id,
name="SetLiquid Group",
type="Group",
parent_uuid="",
lab_node_type="Device",
template_name="",
resource_name="",
footer="",
minimized=True,
param=None,
)
set_liquid_index = 0 set_liquid_index = 0
last_set_liquid_id = last_create_resource_id # set_liquid_from_plate 连接在 create_resource 之后
for labware_id, item in labware_info.items(): for labware_id, item in labware_info.items():
# 跳过 Tip/Rack 类型 # 跳过 Tip/Rack 类型
@@ -430,6 +481,10 @@ def build_protocol_graph(
description=f"Set liquid: {labware_id}", description=f"Set liquid: {labware_id}",
lab_node_type="Reagent", lab_node_type="Reagent",
footer="set_liquid_from_plate-liquid_handler.prcxi", footer="set_liquid_from_plate-liquid_handler.prcxi",
device_name=DEVICE_NAME_DEFAULT,
type=NODE_TYPE_DEFAULT,
parent_uuid=set_liquid_group_id, # 指向 Group 节点
minimized=True, # 折叠显示
param={ param={
"plate": [], # 通过连接传递 "plate": [], # 通过连接传递
"well_names": wells, # 孔位名数组,如 ["A1", "A3", "A5"] "well_names": wells, # 孔位名数组,如 ["A1", "A3", "A5"]
@@ -438,10 +493,7 @@ def build_protocol_graph(
}, },
) )
# ready 连接:上一个节点 -> set_liquid_from_plate # set_liquid_from_plate 之间不需要 ready 连接
if last_set_liquid_id is not None:
G.add_edge(last_set_liquid_id, node_id, source_port="ready", target_port="ready")
last_set_liquid_id = node_id
# 物料流create_resource 的 labware -> set_liquid_from_plate 的 input_plate # 物料流create_resource 的 labware -> set_liquid_from_plate 的 input_plate
create_res_node_id = slot_to_create_resource.get(slot) create_res_node_id = slot_to_create_resource.get(slot)
@@ -451,7 +503,8 @@ def build_protocol_graph(
# set_liquid_from_plate 的输出 output_wells 用于连接 transfer_liquid # set_liquid_from_plate 的输出 output_wells 用于连接 transfer_liquid
resource_last_writer[labware_id] = f"{node_id}:output_wells" resource_last_writer[labware_id] = f"{node_id}:output_wells"
last_control_node_id = last_set_liquid_id # transfer_liquid 之间通过 ready 串联,从 None 开始
last_control_node_id = None
# 端口名称映射JSON 字段名 -> 实际 handle key # 端口名称映射JSON 字段名 -> 实际 handle key
INPUT_PORT_MAPPING = { INPUT_PORT_MAPPING = {
@@ -544,9 +597,11 @@ def build_protocol_graph(
if param_key in params: if param_key in params:
params[param_key] = [] params[param_key] = []
# 更新 step 的 paramfooter # 更新 step 的 paramfooter、device_name 和 type
step_copy = step.copy() step_copy = step.copy()
step_copy["param"] = params step_copy["param"] = params
step_copy["device_name"] = DEVICE_NAME_DEFAULT # 动作节点使用默认设备名
step_copy["type"] = NODE_TYPE_DEFAULT # 节点类型
# 如果有警告,修改 footer 添加警告标记(警告放前面) # 如果有警告,修改 footer 添加警告标记(警告放前面)
if warnings: if warnings: