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Fix/resource UUID and doc fix (#109)

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* Fix ResourceTreeSet load error

* Raise error when using unsupported type to create ResourceTreeSet

* Fix children key error

* Fix children key error

* Fix workstation resource not tracking

* Fix workstation deck & children resource dupe

* Fix workstation deck & children resource dupe

* Fix multiple resource error

* Fix resource tree update

* Fix resource tree update

* Force confirm uuid

* Tip more error log

* Refactor Bioyond workstation and experiment workflow (#105)

Refactored the Bioyond workstation classes to improve parameter handling and workflow management. Updated experiment.py to use BioyondReactionStation with deck and material mappings, and enhanced workflow step parameter mapping and execution logic. Adjusted JSON experiment configs, improved workflow sequence handling, and added UUID assignment to PLR materials. Removed unused station_config and material cache logic, and added detailed docstrings and debug output for workflow methods.

* Fix resource get.
Fix resource parent not found.
Mapping uuid for all resources.

* mount parent uuid

* Add logging configuration based on BasicConfig in main function

* fix workstation node error

* fix workstation node error

* Update boot example

* temp fix for resource get

* temp fix for resource get

* provide error info when cant find plr type

* pack repo info

* fix to plr type error

* fix to plr type error

* Update regular container method

* support no size init

* fix comprehensive_station.json

* fix comprehensive_station.json

* fix type conversion

* fix state loading for regular container

* Update deploy-docs.yml

* Update deploy-docs.yml

---------

Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>
This commit is contained in:
Xuwznln
2025-10-16 17:26:07 +08:00
committed by GitHub
parent c85c49817d
commit 7c440d10ab
24 changed files with 1072 additions and 447 deletions
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79
unilabos/ros/nodes/resource_tracker.py
View File

