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37-biomek-i5i7 (#40)

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* add biomek.py demo implementation

* 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。

* Test

* fix biomek success type

* Convert LH action to biomek.

* Update biomek.py

* 注册表上报handle和schema (param input)

* 修复biomek缺少的字段

* delete 's'

* Remove warnings

* Update biomek.py

* Biomek test

* Update biomek.py

* 新增transfer_biomek的msg

* New transfer_biomek

* Updated transfer_biomek

* 更新transfer_biomek的msg

* 更新transfer_biomek的msg

* 支持Biomek创建

* new action

* fix key name typo

* New parameter for biomek to run.

* Refine

* Update

* new actions

* new actions

* 1

* registry

* fix biomek startup
add action handles

* fix handles not as default entry

* biomek_test.py

biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json

* Update biomek.py

* biomek_test.py

* fix liquid_handler.biomek handles

* host node新增resource add时间统计
create_resource新增handle
bump version to 0.9.2

* 修正物料上传时间
改用biomek_test
增加ResultInfoEncoder
支持返回结果上传

* 正确发送return_info结果

* 同步执行状态信息

* 取消raiseValueError提示

* Update biomek_test.py

* 0608 DONE

* 同步了Biomek.py 现在应可用

* biomek switch back to non-test

* temp disable initialize resource

* Refine biomek

* Refine copy issue

* Refine

---------

Co-authored-by: Junhan Chang <changjh@pku.edu.cn>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>
This commit is contained in:
Xuwznln
2025-06-09 16:57:42 +08:00
committed by GitHub
parent 3470a1cb69
commit 729a0fcf0c
74 changed files with 16032 additions and 131 deletions
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151
unilabos/ros/nodes/base_device_node.py
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@@ -1,5 +1,4 @@
import copy
import functools
import json
import threading
import time
@@ -20,16 +19,29 @@ from rclpy.service import Service
from unilabos_msgs.action import SendCmd
from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response
from unilabos.resources.graphio import convert_resources_to_type, convert_resources_from_type, resource_ulab_to_plr, \
initialize_resources, list_to_nested_dict, dict_to_tree, resource_plr_to_ulab, tree_to_list
from unilabos.resources.graphio import (
convert_resources_to_type,
convert_resources_from_type,
resource_ulab_to_plr,
initialize_resources,
dict_to_tree,
resource_plr_to_ulab,
tree_to_list,
)
from unilabos.ros.msgs.message_converter import (
convert_to_ros_msg,
convert_from_ros_msg,
convert_from_ros_msg_with_mapping,
convert_to_ros_msg_with_mapping, ros_action_to_json_schema,
convert_to_ros_msg_with_mapping,
)
from unilabos_msgs.srv import ResourceAdd, ResourceGet, ResourceDelete, ResourceUpdate, ResourceList, \
SerialCommand # type: ignore
from unilabos_msgs.srv import (
ResourceAdd,
ResourceGet,
ResourceDelete,
ResourceUpdate,
ResourceList,
SerialCommand,
) # type: ignore
from unilabos_msgs.msg import Resource # type: ignore
from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker
@@ -37,7 +49,7 @@ from unilabos.ros.x.rclpyx import get_event_loop
from unilabos.ros.utils.driver_creator import ProtocolNodeCreator, PyLabRobotCreator, DeviceClassCreator
from unilabos.utils.async_util import run_async_func
from unilabos.utils.log import info, debug, warning, error, critical, logger
from unilabos.utils.type_check import get_type_class, TypeEncoder
from unilabos.utils.type_check import get_type_class, TypeEncoder, serialize_result_info
T = TypeVar("T")
@@ -292,7 +304,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
self.create_ros_action_server(action_name, action_value_mapping)
# 创建线程池执行器
self._executor = ThreadPoolExecutor(max_workers=max(len(action_value_mappings), 1), thread_name_prefix=f"ROSDevice{self.device_id}")
self._executor = ThreadPoolExecutor(
max_workers=max(len(action_value_mappings), 1), thread_name_prefix=f"ROSDevice{self.device_id}"
)
# 创建资源管理客户端
self._resource_clients: Dict[str, Client] = {
@@ -334,7 +348,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
other_calling_param["slot"] = slot
# 本地拿到这个物料，可能需要先做初始化?
if isinstance(resources, list):
if len(resources) == 1 and isinstance(resources[0], list) and not initialize_full: # 取消，不存在的情况
if (
len(resources) == 1 and isinstance(resources[0], list) and not initialize_full
): # 取消，不存在的情况
# 预先initialize过，以整组的形式传入
request.resources = [convert_to_ros_msg(Resource, resource_) for resource_ in resources[0]]
elif initialize_full:
@@ -349,6 +365,20 @@ class BaseROS2DeviceNode(Node, Generic[T]):
response = rclient.call(request)
# 应该先add_resource了
res.response = "OK"
# 如果driver自己就有assign的方法，那就使用driver自己的assign方法
if hasattr(self.driver_instance, "create_resource"):
create_resource_func = getattr(self.driver_instance, "create_resource")
create_resource_func(
resource_tracker=self.resource_tracker,
resources=request.resources,
bind_parent_id=bind_parent_id,
bind_location=location,
liquid_input_slot=LIQUID_INPUT_SLOT,
liquid_type=ADD_LIQUID_TYPE,
liquid_volume=LIQUID_VOLUME,
slot_on_deck=slot,
)
return res
# 接下来该根据bind_parent_id进行assign了，目前只有plr可以进行assign，不然没有办法输入到物料系统中
resource = self.resource_tracker.figure_resource({"name": bind_parent_id})
# request.resources = [convert_to_ros_msg(Resource, resources)]
@@ -359,6 +389,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
from pylabrobot.resources import Coordinate
from pylabrobot.resources import OTDeck
from pylabrobot.resources import Plate
contain_model = not isinstance(resource, Deck)
if isinstance(resource, ResourcePLR):
# resources.list()
@@ -366,25 +397,38 @@ class BaseROS2DeviceNode(Node, Generic[T]):
plr_instance = resource_ulab_to_plr(resources_tree[0], contain_model)
if isinstance(plr_instance, Plate):
empty_liquid_info_in = [(None, 0)] * plr_instance.num_items
for liquid_type, liquid_volume, liquid_input_slot in zip(ADD_LIQUID_TYPE, LIQUID_VOLUME, LIQUID_INPUT_SLOT):
for liquid_type, liquid_volume, liquid_input_slot in zip(
ADD_LIQUID_TYPE, LIQUID_VOLUME, LIQUID_INPUT_SLOT
):
empty_liquid_info_in[liquid_input_slot] = (liquid_type, liquid_volume)
plr_instance.set_well_liquids(empty_liquid_info_in)
if isinstance(resource, OTDeck) and "slot" in other_calling_param:
resource.assign_child_at_slot(plr_instance, **other_calling_param)
else:
_discard_slot = other_calling_param.pop("slot", -1)
resource.assign_child_resource(plr_instance, Coordinate(location["x"], location["y"], location["z"]), **other_calling_param)
request2.resources = [convert_to_ros_msg(Resource, r) for r in tree_to_list([resource_plr_to_ulab(resource)])]
resource.assign_child_resource(
plr_instance,
Coordinate(location["x"], location["y"], location["z"]),
**other_calling_param,
)
request2.resources = [
convert_to_ros_msg(Resource, r) for r in tree_to_list([resource_plr_to_ulab(resource)])
]
rclient2.call(request2)
# 发送给ResourceMeshManager
action_client = ActionClient(
self, SendCmd, "/devices/resource_mesh_manager/add_resource_mesh", callback_group=self.callback_group
self,
SendCmd,
"/devices/resource_mesh_manager/add_resource_mesh",
callback_group=self.callback_group,
)
goal = SendCmd.Goal()
goal.command = json.dumps({
"resources": resources,
"bind_parent_id": bind_parent_id,
})
goal.command = json.dumps(
{
"resources": resources,
"bind_parent_id": bind_parent_id,
}
)
future = action_client.send_goal_async(goal, goal_uuid=uuid.uuid4())
def done_cb(*args):
@@ -401,10 +445,16 @@ class BaseROS2DeviceNode(Node, Generic[T]):
# noinspection PyTypeChecker
self._service_server: Dict[str, Service] = {
"query_host_name": self.create_service(
SerialCommand, f"/srv{self.namespace}/query_host_name", query_host_name_cb, callback_group=self.callback_group
SerialCommand,
f"/srv{self.namespace}/query_host_name",
query_host_name_cb,
callback_group=self.callback_group,
),
"append_resource": self.create_service(
SerialCommand, f"/srv{self.namespace}/append_resource", append_resource, callback_group=self.callback_group
SerialCommand,
f"/srv{self.namespace}/append_resource",
append_resource,
callback_group=self.callback_group,
),
}
@@ -433,6 +483,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
registered_devices[self.device_id] = device_info
from unilabos.config.config import BasicConfig
from unilabos.ros.nodes.presets.host_node import HostNode
if not BasicConfig.is_host_mode:
sclient = self.create_client(SerialCommand, "/node_info_update")
# 启动线程执行发送任务
@@ -440,7 +491,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
target=self.send_slave_node_info,
args=(sclient,),
daemon=True,
name=f"ROSDevice{self.device_id}_send_slave_node_info"
name=f"ROSDevice{self.device_id}_send_slave_node_info",
).start()
else:
host_node = HostNode.get_instance(0)
@@ -451,12 +502,18 @@ class BaseROS2DeviceNode(Node, Generic[T]):
sclient.wait_for_service()
request = SerialCommand.Request()
from unilabos.config.config import BasicConfig
request.command = json.dumps({
"SYNC_SLAVE_NODE_INFO": {
"machine_name": BasicConfig.machine_name,
"type": "slave",
"edge_device_id": self.device_id
}}, ensure_ascii=False, cls=TypeEncoder)
request.command = json.dumps(
{
"SYNC_SLAVE_NODE_INFO": {
"machine_name": BasicConfig.machine_name,
"type": "slave",
"edge_device_id": self.device_id,
}
},
ensure_ascii=False,
cls=TypeEncoder,
)
# 发送异步请求并等待结果
future = sclient.call_async(request)
@@ -529,6 +586,11 @@ class BaseROS2DeviceNode(Node, Generic[T]):
"""创建动作执行回调函数"""
async def execute_callback(goal_handle: ServerGoalHandle):
# 初始化结果信息变量
execution_error = ""
execution_success = False
action_return_value = None
self.lab_logger().info(f"执行动作: {action_name}")
goal = goal_handle.request
@@ -568,7 +630,11 @@ class BaseROS2DeviceNode(Node, Generic[T]):
current_resources.extend(response.resources)
else:
r = ResourceGet.Request()
r.id = action_kwargs[k]["id"] if v == "unilabos_msgs/Resource" else action_kwargs[k][0]["id"]
r.id = (
action_kwargs[k]["id"]
if v == "unilabos_msgs/Resource"
else action_kwargs[k][0]["id"]
)
r.with_children = True
response = await self._resource_clients["resource_get"].call_async(r)
current_resources.extend(response.resources)
@@ -591,7 +657,19 @@ class BaseROS2DeviceNode(Node, Generic[T]):
if asyncio.iscoroutinefunction(ACTION):
try:
self.lab_logger().info(f"异步执行动作 {ACTION}")
future = ROS2DeviceNode.run_async_func(ACTION, **action_kwargs)
future = ROS2DeviceNode.run_async_func(ACTION, trace_error=False, **action_kwargs)
def _handle_future_exception(fut):
nonlocal execution_error, execution_success, action_return_value
try:
action_return_value = fut.result()
execution_success = True
except Exception as e:
execution_error = traceback.format_exc()
error(f"异步任务 {ACTION.__name__} 报错了")
error(traceback.format_exc())
future.add_done_callback(_handle_future_exception)
except Exception as e:
self.lab_logger().error(f"创建异步任务失败: {traceback.format_exc()}")
raise e
@@ -600,9 +678,12 @@ class BaseROS2DeviceNode(Node, Generic[T]):
future = self._executor.submit(ACTION, **action_kwargs)
def _handle_future_exception(fut):
nonlocal execution_error, execution_success, action_return_value
try:
fut.result()
action_return_value = fut.result()
execution_success = True
except Exception as e:
execution_error = traceback.format_exc()
error(f"同步任务 {ACTION.__name__} 报错了")
error(traceback.format_exc())
@@ -693,6 +774,8 @@ class BaseROS2DeviceNode(Node, Generic[T]):
for attr_name in result_msg_types.keys():
if attr_name in ["success", "reached_goal"]:
setattr(result_msg, attr_name, True)
elif attr_name == "return_info":
setattr(result_msg, attr_name, serialize_result_info(execution_error, execution_success, action_return_value))
self.lab_logger().info(f"动作 {action_name} 完成并返回结果")
return result_msg
@@ -738,8 +821,8 @@ class ROS2DeviceNode:
return cls._loop
@classmethod
def run_async_func(cls, func, **kwargs):
return run_async_func(func, loop=cls._loop, **kwargs)
def run_async_func(cls, func, trace_error=True, **kwargs):
return run_async_func(func, loop=cls._loop, trace_error=trace_error, **kwargs)
@property
def driver_instance(self):
@@ -791,7 +874,11 @@ class ROS2DeviceNode:
self.resource_tracker = DeviceNodeResourceTracker()
# use_pylabrobot_creator 使用 cls的包路径检测
use_pylabrobot_creator = driver_class.__module__.startswith("pylabrobot") or driver_class.__name__ == "LiquidHandlerAbstract"
use_pylabrobot_creator = (
driver_class.__module__.startswith("pylabrobot")
or driver_class.__name__ == "LiquidHandlerAbstract"
or driver_class.__name__ == "LiquidHandlerBiomek"
)
# TODO: 要在创建之前预先请求服务器是否有当前id的物料，放到resource_tracker中，让pylabrobot进行创建
# 创建设备类实例