@@ -1,3 +1,4 @@
import traceback
import uuid
from pydantic import BaseModel, field_serializer, field_validator
from pydantic import Field
@@ -140,7 +141,7 @@ class ResourceDictInstance(object):
def get_nested_dict(self) -> Dict[str, Any]:
"""获取资源实例的嵌套字典表示"""
res_dict = self.res_content.model_dump(by_alias=True)
res_dict["children"] = {child.res_content.name: child.get_nested_dict() for child in self.children}
res_dict["children"] = {child.res_content.id: child.get_nested_dict() for child in self.children}
res_dict["parent"] = self.res_content.parent_instance_name
res_dict["position"] = self.res_content.position.position.model_dump()
return res_dict
@@ -213,7 +214,7 @@ class ResourceTreeInstance(object):
if node.res_content.uuid:
known_uuids.add(node.res_content.uuid)
else:
print(f"警告: 资源 {node.res_content.id} 没有uuid")
logger.warning(f"警告: 资源 {node.res_content.id} 没有uuid")
# 验证并递归处理子节点
for child in node.children:
@@ -289,8 +290,6 @@ class ResourceTreeSet(object):
elif isinstance(resource_list[0], ResourceTreeInstance):
# 已经是ResourceTree列表
self.trees = cast(List[ResourceTreeInstance], resource_list)
elif isinstance(resource_list[0], list):
pass
else:
raise TypeError(
f"不支持的类型: {type(resource_list[0])}。"
@@ -307,10 +306,7 @@ class ResourceTreeSet(object):
replace_info = {
"plate": "plate",
"well": "well",
"tip_spot": "container",
"trash": "container",
"deck": "deck",
"tip_rack": "container",
}
if source in replace_info:
return replace_info[source]
@@ -320,7 +316,12 @@ class ResourceTreeSet(object):
def build_uuid_mapping(res: "PLRResource", uuid_list: list):
"""递归构建uuid映射字典"""
uuid_list.append(getattr(res, "unilabos_uuid", ""))
uid = getattr(res, "unilabos_uuid", "")
if not uid:
uid = str(uuid.uuid4())
res.unilabos_uuid = uid
logger.warning(f"{res}没有uuid，请设置后再传入，默认填充{uid}！\n{traceback.format_exc()}")
uuid_list.append(uid)
for child in res.children:
build_uuid_mapping(child, uuid_list)
@@ -384,7 +385,7 @@ class ResourceTreeSet(object):
import inspect
# 类型映射
TYPE_MAP = {"plate": "plate", "well": "well", "container": "tip_spot", "deck": "deck", "tip_rack": "tip_rack"}
TYPE_MAP = {"plate": "Plate", "well": "Well", "deck": "Deck"}
def collect_node_data(node: ResourceDictInstance, name_to_uuid: dict, all_states: dict):
"""一次遍历收集 name_to_uuid 和 all_states"""
@@ -396,13 +397,13 @@ class ResourceTreeSet(object):
def node_to_plr_dict(node: ResourceDictInstance, has_model: bool):
"""转换节点为 PLR 字典格式"""
res = node.res_content
plr_type = TYPE_MAP.get(res.type, "tip_spot")
plr_type = TYPE_MAP.get(res.type, res.type)
if res.type not in TYPE_MAP:
logger.warning(f"未知类型 {res.type}，使用默认类型 tip_spot")
logger.warning(f"未知类型 {res.type}")
d = {
"name": res.name,
"type": plr_type,
"type": res.config.get("type", plr_type),
"size_x": res.config.get("size_x", 0),
"size_y": res.config.get("size_y", 0),
"size_z": res.config.get("size_z", 0),
@@ -413,7 +414,7 @@ class ResourceTreeSet(object):
"type": "Coordinate",
},
"rotation": {"x": 0, "y": 0, "z": 0, "type": "Rotation"},
"category": plr_type,
"category": res.config.get("category", plr_type),
"children": [node_to_plr_dict(child, has_model) for child in node.children],
"parent_name": res.parent_instance_name,
**res.config,
@@ -435,7 +436,7 @@ class ResourceTreeSet(object):
try:
sub_cls = find_subclass(plr_dict["type"], PLRResource)
if sub_cls is None:
raise ValueError(f"无法找到类型 {plr_dict['type']} 对应的 PLR 资源类")
raise ValueError(f"无法找到类型 {plr_dict['type']} 对应的 PLR 资源类。原始信息：{tree.root_node.res_content}")
spec = inspect.signature(sub_cls)
if "category" not in spec.parameters:
plr_dict.pop("category", None)
@@ -715,16 +716,9 @@ class ResourceTreeSet(object):
Returns:
ResourceTreeSet: 反序列化后的资源树集合
"""
# 将每个字典转换为 ResourceInstanceDict
# FIXME: 需要重新确定parent关系
nested_lists = []
for tree_data in data:
flatten_instances = [
ResourceDictInstance.get_resource_instance_from_dict(node_dict) for node_dict in tree_data
]
nested_lists.append(flatten_instances)
# 使用现有的构造函数创建 ResourceTreeSet
nested_lists.extend(ResourceTreeSet.from_raw_list(tree_data).trees)
return cls(nested_lists)
@@ -777,7 +771,8 @@ class DeviceNodeResourceTracker(object):
else:
return getattr(resource, uuid_attr, None)
def _set_resource_uuid(self, resource, new_uuid: str):
@classmethod
def set_resource_uuid(cls, resource, new_uuid: str):
"""
设置资源的 uuid，统一处理 dict 和 instance 两种类型
@@ -830,7 +825,7 @@ class DeviceNodeResourceTracker(object):
resource_name = self._get_resource_attr(res, "name")
if resource_name and resource_name in name_to_uuid_map:
new_uuid = name_to_uuid_map[resource_name]
self._set_resource_uuid(res, new_uuid)
self.set_resource_uuid(res, new_uuid)
self.uuid_to_resources[new_uuid] = res
logger.debug(f"设置资源UUID: {resource_name} -> {new_uuid}")
return 1
@@ -842,7 +837,7 @@ class DeviceNodeResourceTracker(object):
"""
递归遍历资源树，更新所有节点的uuid
Args:
Args:0
resource: 资源对象（可以是dict或实例）
uuid_map: uuid映射字典，{old_uuid: new_uuid}
@@ -852,17 +847,18 @@ class DeviceNodeResourceTracker(object):
def process(res):
current_uuid = self._get_resource_attr(res, "uuid", "unilabos_uuid")
replaced = 0
if current_uuid and current_uuid in uuid_map:
new_uuid = uuid_map[current_uuid]
if current_uuid != new_uuid:
self._set_resource_uuid(res, new_uuid)
self.set_resource_uuid(res, new_uuid)
# 更新uuid_to_resources映射
if current_uuid in self.uuid_to_resources:
self.uuid_to_resources.pop(current_uuid)
self.uuid_to_resources[new_uuid] = res
logger.debug(f"更新uuid: {current_uuid} -> {new_uuid}")
return 1
return 0
replaced = 1
return replaced
return self._traverse_and_process(resource, process)
@@ -877,8 +873,9 @@ class DeviceNodeResourceTracker(object):
def process(res):
current_uuid = self._get_resource_attr(res, "uuid", "unilabos_uuid")
if current_uuid:
old = self.uuid_to_resources.get(current_uuid)
self.uuid_to_resources[current_uuid] = res
logger.debug(f"收集资源UUID映射: {current_uuid} -> {res}")
logger.debug(f"收集资源UUID映射: {current_uuid} -> {res} {'' if old is None else f'(覆盖旧值: {old})'}")
return 0
self._traverse_and_process(resource, process)
@@ -913,9 +910,23 @@ class DeviceNodeResourceTracker(object):
Args:
resource: 资源对象（可以是dict或实例）
"""
root_uuids = {}
for r in self.resources:
res_uuid = r.get("uuid") if isinstance(r, dict) else getattr(r, "unilabos_uuid", None)
if res_uuid:
root_uuids[res_uuid] = r
if id(r) == id(resource):
return
# 这里只做uuid的根节点比较
if isinstance(resource, dict):
res_uuid = resource.get("uuid")
else:
res_uuid = getattr(resource, "unilabos_uuid", None)
if res_uuid in root_uuids:
old_res = root_uuids[res_uuid]
# self.remove_resource(old_res)
logger.warning(f"资源{resource}已存在，旧资源: {old_res}")
self.resources.append(resource)
# 递归收集uuid映射
self._collect_uuid_mapping(resource)
@@ -1046,13 +1057,19 @@ class DeviceNodeResourceTracker(object):
) -> List[Tuple[Any, Any]]:
res_list = []
# print(resource, target_resource_cls_type, identifier_key, compare_value)
children = getattr(resource, "children", [])
children = []
if not isinstance(resource, dict):
children = getattr(resource, "children", [])
else:
children = resource.get("children")
if children is not None:
children = list(children.values()) if isinstance(children, dict) else children
for child in children:
res_list.extend(
self.loop_find_resource(child, target_resource_cls_type, identifier_key, compare_value, resource)
)
if issubclass(type(resource), target_resource_cls_type):
if target_resource_cls_type == dict:
if type(resource) == dict:
# 对于字典类型，直接检查 identifier_key
if identifier_key in resource:
if resource[identifier_key] == compare_value: