workflow upload & set liquid fix & add set liquid with plate

fix upload workflow json

save class name when deserialize & protocol execute test

Support root node change pos

add unilabos_class

gather query

.conda/base/recipe.yaml

@@ -41,7 +41,6 @@ requirements:
   - networkx
   - typing_extensions
   - websockets
-  - opentrons_shared_data
   - pint
   - fastapi
   - jinja2

docs/user_guide/best_practice.md

@@ -439,6 +439,9 @@ unilab --ak your_ak --sk your_sk -g test/experiments/mock_devices/mock_all.json
 1. 访问 Web 界面，进入"仪器耗材"模块
 2. 在"仪器设备"区域找到并添加上述设备
 3. 在"物料耗材"区域找到并添加容器
+4. 在workstation中配置protocol_type包含PumpTransferProtocol
+
+![添加Protocol类型](image/add_protocol.png)
 
 ![物料列表](image/material.png)
 

tests/workflow/test.json

@@ -0,0 +1,213 @@
+{
+  "workflow": [
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines",
+        "targets": "Liquid_1",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines",
+        "targets": "Liquid_2",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines",
+        "targets": "Liquid_3",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines_2",
+        "targets": "Liquid_4",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines_2",
+        "targets": "Liquid_5",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines_2",
+        "targets": "Liquid_6",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines_3",
+        "targets": "dest_set",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines_3",
+        "targets": "dest_set_2",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "cell_lines_3",
+        "targets": "dest_set_3",
+        "asp_vol": 100.0,
+        "dis_vol": 74.75,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 95.5
+      }
+    }
+  ],
+  "reagent": {
+    "Liquid_1": {
+      "slot": 1,
+      "well": [
+        "A4",
+        "A7",
+        "A10"
+      ],
+      "labware": "rep 1"
+    },
+    "Liquid_4": {
+      "slot": 1,
+      "well": [
+        "A4",
+        "A7",
+        "A10"
+      ],
+      "labware": "rep 1"
+    },
+    "dest_set": {
+      "slot": 1,
+      "well": [
+        "A4",
+        "A7",
+        "A10"
+      ],
+      "labware": "rep 1"
+    },
+    "Liquid_2": {
+      "slot": 2,
+      "well": [
+        "A3",
+        "A5",
+        "A8"
+      ],
+      "labware": "rep 2"
+    },
+    "Liquid_5": {
+      "slot": 2,
+      "well": [
+        "A3",
+        "A5",
+        "A8"
+      ],
+      "labware": "rep 2"
+    },
+    "dest_set_2": {
+      "slot": 2,
+      "well": [
+        "A3",
+        "A5",
+        "A8"
+      ],
+      "labware": "rep 2"
+    },
+    "Liquid_3": {
+      "slot": 3,
+      "well": [
+        "A4",
+        "A6",
+        "A10"
+      ],
+      "labware": "rep 3"
+    },
+    "Liquid_6": {
+      "slot": 3,
+      "well": [
+        "A4",
+        "A6",
+        "A10"
+      ],
+      "labware": "rep 3"
+    },
+    "dest_set_3": {
+      "slot": 3,
+      "well": [
+        "A4",
+        "A6",
+        "A10"
+      ],
+      "labware": "rep 3"
+    },
+    "cell_lines": {
+      "slot": 4,
+      "well": [
+        "A1",
+        "A3",
+        "A5"
+      ],
+      "labware": "DRUG + YOYO-MEDIA"
+    },
+    "cell_lines_2": {
+      "slot": 4,
+      "well": [
+        "A1",
+        "A3",
+        "A5"
+      ],
+      "labware": "DRUG + YOYO-MEDIA"
+    },
+    "cell_lines_3": {
+      "slot": 4,
+      "well": [
+        "A1",
+        "A3",
+        "A5"
+      ],
+      "labware": "DRUG + YOYO-MEDIA"
+    }
+  }
+}

unilabos/app/web/client.py

@@ -74,7 +74,8 @@ class HTTPClient:
             Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid}
         """
         with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_add.json"), "w", encoding="utf-8") as f:
-            f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4))
+            payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}
+            f.write(json.dumps(payload, indent=4))
         # 从序列化数据中提取所有节点的UUID（保存旧UUID）
         old_uuids = {n.res_content.uuid: n for n in resources.all_nodes}
         if not self.initialized or first_add:
@@ -333,6 +334,65 @@ class HTTPClient:
                 logger.error(f"响应内容: {response.text}")
         return None
 
+    def workflow_import(
+        self,
+        name: str,
+        workflow_uuid: str,
+        workflow_name: str,
+        nodes: List[Dict[str, Any]],
+        edges: List[Dict[str, Any]],
+        tags: Optional[List[str]] = None,
+        published: bool = False,
+    ) -> Dict[str, Any]:
+        """
+        导入工作流到服务器
+
+        Args:
+            name: 工作流名称（顶层）
+            workflow_uuid: 工作流UUID
+            workflow_name: 工作流名称（data内部）
+            nodes: 工作流节点列表
+            edges: 工作流边列表
+            tags: 工作流标签列表，默认为空列表
+            published: 是否发布工作流，默认为False
+
+        Returns:
+            Dict: API响应数据，包含 code 和 data (uuid, name)
+        """
+        payload = {
+            "name": name,
+            "data": {
+                "workflow_uuid": workflow_uuid,
+                "workflow_name": workflow_name,
+                "nodes": nodes,
+                "edges": edges,
+                "tags": tags if tags is not None else [],
+                "published": published,
+            },
+        }
+        # 保存请求到文件
+        with open(os.path.join(BasicConfig.working_dir, "req_workflow_upload.json"), "w", encoding="utf-8") as f:
+            f.write(json.dumps(payload, indent=4, ensure_ascii=False))
+
+        response = requests.post(
+            f"{self.remote_addr}/lab/workflow/owner/import",
+            json=payload,
+            headers={"Authorization": f"Lab {self.auth}"},
+            timeout=60,
+        )
+        # 保存响应到文件
+        with open(os.path.join(BasicConfig.working_dir, "res_workflow_upload.json"), "w", encoding="utf-8") as f:
+            f.write(f"{response.status_code}" + "\n" + response.text)
+
+        if response.status_code == 200:
+            res = response.json()
+            if "code" in res and res["code"] != 0:
+                logger.error(f"导入工作流失败: {response.text}")
+            return res
+        else:
+            logger.error(f"导入工作流失败: {response.status_code}, {response.text}")
+            return {"code": response.status_code, "message": response.text}
+
 
 # 创建默认客户端实例
 http_client = HTTPClient()

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -30,9 +30,30 @@ from pylabrobot.liquid_handling.standard import (
     ResourceMove,
     ResourceDrop,
 )
-from pylabrobot.resources import ResourceHolder, ResourceStack, Tip, Deck, Plate, Well, TipRack, Resource, Container, Coordinate, TipSpot, Trash, PlateAdapter, TubeRack
+from pylabrobot.resources import (
+    ResourceHolder,
+    ResourceStack,
+    Tip,
+    Deck,
+    Plate,
+    Well,
+    TipRack,
+    Resource,
+    Container,
+    Coordinate,
+    TipSpot,
+    Trash,
+    PlateAdapter,
+    TubeRack,
+)
 
-from unilabos.devices.liquid_handling.liquid_handler_abstract import LiquidHandlerAbstract, SimpleReturn
+from unilabos.devices.liquid_handling.liquid_handler_abstract import (
+    LiquidHandlerAbstract,
+    SimpleReturn,
+    SetLiquidReturn,
+    SetLiquidFromPlateReturn,
+)
+from unilabos.registry.placeholder_type import ResourceSlot
 from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
 
 
@@ -80,6 +101,7 @@ class PRCXI9300Deck(Deck):
         self.slots[slot - 1] = resource
         super().assign_child_resource(resource, location=self.slot_locations[slot - 1])
 
+
 class PRCXI9300Container(Plate):
     """PRCXI 9300 的专用 Container 类，继承自 Plate，用于槽位定位和未知模块。
 
@@ -108,20 +130,29 @@ class PRCXI9300Container(Plate):
     def serialize_state(self) -> Dict[str, Dict[str, Any]]:
         data = super().serialize_state()
         data.update(self._unilabos_state)
-        return data   
+        return data
+
+
 class PRCXI9300Plate(Plate):
-    """ 
+    """
     专用孔板类：
     1. 继承自 PLR 原生 Plate，保留所有物理特性。
     2. 增加 material_info 参数，用于在初始化时直接绑定 Unilab UUID。
     """
-    def __init__(self, name: str, size_x: float, size_y: float, size_z: float, 
-                 category: str = "plate", 
-                 ordered_items: collections.OrderedDict = None, 
-                 ordering: Optional[collections.OrderedDict] = None,
-                 model: Optional[str] = None, 
-                 material_info: Optional[Dict[str, Any]] = None, 
-                 **kwargs):
+
+    def __init__(
+        self,
+        name: str,
+        size_x: float,
+        size_y: float,
+        size_z: float,
+        category: str = "plate",
+        ordered_items: collections.OrderedDict = None,
+        ordering: Optional[collections.OrderedDict] = None,
+        model: Optional[str] = None,
+        material_info: Optional[Dict[str, Any]] = None,
+        **kwargs,
+    ):
         # 如果 ordered_items 不为 None，直接使用
         if ordered_items is not None:
             items = ordered_items
@@ -142,40 +173,34 @@ class PRCXI9300Plate(Plate):
         else:
             items = None
             ordering_param = None
-        
+
         # 根据情况传递不同的参数
         if items is not None:
-            super().__init__(name, size_x, size_y, size_z, 
-                             ordered_items=items,
-                             category=category,
-                             model=model, **kwargs)
+            super().__init__(
+                name, size_x, size_y, size_z, ordered_items=items, category=category, model=model, **kwargs
+            )
         elif ordering_param is not None:
             # 传递 ordering 参数，让 Plate 自己创建 Well 对象
-            super().__init__(name, size_x, size_y, size_z, 
-                             ordering=ordering_param,
-                             category=category,
-                             model=model, **kwargs)
+            super().__init__(
+                name, size_x, size_y, size_z, ordering=ordering_param, category=category, model=model, **kwargs
+            )
         else:
-            super().__init__(name, size_x, size_y, size_z, 
-                             category=category,
-                             model=model, **kwargs)
-        
+            super().__init__(name, size_x, size_y, size_z, category=category, model=model, **kwargs)
+
         self._unilabos_state = {}
         if material_info:
             self._unilabos_state["Material"] = material_info
-        
 
     def load_state(self, state: Dict[str, Any]) -> None:
         super().load_state(state)
         self._unilabos_state = state
 
-
     def serialize_state(self) -> Dict[str, Dict[str, Any]]:
         try:
             data = super().serialize_state()
         except AttributeError:
             data = {}
-        if hasattr(self, '_unilabos_state') and self._unilabos_state:
+        if hasattr(self, "_unilabos_state") and self._unilabos_state:
             safe_state = {}
             for k, v in self._unilabos_state.items():
                 # 如果是 Material 字典，深入检查
@@ -188,23 +213,32 @@ class PRCXI9300Plate(Plate):
                         else:
                             # 打印日志提醒（可选）
                             # print(f"Warning: Removing non-serializable key {mk} from {self.name}")
-                            pass 
+                            pass
                     safe_state[k] = safe_material
                 # 其他顶层属性也进行类型检查
                 elif isinstance(v, (str, int, float, bool, list, dict, type(None))):
                     safe_state[k] = v
-            
+
             data.update(safe_state)
-        return data            # 其他顶层属性也进行类型检查
+        return data  # 其他顶层属性也进行类型检查
+
+
 class PRCXI9300TipRack(TipRack):
-    """ 专用吸头盒类 """
-    def __init__(self, name: str, size_x: float, size_y: float, size_z: float, 
-                 category: str = "tip_rack", 
-                 ordered_items: collections.OrderedDict = None, 
-                 ordering: Optional[collections.OrderedDict] = None,
-                 model: Optional[str] = None,
-                 material_info: Optional[Dict[str, Any]] = None,
-                 **kwargs):
+    """专用吸头盒类"""
+
+    def __init__(
+        self,
+        name: str,
+        size_x: float,
+        size_y: float,
+        size_z: float,
+        category: str = "tip_rack",
+        ordered_items: collections.OrderedDict = None,
+        ordering: Optional[collections.OrderedDict] = None,
+        model: Optional[str] = None,
+        material_info: Optional[Dict[str, Any]] = None,
+        **kwargs,
+    ):
         # 如果 ordered_items 不为 None，直接使用
         if ordered_items is not None:
             items = ordered_items
@@ -225,27 +259,23 @@ class PRCXI9300TipRack(TipRack):
         else:
             items = None
             ordering_param = None
-        
+
         # 根据情况传递不同的参数
         if items is not None:
-            super().__init__(name, size_x, size_y, size_z, 
-                             ordered_items=items,
-                             category=category, 
-                             model=model, **kwargs)
+            super().__init__(
+                name, size_x, size_y, size_z, ordered_items=items, category=category, model=model, **kwargs
+            )
         elif ordering_param is not None:
             # 传递 ordering 参数，让 TipRack 自己创建 Tip 对象
-            super().__init__(name, size_x, size_y, size_z, 
-                             ordering=ordering_param,
-                             category=category, 
-                             model=model, **kwargs)
+            super().__init__(
+                name, size_x, size_y, size_z, ordering=ordering_param, category=category, model=model, **kwargs
+            )
         else:
-            super().__init__(name, size_x, size_y, size_z, 
-                             category=category, 
-                             model=model, **kwargs)
+            super().__init__(name, size_x, size_y, size_z, category=category, model=model, **kwargs)
         self._unilabos_state = {}
         if material_info:
             self._unilabos_state["Material"] = material_info
-            
+
     def load_state(self, state: Dict[str, Any]) -> None:
         super().load_state(state)
         self._unilabos_state = state
@@ -255,7 +285,7 @@ class PRCXI9300TipRack(TipRack):
             data = super().serialize_state()
         except AttributeError:
             data = {}
-        if hasattr(self, '_unilabos_state') and self._unilabos_state:
+        if hasattr(self, "_unilabos_state") and self._unilabos_state:
             safe_state = {}
             for k, v in self._unilabos_state.items():
                 # 如果是 Material 字典，深入检查
@@ -268,26 +298,33 @@ class PRCXI9300TipRack(TipRack):
                         else:
                             # 打印日志提醒（可选）
                             # print(f"Warning: Removing non-serializable key {mk} from {self.name}")
-                            pass 
+                            pass
                     safe_state[k] = safe_material
                 # 其他顶层属性也进行类型检查
                 elif isinstance(v, (str, int, float, bool, list, dict, type(None))):
                     safe_state[k] = v
-            
+
             data.update(safe_state)
         return data
-    
+
+
 class PRCXI9300Trash(Trash):
     """PRCXI 9300 的专用 Trash 类，继承自 Trash。
 
     该类定义了 PRCXI 9300 的工作台布局和槽位信息。
     """
 
-    def __init__(self, name: str, size_x: float, size_y: float, size_z: float, 
-                 category: str = "trash", 
-                 material_info: Optional[Dict[str, Any]] = None,
-                 **kwargs):
-        
+    def __init__(
+        self,
+        name: str,
+        size_x: float,
+        size_y: float,
+        size_z: float,
+        category: str = "trash",
+        material_info: Optional[Dict[str, Any]] = None,
+        **kwargs,
+    ):
+
         if name != "trash":
             print(f"Warning: PRCXI9300Trash usually expects name='trash' for backend logic, but got '{name}'.")
         super().__init__(name, size_x, size_y, size_z, **kwargs)
@@ -306,7 +343,7 @@ class PRCXI9300Trash(Trash):
             data = super().serialize_state()
         except AttributeError:
             data = {}
-        if hasattr(self, '_unilabos_state') and self._unilabos_state:
+        if hasattr(self, "_unilabos_state") and self._unilabos_state:
             safe_state = {}
             for k, v in self._unilabos_state.items():
                 # 如果是 Material 字典，深入检查
@@ -319,29 +356,37 @@ class PRCXI9300Trash(Trash):
                         else:
                             # 打印日志提醒（可选）
                             # print(f"Warning: Removing non-serializable key {mk} from {self.name}")
-                            pass 
+                            pass
                     safe_state[k] = safe_material
                 # 其他顶层属性也进行类型检查
                 elif isinstance(v, (str, int, float, bool, list, dict, type(None))):
                     safe_state[k] = v
-            
+
             data.update(safe_state)
         return data
 
+
 class PRCXI9300TubeRack(TubeRack):
     """
     专用管架类：用于 EP 管架、试管架等。
     继承自 PLR 的 TubeRack，并支持注入 material_info (UUID)。
     """
-    def __init__(self, name: str, size_x: float, size_y: float, size_z: float, 
-                 category: str = "tube_rack", 
-                 items: Optional[Dict[str, Any]] = None,
-                 ordered_items: Optional[OrderedDict] = None,
-                 ordering: Optional[OrderedDict] = None,
-                 model: Optional[str] = None,
-                 material_info: Optional[Dict[str, Any]] = None, 
-                 **kwargs):
-        
+
+    def __init__(
+        self,
+        name: str,
+        size_x: float,
+        size_y: float,
+        size_z: float,
+        category: str = "tube_rack",
+        items: Optional[Dict[str, Any]] = None,
+        ordered_items: Optional[OrderedDict] = None,
+        ordering: Optional[OrderedDict] = None,
+        model: Optional[str] = None,
+        material_info: Optional[Dict[str, Any]] = None,
+        **kwargs,
+    ):
+
         # 如果 ordered_items 不为 None，直接使用
         if ordered_items is not None:
             items_to_pass = ordered_items
@@ -367,24 +412,16 @@ class PRCXI9300TubeRack(TubeRack):
         else:
             items_to_pass = None
             ordering_param = None
-        
+
         # 根据情况传递不同的参数
         if items_to_pass is not None:
-            super().__init__(name, size_x, size_y, size_z, 
-                             ordered_items=items_to_pass, 
-                             model=model, 
-                             **kwargs)
+            super().__init__(name, size_x, size_y, size_z, ordered_items=items_to_pass, model=model, **kwargs)
         elif ordering_param is not None:
             # 传递 ordering 参数，让 TubeRack 自己创建 Tube 对象
-            super().__init__(name, size_x, size_y, size_z, 
-                             ordering=ordering_param,
-                             model=model, 
-                             **kwargs)
+            super().__init__(name, size_x, size_y, size_z, ordering=ordering_param, model=model, **kwargs)
         else:
-            super().__init__(name, size_x, size_y, size_z, 
-                             model=model, 
-                             **kwargs)
-        
+            super().__init__(name, size_x, size_y, size_z, model=model, **kwargs)
+
         self._unilabos_state = {}
         if material_info:
             self._unilabos_state["Material"] = material_info
@@ -394,7 +431,7 @@ class PRCXI9300TubeRack(TubeRack):
             data = super().serialize_state()
         except AttributeError:
             data = {}
-        if hasattr(self, '_unilabos_state') and self._unilabos_state:
+        if hasattr(self, "_unilabos_state") and self._unilabos_state:
             safe_state = {}
             for k, v in self._unilabos_state.items():
                 # 如果是 Material 字典，深入检查
@@ -407,33 +444,41 @@ class PRCXI9300TubeRack(TubeRack):
                         else:
                             # 打印日志提醒（可选）
                             # print(f"Warning: Removing non-serializable key {mk} from {self.name}")
-                            pass 
+                            pass
                     safe_state[k] = safe_material
                 # 其他顶层属性也进行类型检查
                 elif isinstance(v, (str, int, float, bool, list, dict, type(None))):
                     safe_state[k] = v
-            
+
             data.update(safe_state)
         return data
 
+
 class PRCXI9300PlateAdapter(PlateAdapter):
     """
     专用板式适配器类：用于承载 Plate 的底座（如 PCR 适配器、磁吸架等）。
     支持注入 material_info (UUID)。
     """
-    def __init__(self, name: str, size_x: float, size_y: float, size_z: float, 
-                 category: str = "plate_adapter", 
-                 model: Optional[str] = None,
-                 material_info: Optional[Dict[str, Any]] = None, 
-                 # 参数给予默认值 (标准96孔板尺寸)
-                 adapter_hole_size_x: float = 127.76, 
-                 adapter_hole_size_y: float = 85.48, 
-                 adapter_hole_size_z: float = 10.0, # 假设凹槽深度或板子放置高度
-                 dx: Optional[float] = None,
-                 dy: Optional[float] = None,
-                 dz: float = 0.0, # 默认Z轴偏移
-                 **kwargs):
-        
+
+    def __init__(
+        self,
+        name: str,
+        size_x: float,
+        size_y: float,
+        size_z: float,
+        category: str = "plate_adapter",
+        model: Optional[str] = None,
+        material_info: Optional[Dict[str, Any]] = None,
+        # 参数给予默认值 (标准96孔板尺寸)
+        adapter_hole_size_x: float = 127.76,
+        adapter_hole_size_y: float = 85.48,
+        adapter_hole_size_z: float = 10.0,  # 假设凹槽深度或板子放置高度
+        dx: Optional[float] = None,
+        dy: Optional[float] = None,
+        dz: float = 0.0,  # 默认Z轴偏移
+        **kwargs,
+    ):
+
         # 自动居中计算：如果未指定 dx/dy，则根据适配器尺寸和孔尺寸计算居中位置
         if dx is None:
             dx = (size_x - adapter_hole_size_x) / 2
@@ -441,20 +486,20 @@ class PRCXI9300PlateAdapter(PlateAdapter):
             dy = (size_y - adapter_hole_size_y) / 2
 
         super().__init__(
-            name=name, 
-            size_x=size_x, 
-            size_y=size_y, 
-            size_z=size_z, 
+            name=name,
+            size_x=size_x,
+            size_y=size_y,
+            size_z=size_z,
             dx=dx,
             dy=dy,
             dz=dz,
             adapter_hole_size_x=adapter_hole_size_x,
             adapter_hole_size_y=adapter_hole_size_y,
             adapter_hole_size_z=adapter_hole_size_z,
-            model=model, 
-            **kwargs
+            model=model,
+            **kwargs,
         )
-        
+
         self._unilabos_state = {}
         if material_info:
             self._unilabos_state["Material"] = material_info
@@ -464,7 +509,7 @@ class PRCXI9300PlateAdapter(PlateAdapter):
             data = super().serialize_state()
         except AttributeError:
             data = {}
-        if hasattr(self, '_unilabos_state') and self._unilabos_state:
+        if hasattr(self, "_unilabos_state") and self._unilabos_state:
             safe_state = {}
             for k, v in self._unilabos_state.items():
                 # 如果是 Material 字典，深入检查
@@ -477,15 +522,16 @@ class PRCXI9300PlateAdapter(PlateAdapter):
                         else:
                             # 打印日志提醒（可选）
                             # print(f"Warning: Removing non-serializable key {mk} from {self.name}")
-                            pass 
+                            pass
                     safe_state[k] = safe_material
                 # 其他顶层属性也进行类型检查
                 elif isinstance(v, (str, int, float, bool, list, dict, type(None))):
                     safe_state[k] = v
-            
+
             data.update(safe_state)
         return data
 
+
 class PRCXI9300Handler(LiquidHandlerAbstract):
     support_touch_tip = False
 
@@ -518,7 +564,9 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
                 if "Material" in child.children[0]._unilabos_state:
                     number = int(child.name.replace("T", ""))
                     tablets_info.append(
-                        WorkTablets(Number=number, Code=f"T{number}", Material=child.children[0]._unilabos_state["Material"])
+                        WorkTablets(
+                            Number=number, Code=f"T{number}", Material=child.children[0]._unilabos_state["Material"]
+                        )
                     )
         if is_9320:
             print("当前设备是9320")
@@ -538,9 +586,14 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         super().post_init(ros_node)
         self._unilabos_backend.post_init(ros_node)
 
-    def set_liquid(self, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SimpleReturn:
+    def set_liquid(self, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SetLiquidReturn:
         return super().set_liquid(wells, liquid_names, volumes)
 
+    def set_liquid_from_plate(
+        self, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float]
+    ) -> SetLiquidFromPlateReturn:
+        return super().set_liquid_from_plate(plate, well_names, liquid_names, volumes)
+
     def set_group(self, group_name: str, wells: List[Well], volumes: List[float]):
         return super().set_group(group_name, wells, volumes)
 
@@ -799,7 +852,8 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         return await self._unilabos_backend.shaker_action(time, module_no, amplitude, is_wait)
 
     async def heater_action(self, temperature: float, time: int):
-        return await self._unilabos_backend.heater_action(temperature, time)  
+        return await self._unilabos_backend.heater_action(temperature, time)
+
     async def move_plate(
         self,
         plate: Plate,
@@ -822,10 +876,11 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
             drop_direction,
             pickup_direction,
             pickup_distance_from_top,
-            target_plate_number = to,
+            target_plate_number=to,
             **backend_kwargs,
         )
 
+
 class PRCXI9300Backend(LiquidHandlerBackend):
     """PRCXI 9300 的后端实现，继承自 LiquidHandlerBackend。
 
@@ -878,31 +933,28 @@ class PRCXI9300Backend(LiquidHandlerBackend):
         self.steps_todo_list.append(step)
         return step
 
-
     async def pick_up_resource(self, pickup: ResourcePickup, **backend_kwargs):
-        
-        resource=pickup.resource
-        offset=pickup.offset
-        pickup_distance_from_top=pickup.pickup_distance_from_top
-        direction=pickup.direction
+
+        resource = pickup.resource
+        offset = pickup.offset
+        pickup_distance_from_top = pickup.pickup_distance_from_top
+        direction = pickup.direction
 
         plate_number = int(resource.parent.name.replace("T", ""))
         is_whole_plate = True
         balance_height = 0
         step = self.api_client.clamp_jaw_pick_up(plate_number, is_whole_plate, balance_height)
-        
+
         self.steps_todo_list.append(step)
         return step
 
     async def drop_resource(self, drop: ResourceDrop, **backend_kwargs):
 
-
         plate_number = None
         target_plate_number = backend_kwargs.get("target_plate_number", None)
         if target_plate_number is not None:
             plate_number = int(target_plate_number.name.replace("T", ""))
 
-
         is_whole_plate = True
         balance_height = 0
         if plate_number is None:
@@ -911,7 +963,6 @@ class PRCXI9300Backend(LiquidHandlerBackend):
         self.steps_todo_list.append(step)
         return step
 
-
     async def heater_action(self, temperature: float, time: int):
         print(f"\n\nHeater action: temperature={temperature}, time={time}\n\n")
         # return await self.api_client.heater_action(temperature, time)
@@ -968,7 +1019,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
                 error_code = self.api_client.get_error_code()
                 if error_code:
                     print(f"PRCXI9300 error code detected: {error_code}")
-                
+
                 # 清除错误代码
                 self.api_client.clear_error_code()
                 print("PRCXI9300 error code cleared.")
@@ -976,11 +1027,11 @@ class PRCXI9300Backend(LiquidHandlerBackend):
                 # 执行重置
                 print("Starting PRCXI9300 reset...")
                 self.api_client.call("IAutomation", "Reset")
-                
+
                 # 检查重置状态并等待完成
                 while not self.is_reset_ok:
                     print("Waiting for PRCXI9300 to reset...")
-                    if hasattr(self, '_ros_node') and self._ros_node is not None:
+                    if hasattr(self, "_ros_node") and self._ros_node is not None:
                         await self._ros_node.sleep(1)
                     else:
                         await asyncio.sleep(1)
@@ -998,7 +1049,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
         """Pick up tips from the specified resource."""
         # INSERT_YOUR_CODE
         # Ensure use_channels is converted to a list of ints if it's an array
-        if hasattr(use_channels, 'tolist'):
+        if hasattr(use_channels, "tolist"):
             _use_channels = use_channels.tolist()
         else:
             _use_channels = list(use_channels) if use_channels is not None else None
@@ -1052,7 +1103,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
 
     async def drop_tips(self, ops: List[Drop], use_channels: List[int] = None):
         """Pick up tips from the specified resource."""
-        if hasattr(use_channels, 'tolist'):
+        if hasattr(use_channels, "tolist"):
             _use_channels = use_channels.tolist()
         else:
             _use_channels = list(use_channels) if use_channels is not None else None
@@ -1135,7 +1186,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
         none_keys: List[str] = [],
     ):
         """Mix liquid in the specified resources."""
-        
+
         plate_indexes = []
         for op in targets:
             deck = op.parent.parent.parent
@@ -1178,7 +1229,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
 
     async def aspirate(self, ops: List[SingleChannelAspiration], use_channels: List[int] = None):
         """Aspirate liquid from the specified resources."""
-        if hasattr(use_channels, 'tolist'):
+        if hasattr(use_channels, "tolist"):
             _use_channels = use_channels.tolist()
         else:
             _use_channels = list(use_channels) if use_channels is not None else None
@@ -1235,7 +1286,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
 
     async def dispense(self, ops: List[SingleChannelDispense], use_channels: List[int] = None):
         """Dispense liquid into the specified resources."""
-        if hasattr(use_channels, 'tolist'):
+        if hasattr(use_channels, "tolist"):
             _use_channels = use_channels.tolist()
         else:
             _use_channels = list(use_channels) if use_channels is not None else None
@@ -1416,7 +1467,6 @@ class PRCXI9300Api:
                 time.sleep(1)
         return success
 
-
     def call(self, service: str, method: str, params: Optional[list] = None) -> Any:
         payload = json.dumps(
             {"ServiceName": service, "MethodName": method, "Paramters": params or []}, separators=(",", ":")
@@ -1543,7 +1593,7 @@ class PRCXI9300Api:
         assist_fun5: str = "",
         liquid_method: str = "NormalDispense",
         axis: str = "Left",
-        ) -> Dict[str, Any]:
+    ) -> Dict[str, Any]:
         return {
             "StepAxis": axis,
             "Function": "Imbibing",
@@ -1621,7 +1671,7 @@ class PRCXI9300Api:
         assist_fun5: str = "",
         liquid_method: str = "NormalDispense",
         axis: str = "Left",
-        ) -> Dict[str, Any]:
+    ) -> Dict[str, Any]:
         return {
             "StepAxis": axis,
             "Function": "Blending",
@@ -1681,11 +1731,11 @@ class PRCXI9300Api:
             "LiquidDispensingMethod": liquid_method,
         }
 
-    def clamp_jaw_pick_up(self,
+    def clamp_jaw_pick_up(
+        self,
         plate_no: int,
         is_whole_plate: bool,
         balance_height: int,
-
     ) -> Dict[str, Any]:
         return {
             "StepAxis": "ClampingJaw",
@@ -1695,7 +1745,7 @@ class PRCXI9300Api:
             "HoleRow": 1,
             "HoleCol": 1,
             "BalanceHeight": balance_height,
-            "PlateOrHoleNum": f"T{plate_no}"
+            "PlateOrHoleNum": f"T{plate_no}",
         }
 
     def clamp_jaw_drop(
@@ -1703,7 +1753,6 @@ class PRCXI9300Api:
         plate_no: int,
         is_whole_plate: bool,
         balance_height: int,
-
     ) -> Dict[str, Any]:
         return {
             "StepAxis": "ClampingJaw",
@@ -1713,7 +1762,7 @@ class PRCXI9300Api:
             "HoleRow": 1,
             "HoleCol": 1,
             "BalanceHeight": balance_height,
-            "PlateOrHoleNum": f"T{plate_no}"
+            "PlateOrHoleNum": f"T{plate_no}",
         }
 
     def shaker_action(self, time: int, module_no: int, amplitude: int, is_wait: bool):
@@ -1726,6 +1775,7 @@ class PRCXI9300Api:
             "AssistFun4": is_wait,
         }
 
+
 class DefaultLayout:
 
     def __init__(self, product_name: str = "PRCXI9300"):
@@ -2104,7 +2154,9 @@ if __name__ == "__main__":
             size_y=50,
             size_z=10,
             category="tip_rack",
-            ordered_items=collections.OrderedDict({k: f"{child_prefix}_{k}" for k, v in tip_racks["ordering"].items()}),
+            ordered_items=collections.OrderedDict(
+                {k: f"{child_prefix}_{k}" for k, v in tip_racks["ordering"].items()}
+            ),
         )
         tip_rack_serialized = tip_rack.serialize()
         tip_rack_serialized["parent_name"] = deck.name
@@ -2299,43 +2351,37 @@ if __name__ == "__main__":
 
     A = tree_to_list([resource_plr_to_ulab(deck)])
     with open("deck.json", "w", encoding="utf-8") as f:
-        A.insert(0, {
-            "id": "PRCXI",
-            "name": "PRCXI",
-            "parent": None,
-            "type": "device",
-            "class": "liquid_handler.prcxi",
-            "position": {
-                "x": 0,
-                "y": 0,
-                "z": 0
-            },
-            "config": {
-                "deck": {
-                    "_resource_child_name": "PRCXI_Deck",
-                    "_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck"
+        A.insert(
+            0,
+            {
+                "id": "PRCXI",
+                "name": "PRCXI",
+                "parent": None,
+                "type": "device",
+                "class": "liquid_handler.prcxi",
+                "position": {"x": 0, "y": 0, "z": 0},
+                "config": {
+                    "deck": {
+                        "_resource_child_name": "PRCXI_Deck",
+                        "_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck",
+                    },
+                    "host": "192.168.0.121",
+                    "port": 9999,
+                    "timeout": 10.0,
+                    "axis": "Right",
+                    "channel_num": 1,
+                    "setup": False,
+                    "debug": True,
+                    "simulator": True,
+                    "matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb",
+                    "is_9320": True,
                 },
-                "host": "192.168.0.121",
-                "port": 9999,
-                "timeout": 10.0,
-                "axis": "Right",
-                "channel_num": 1,
-                "setup": False,
-                "debug": True,
-                "simulator": True,
-                "matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb",
-                "is_9320": True
+                "data": {},
+                "children": ["PRCXI_Deck"],
             },
-            "data": {},
-            "children": [
-                "PRCXI_Deck"
-            ]
-        })
+        )
         A[1]["parent"] = "PRCXI"
-        json.dump({
-            "nodes": A,
-            "links": []
-        }, f, indent=4, ensure_ascii=False)
+        json.dump({"nodes": A, "links": []}, f, indent=4, ensure_ascii=False)
 
     handler = PRCXI9300Handler(
         deck=deck,
@@ -2377,7 +2423,6 @@ if __name__ == "__main__":
     time.sleep(5)
     os._exit(0)
 
-
     prcxi_api = PRCXI9300Api(host="192.168.0.121", port=9999)
     prcxi_api.list_matrices()
     prcxi_api.get_all_materials()

unilabos/registry/devices/liquid_handler.yaml

@@ -9284,7 +9284,13 @@ liquid_handler.prcxi:
             data_source: handle
             data_type: resource
             handler_key: input_wells
-            label: InputWells
+            label: 待设定液体孔
+          output:
+          - data_key: wells.@flatten
+            data_source: executor
+            data_type: resource
+            handler_key: output_wells
+            label: 已设定液体孔
         placeholder_keys:
           wells: unilabos_resources
         result: {}
@@ -9400,6 +9406,163 @@ liquid_handler.prcxi:
           title: LiquidHandlerSetLiquid
           type: object
         type: LiquidHandlerSetLiquid
+      set_liquid_from_plate:
+        feedback: {}
+        goal: {}
+        goal_default:
+          liquid_names: null
+          plate: null
+          volumes: null
+          well_names: null
+        handles:
+          input:
+          - data_key: plate
+            data_source: handle
+            data_type: resource
+            handler_key: input_plate
+            label: 待设定液体板
+          output:
+          - data_key: plate.@flatten
+            data_source: executor
+            data_type: resource
+            handler_key: output_plate
+            label: 已设定液体板
+          - data_key: wells.@flatten
+            data_source: executor
+            data_type: resource
+            handler_key: output_wells
+            label: 已设定液体孔
+          - data_key: volumes
+            data_source: executor
+            data_type: number_array
+            handler_key: output_volumes
+            label: 各孔设定体积
+        placeholder_keys:
+          plate: unilabos_resources
+        result: {}
+        schema:
+          description: ''
+          properties:
+            feedback: {}
+            goal:
+              properties:
+                liquid_names:
+                  items:
+                    type: string
+                  type: array
+                plate:
+                  properties:
+                    category:
+                      type: string
+                    children:
+                      items:
+                        type: string
+                      type: array
+                    config:
+                      type: string
+                    data:
+                      type: string
+                    id:
+                      type: string
+                    name:
+                      type: string
+                    parent:
+                      type: string
+                    pose:
+                      properties:
+                        orientation:
+                          properties:
+                            w:
+                              type: number
+                            x:
+                              type: number
+                            y:
+                              type: number
+                            z:
+                              type: number
+                          required:
+                          - x
+                          - y
+                          - z
+                          - w
+                          title: orientation
+                          type: object
+                        position:
+                          properties:
+                            x:
+                              type: number
+                            y:
+                              type: number
+                            z:
+                              type: number
+                          required:
+                          - x
+                          - y
+                          - z
+                          title: position
+                          type: object
+                      required:
+                      - position
+                      - orientation
+                      title: pose
+                      type: object
+                    sample_id:
+                      type: string
+                    type:
+                      type: string
+                  required:
+                  - id
+                  - name
+                  - sample_id
+                  - children
+                  - parent
+                  - type
+                  - category
+                  - pose
+                  - config
+                  - data
+                  title: plate
+                  type: object
+                volumes:
+                  items:
+                    type: number
+                  type: array
+                well_names:
+                  items:
+                    type: string
+                  type: array
+              required:
+              - plate
+              - well_names
+              - liquid_names
+              - volumes
+              type: object
+            result:
+              properties:
+                plate:
+                  items: {}
+                  title: Plate
+                  type: array
+                volumes:
+                  items:
+                    type: number
+                  title: Volumes
+                  type: array
+                wells:
+                  items: {}
+                  title: Wells
+                  type: array
+              required:
+              - plate
+              - wells
+              - volumes
+              title: SetLiquidFromPlateReturn
+              type: object
+          required:
+          - goal
+          title: set_liquid_from_plate参数
+          type: object
+        type: UniLabJsonCommand
       set_tiprack:
         feedback: {}
         goal:
@@ -9743,7 +9906,34 @@ liquid_handler.prcxi:
           touch_tip: false
           use_channels:
           - 0
-        handles: {}
+        handles:
+          input:
+          - data_key: sources
+            data_source: handle
+            data_type: resource
+            handler_key: sources_identifier
+            label: 待移动液体
+          - data_key: targets
+            data_source: handle
+            data_type: resource
+            handler_key: targets_identifier
+            label: 转移目标
+          - data_key: tip_rack
+            data_source: handle
+            data_type: resource
+            handler_key: tip_rack_identifier
+            label: 墙头盒
+          output:
+          - data_key: liquid
+            data_source: handle
+            data_type: resource
+            handler_key: sources_out
+            label: sources
+          - data_key: liquid
+            data_source: executor
+            data_type: resource
+            handler_key: targets_out
+            label: targets
         placeholder_keys:
           sources: unilabos_resources
           targets: unilabos_resources

unilabos/registry/registry.py

@@ -163,6 +163,7 @@ class Registry:
                                     "res_id": "unilabos_resources",  # 将当前实验室的全部物料id作为下拉框可选择
                                     "device_id": "unilabos_devices",  # 将当前实验室的全部设备id作为下拉框可选择
                                     "parent": "unilabos_nodes",  # 将当前实验室的设备/物料作为下拉框可选择
+                                    "class_name": "unilabos_class",
                                 },
                             },
                             "test_latency": {

unilabos/resources/graphio.py

@@ -260,7 +260,7 @@ def read_node_link_json(
     resource_tree_set = canonicalize_nodes_data(nodes)
 
     # 标准化边数据
-    links = data.get("links", [])
+    links = data.get("links", data.get("edges", []))
     standardized_links = canonicalize_links_ports(links, resource_tree_set)
 
     # 构建 NetworkX 图（需要转换回 dict 格式）
@@ -597,6 +597,8 @@ def resource_plr_to_ulab(resource_plr: "ResourcePLR", parent_name: str = None, w
             "tube": "tube",
             "bottle_carrier": "bottle_carrier",
             "plate_adapter": "plate_adapter",
+            "electrode_sheet": "electrode_sheet",
+            "material_hole": "material_hole",
         }
         if source in replace_info:
             return replace_info[source]

unilabos/resources/resource_tracker.py

@@ -13,6 +13,9 @@ if TYPE_CHECKING:
     from pylabrobot.resources import Resource as PLRResource
 
 
+EXTRA_CLASS = "unilabos_resource_class"
+
+
 class ResourceDictPositionSize(BaseModel):
     depth: float = Field(description="Depth", default=0.0)  # z
     width: float = Field(description="Width", default=0.0)  # x
@@ -393,7 +396,7 @@ class ResourceTreeSet(object):
                 "parent": parent_resource,  # 直接传入 ResourceDict 对象
                 "parent_uuid": parent_uuid,  # 使用 parent_uuid 而不是 parent 对象
                 "type": replace_plr_type(d.get("category", "")),
-                "class": d.get("class", ""),
+                "class": extra.get(EXTRA_CLASS, ""),
                 "position": pos,
                 "pose": pos,
                 "config": {
@@ -443,7 +446,7 @@ class ResourceTreeSet(object):
             trees.append(tree_instance)
         return cls(trees)
 
-    def to_plr_resources(self) -> List["PLRResource"]:
+    def to_plr_resources(self, skip_devices=True) -> List["PLRResource"]:
         """
         将 ResourceTreeSet 转换为 PLR 资源列表
 
@@ -468,6 +471,7 @@ class ResourceTreeSet(object):
             name_to_uuid[node.res_content.name] = node.res_content.uuid
             all_states[node.res_content.name] = node.res_content.data
             name_to_extra[node.res_content.name] = node.res_content.extra
+            name_to_extra[node.res_content.name][EXTRA_CLASS] = node.res_content.klass
             for child in node.children:
                 collect_node_data(child, name_to_uuid, all_states, name_to_extra)
 
@@ -512,7 +516,10 @@ class ResourceTreeSet(object):
             plr_dict = node_to_plr_dict(tree.root_node, has_model)
             try:
                 sub_cls = find_subclass(plr_dict["type"], PLRResource)
-                if sub_cls is None:
+                if skip_devices and plr_dict["type"] == "device":
+                    logger.info(f"跳过更新 {plr_dict['name']} 设备是class")
+                    continue
+                elif sub_cls is None:
                     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}"
                     )
@@ -520,6 +527,10 @@ class ResourceTreeSet(object):
                 if "category" not in spec.parameters:
                     plr_dict.pop("category", None)
                 plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True)
+                from pylabrobot.resources import Coordinate
+                from pylabrobot.serializer import deserialize
+                location = cast(Coordinate, deserialize(plr_dict["location"]))
+                plr_resource.location = location
                 plr_resource.load_all_state(all_states)
                 # 使用 DeviceNodeResourceTracker 设置 UUID 和 Extra
                 tracker.loop_set_uuid(plr_resource, name_to_uuid)
@@ -986,7 +997,7 @@ class DeviceNodeResourceTracker(object):
                 extra = name_to_extra_map[resource_name]
                 self.set_resource_extra(res, extra)
                 if len(extra):
-                    logger.debug(f"设置资源Extra: {resource_name} -> {extra}")
+                    logger.trace(f"设置资源Extra: {resource_name} -> {extra}")
                 return 1
             return 0
 

unilabos/ros/nodes/base_device_node.py

@@ -884,6 +884,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                                 parent_appended = True
 
                 # 加载状态
+                original_instance.location = plr_resource.location
+                original_instance.rotation = plr_resource.rotation
+                original_instance.barcode = plr_resource.barcode
                 original_instance.load_all_state(states)
                 child_count = len(original_instance.get_all_children())
                 self.lab_logger().info(
@@ -1319,19 +1322,32 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                             resource_inputs = action_kwargs[k] if is_sequence else [action_kwargs[k]]
 
                             # 批量查询资源
-                            queried_resources = []
-                            for resource_data in resource_inputs:
+                            queried_resources: list = [None] * len(resource_inputs)
+                            uuid_indices: list[tuple[int, str, dict]] = []  # (index, uuid, resource_data)
+
+                            # 第一遍：处理没有uuid的资源，收集有uuid的资源信息
+                            for idx, resource_data in enumerate(resource_inputs):
                                 unilabos_uuid = resource_data.get("data", {}).get("unilabos_uuid")
                                 if unilabos_uuid is None:
                                     plr_resource = await self.get_resource_with_dir(
                                         resource_id=resource_data["id"], with_children=True
                                     )
+                                    if "sample_id" in resource_data:
+                                        plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"]
+                                    queried_resources[idx] = plr_resource
                                 else:
-                                    resource_tree = await self.get_resource([unilabos_uuid])
-                                    plr_resource = resource_tree.to_plr_resources()[0]
-                                if "sample_id" in resource_data:
-                                    plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"]
-                                queried_resources.append(plr_resource)
+                                    uuid_indices.append((idx, unilabos_uuid, resource_data))
+
+                            # 第二遍：批量查询有uuid的资源
+                            if uuid_indices:
+                                uuids = [item[1] for item in uuid_indices]
+                                resource_tree = await self.get_resource(uuids)
+                                plr_resources = resource_tree.to_plr_resources()
+                                for i, (idx, _, resource_data) in enumerate(uuid_indices):
+                                    plr_resource = plr_resources[i]
+                                    if "sample_id" in resource_data:
+                                        plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"]
+                                    queried_resources[idx] = plr_resource
 
                             self.lab_logger().debug(f"资源查询结果: 共 {len(queried_resources)} 个资源")
 

unilabos/ros/nodes/presets/host_node.py

@@ -808,6 +808,7 @@ class HostNode(BaseROS2DeviceNode):
         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}: {action_kwargs}")
         self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {goal_msg}")
         action_client.wait_for_server()
         goal_uuid_obj = UUID(uuid=list(u.bytes))

unilabos/ros/nodes/presets/workstation.py

@@ -6,8 +6,6 @@ from typing import List, Dict, Any, Optional, TYPE_CHECKING
 
 import rclpy
 from rosidl_runtime_py import message_to_ordereddict
-from unilabos_msgs.msg import Resource
-from unilabos_msgs.srv import ResourceUpdate
 
 from unilabos.messages import *  # type: ignore  # protocol names
 from rclpy.action import ActionServer, ActionClient
@@ -15,7 +13,6 @@ from rclpy.action.server import ServerGoalHandle
 from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response
 
 from unilabos.compile import action_protocol_generators
-from unilabos.resources.graphio import nested_dict_to_list
 from unilabos.ros.initialize_device import initialize_device_from_dict
 from unilabos.ros.msgs.message_converter import (
     get_action_type,
@@ -231,15 +228,15 @@ class ROS2WorkstationNode(BaseROS2DeviceNode):
                         try:
                             # 统一处理单个或多个资源
                             resource_id = (
-                                protocol_kwargs[k]["id"] if v == "unilabos_msgs/Resource" else protocol_kwargs[k][0]["id"]
+                                protocol_kwargs[k]["id"]
+                                if v == "unilabos_msgs/Resource"
+                                else protocol_kwargs[k][0]["id"]
                             )
                             resource_uuid = protocol_kwargs[k].get("uuid", None)
                             r = SerialCommand_Request()
                             r.command = json.dumps({"id": resource_id, "uuid": resource_uuid, "with_children": True})
                             # 发送请求并等待响应
-                            response: SerialCommand_Response = await self._resource_clients[
-                                "resource_get"
-                            ].call_async(
+                            response: SerialCommand_Response = await self._resource_clients["resource_get"].call_async(
                                 r
                             )  # type: ignore
                             raw_data = json.loads(response.response)
@@ -307,12 +304,52 @@ class ROS2WorkstationNode(BaseROS2DeviceNode):
 
                 # 向Host更新物料当前状态
                 for k, v in goal.get_fields_and_field_types().items():
-                    if v in ["unilabos_msgs/Resource", "sequence<unilabos_msgs/Resource>"]:
-                        r = ResourceUpdate.Request()
-                        r.resources = [
-                            convert_to_ros_msg(Resource, rs) for rs in nested_dict_to_list(protocol_kwargs[k])
-                        ]
-                        response = await self._resource_clients["resource_update"].call_async(r)
+                    if v not in ["unilabos_msgs/Resource", "sequence<unilabos_msgs/Resource>"]:
+                        continue
+                    self.lab_logger().info(f"更新资源状态: {k}")
+                    try:
+                        # 去重：使用 seen 集合获取唯一的资源对象
+                        seen = set()
+                        unique_resources = []
+
+                        # 获取资源数据，统一转换为列表
+                        resource_data = protocol_kwargs[k]
+                        is_sequence = v != "unilabos_msgs/Resource"
+                        if not is_sequence:
+                            resource_list = [resource_data] if isinstance(resource_data, dict) else resource_data
+                        else:
+                            # 处理序列类型，可能是嵌套列表
+                            resource_list = []
+                            if isinstance(resource_data, list):
+                                for item in resource_data:
+                                    if isinstance(item, list):
+                                        resource_list.extend(item)
+                                    else:
+                                        resource_list.append(item)
+                            else:
+                                resource_list = [resource_data]
+
+                        for res_data in resource_list:
+                            if not isinstance(res_data, dict):
+                                continue
+                            res_name = res_data.get("id") or res_data.get("name")
+                            if not res_name:
+                                continue
+
+                            # 使用 resource_tracker 获取本地 PLR 实例
+                            plr = self.resource_tracker.figure_resource({"name": res_name}, try_mode=False)
+                            # 获取父资源
+                            res = self.resource_tracker.parent_resource(plr)
+                            if id(res) not in seen:
+                                seen.add(id(res))
+                                unique_resources.append(res)
+
+                        # 使用新的资源树接口更新
+                        if unique_resources:
+                            await self.update_resource(unique_resources)
+                    except Exception as e:
+                        self.lab_logger().error(f"资源更新失败: {e}")
+                        self.lab_logger().error(traceback.format_exc())
 
                 # 设置成功状态和返回值
                 execution_success = True

unilabos/workflow/common.py

@@ -0,0 +1,770 @@
+"""
+工作流转换模块 - JSON 到 WorkflowGraph 的转换流程
+
+==================== 输入格式 (JSON) ====================
+
+{
+    "workflow": [
+        {"action": "transfer_liquid", "action_args": {"sources": "cell_lines", "targets": "Liquid_1", "asp_vol": 100.0, "dis_vol": 74.75, ...}},
+        ...
+    ],
+    "reagent": {
+        "cell_lines": {"slot": 4, "well": ["A1", "A3", "A5"], "labware": "DRUG + YOYO-MEDIA"},
+        "Liquid_1": {"slot": 1, "well": ["A4", "A7", "A10"], "labware": "rep 1"},
+        ...
+    }
+}
+
+==================== 转换步骤 ====================
+
+第一步: 按 slot 去重创建 create_resource 节点（创建板子）
+--------------------------------------------------------------------------------
+- 遍历所有 reagent，按 slot 去重，为每个唯一的 slot 创建一个板子
+- 生成参数:
+    res_id: plate_slot_{slot}
+    device_id: /PRCXI
+    class_name: PRCXI_BioER_96_wellplate
+    parent: /PRCXI/PRCXI_Deck/T{slot}
+    slot_on_deck: "{slot}"
+- 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
+
+示例: slot=1, slot=4 -> 创建 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）
+--------------------------------------------------------------------------------
+- 遍历所有 reagent，为每个试剂创建 set_liquid_from_plate 节点
+- 生成参数:
+    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）
+    liquid_names: ["cell_lines", "cell_lines", "cell_lines"]（与 well 数量一致）
+    volumes: [1e5, 1e5, 1e5]（与 well 数量一致，默认体积）
+- 输入连接: create_resource (labware) -> set_liquid_from_plate (input_plate)
+- 输出端口: output_wells（用于连接 transfer_liquid）
+- 控制流: set_liquid_from_plate 连接在所有 create_resource 之后，通过 ready 端口串联
+
+第三步: 解析 workflow，创建 transfer_liquid 等动作节点
+--------------------------------------------------------------------------------
+- 遍历 workflow 数组，为每个动作创建步骤节点
+- 参数重命名: asp_vol -> asp_vols, dis_vol -> dis_vols, asp_flow_rate -> asp_flow_rates, dis_flow_rate -> dis_flow_rates
+- 参数扩展: 根据 targets 的 wells 数量，将单值扩展为数组
+    例: asp_vol=100.0, targets 有 3 个 wells -> asp_vols=[100.0, 100.0, 100.0]
+- 连接处理: 如果 sources/targets 已通过 set_liquid_from_plate 连接，参数值改为 []
+- 输入连接: set_liquid_from_plate (output_wells) -> transfer_liquid (sources_identifier / targets_identifier)
+- 输出端口: sources_out, targets_out（用于连接下一个 transfer_liquid）
+
+==================== 连接关系图 ====================
+
+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 -> ...
+
+物料流:
+    [create_resource] --labware--> [set_liquid_from_plate] --output_wells--> [transfer_liquid] --sources_out/targets_out--> [下一个 transfer_liquid]
+          (slot=1)                    (cell_lines)           (input_plate)     (sources_identifier)                          (sources_identifier)
+          (slot=4)                    (Liquid_1)                               (targets_identifier)                          (targets_identifier)
+
+==================== 端口映射 ====================
+
+create_resource:
+    输出: labware
+
+set_liquid_from_plate:
+    输入: input_plate
+    输出: output_plate, output_wells
+
+transfer_liquid:
+    输入: sources -> sources_identifier, targets -> targets_identifier
+    输出: sources -> sources_out, targets -> targets_out
+
+==================== 校验规则 ====================
+
+- 检查 sources/targets 是否在 reagent 中定义
+- 检查 sources 和 targets 的 wells 数量是否匹配
+- 检查参数数组长度是否与 wells 数量一致
+- 如有问题，在 footer 中添加 [WARN: ...] 标记
+"""
+
+import re
+import uuid
+
+import networkx as nx
+from networkx.drawing.nx_agraph import to_agraph
+import matplotlib.pyplot as plt
+from typing import Dict, List, Any, Tuple, Optional
+
+Json = Dict[str, Any]
+
+
+# ==================== 默认配置 ====================
+
+# create_resource 节点默认参数
+CREATE_RESOURCE_DEFAULTS = {
+    "device_id": "/PRCXI",
+    "parent_template": "/PRCXI/PRCXI_Deck/T{slot}",  # {slot} 会被替换为实际的 slot 值
+    "class_name": "PRCXI_BioER_96_wellplate",
+}
+
+# 默认液体体积 (uL)
+DEFAULT_LIQUID_VOLUME = 1e5
+
+# 参数重命名映射：单数 -> 复数（用于 transfer_liquid 等动作）
+PARAM_RENAME_MAPPING = {
+    "asp_vol": "asp_vols",
+    "dis_vol": "dis_vols",
+    "asp_flow_rate": "asp_flow_rates",
+    "dis_flow_rate": "dis_flow_rates",
+}
+
+
+# ---------------- Graph ----------------
+
+
+class WorkflowGraph:
+    """简单的有向图实现：使用 params 单层参数；inputs 内含连线；支持 node-link 导出"""
+
+    def __init__(self):
+        self.nodes: Dict[str, Dict[str, Any]] = {}
+        self.edges: List[Dict[str, Any]] = []
+
+    def add_node(self, node_id: str, **attrs):
+        self.nodes[node_id] = attrs
+
+    def add_edge(self, source: str, target: str, **attrs):
+        # 将 source_port/target_port 映射为服务端期望的 source_handle_key/target_handle_key
+        source_handle_key = attrs.pop("source_port", "") or attrs.pop("source_handle_key", "")
+        target_handle_key = attrs.pop("target_port", "") or attrs.pop("target_handle_key", "")
+
+        edge = {
+            "source": source,
+            "target": target,
+            "source_node_uuid": source,
+            "target_node_uuid": target,
+            "source_handle_key": source_handle_key,
+            "source_handle_io": attrs.pop("source_handle_io", "source"),
+            "target_handle_key": target_handle_key,
+            "target_handle_io": attrs.pop("target_handle_io", "target"),
+            **attrs,
+        }
+        self.edges.append(edge)
+
+    def _materialize_wiring_into_inputs(
+        self,
+        obj: Any,
+        inputs: Dict[str, Any],
+        variable_sources: Dict[str, Dict[str, Any]],
+        target_node_id: str,
+        base_path: List[str],
+    ):
+        has_var = False
+
+        def walk(node: Any, path: List[str]):
+            nonlocal has_var
+            if isinstance(node, dict):
+                if "__var__" in node:
+                    has_var = True
+                    varname = node["__var__"]
+                    placeholder = f"${{{varname}}}"
+                    src = variable_sources.get(varname)
+                    if src:
+                        key = ".".join(path)  # e.g. "params.foo.bar.0"
+                        inputs[key] = {"node": src["node_id"], "output": src.get("output_name", "result")}
+                        self.add_edge(
+                            str(src["node_id"]),
+                            target_node_id,
+                            source_handle_io=src.get("output_name", "result"),
+                            target_handle_io=key,
+                        )
+                    return placeholder
+                return {k: walk(v, path + [k]) for k, v in node.items()}
+            if isinstance(node, list):
+                return [walk(v, path + [str(i)]) for i, v in enumerate(node)]
+            return node
+
+        replaced = walk(obj, base_path[:])
+        return replaced, has_var
+
+    def add_workflow_node(
+        self,
+        node_id: int,
+        *,
+        device_key: Optional[str] = None,  # 实例名，如 "ser"
+        resource_name: Optional[str] = None,  # registry key（原 device_class）
+        module: Optional[str] = None,
+        template_name: Optional[str] = None,  # 动作/模板名（原 action_key）
+        params: Dict[str, Any],
+        variable_sources: Dict[str, Dict[str, Any]],
+        add_ready_if_no_vars: bool = True,
+        prev_node_id: Optional[int] = None,
+        **extra_attrs,
+    ) -> None:
+        """添加工作流节点：params 单层；自动变量连线与 ready 串联；支持附加属性"""
+        node_id_str = str(node_id)
+        inputs: Dict[str, Any] = {}
+
+        params, has_var = self._materialize_wiring_into_inputs(
+            params, inputs, variable_sources, node_id_str, base_path=["params"]
+        )
+
+        if add_ready_if_no_vars and not has_var:
+            last_id = str(prev_node_id) if prev_node_id is not None else "-1"
+            inputs["ready"] = {"node": int(last_id), "output": "ready"}
+            self.add_edge(last_id, node_id_str, source_handle_io="ready", target_handle_io="ready")
+
+        node_obj = {
+            "device_key": device_key,
+            "resource_name": resource_name,  # ✅ 新名字
+            "module": module,
+            "template_name": template_name,  # ✅ 新名字
+            "params": params,
+            "inputs": inputs,
+        }
+        node_obj.update(extra_attrs or {})
+        self.add_node(node_id_str, parameters=node_obj)
+
+    # 顺序工作流导出（连线在 inputs，不返回 edges）
+    def to_dict(self) -> List[Dict[str, Any]]:
+        result = []
+        for node_id, attrs in self.nodes.items():
+            node = {"uuid": node_id}
+            params = dict(attrs.get("parameters", {}) or {})
+            flat = {k: v for k, v in attrs.items() if k != "parameters"}
+            flat.update(params)
+            node.update(flat)
+            result.append(node)
+        return sorted(result, key=lambda n: int(n["uuid"]) if str(n["uuid"]).isdigit() else n["uuid"])
+
+    # node-link 导出（含 edges）
+    def to_node_link_dict(self) -> Dict[str, Any]:
+        nodes_list = []
+        for node_id, attrs in self.nodes.items():
+            node_attrs = attrs.copy()
+            params = node_attrs.pop("parameters", {}) or {}
+            node_attrs.update(params)
+            nodes_list.append({"uuid": node_id, **node_attrs})
+        return {
+            "directed": True,
+            "multigraph": False,
+            "graph": {},
+            "nodes": nodes_list,
+            "edges": self.edges,
+            "links": self.edges,
+        }
+
+
+def refactor_data(
+    data: List[Dict[str, Any]],
+    action_resource_mapping: Optional[Dict[str, str]] = None,
+) -> List[Dict[str, Any]]:
+    """统一的数据重构函数，根据操作类型自动选择模板
+
+    Args:
+        data: 原始步骤数据列表
+        action_resource_mapping: action 到 resource_name 的映射字典，可选
+    """
+    refactored_data = []
+
+    # 定义操作映射，包含生物实验和有机化学的所有操作
+    OPERATION_MAPPING = {
+        # 生物实验操作
+        "transfer_liquid": "transfer_liquid",
+        "transfer": "transfer",
+        "incubation": "incubation",
+        "move_labware": "move_labware",
+        "oscillation": "oscillation",
+        # 有机化学操作
+        "HeatChillToTemp": "HeatChillProtocol",
+        "StopHeatChill": "HeatChillStopProtocol",
+        "StartHeatChill": "HeatChillStartProtocol",
+        "HeatChill": "HeatChillProtocol",
+        "Dissolve": "DissolveProtocol",
+        "Transfer": "TransferProtocol",
+        "Evaporate": "EvaporateProtocol",
+        "Recrystallize": "RecrystallizeProtocol",
+        "Filter": "FilterProtocol",
+        "Dry": "DryProtocol",
+        "Add": "AddProtocol",
+    }
+
+    UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
+
+    for step in data:
+        operation = step.get("action")
+        if not operation or operation in UNSUPPORTED_OPERATIONS:
+            continue
+
+        # 处理重复操作
+        if operation == "Repeat":
+            times = step.get("times", step.get("parameters", {}).get("times", 1))
+            sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
+            for i in range(int(times)):
+                sub_data = refactor_data(sub_steps, action_resource_mapping)
+                refactored_data.extend(sub_data)
+            continue
+
+        # 获取模板名称
+        template_name = OPERATION_MAPPING.get(operation)
+        if not template_name:
+            # 自动推断模板类型
+            if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
+                template_name = f"biomek-{operation}"
+            else:
+                template_name = f"{operation}Protocol"
+
+        # 获取 resource_name
+        resource_name = f"device.{operation.lower()}"
+        if action_resource_mapping:
+            resource_name = action_resource_mapping.get(operation, resource_name)
+
+        # 获取步骤编号，生成 name 字段
+        step_number = step.get("step_number")
+        name = f"Step {step_number}" if step_number is not None else None
+
+        # 创建步骤数据
+        step_data = {
+            "template_name": template_name,
+            "resource_name": resource_name,
+            "description": step.get("description", step.get("purpose", f"{operation} operation")),
+            "lab_node_type": "Device",
+            "param": step.get("parameters", step.get("action_args", {})),
+            "footer": f"{template_name}-{resource_name}",
+        }
+        if name:
+            step_data["name"] = name
+        refactored_data.append(step_data)
+
+    return refactored_data
+
+
+def build_protocol_graph(
+    labware_info: Dict[str, Dict[str, Any]],
+    protocol_steps: List[Dict[str, Any]],
+    workstation_name: str,
+    action_resource_mapping: Optional[Dict[str, str]] = None,
+) -> WorkflowGraph:
+    """统一的协议图构建函数，根据设备类型自动选择构建逻辑
+
+    Args:
+        labware_info: labware 信息字典，格式为 {name: {slot, well, labware, ...}, ...}
+        protocol_steps: 协议步骤列表
+        workstation_name: 工作站名称
+        action_resource_mapping: action 到 resource_name 的映射字典，可选
+    """
+    G = WorkflowGraph()
+    resource_last_writer = {}  # reagent_name -> "node_id:port"
+    slot_to_create_resource = {}  # slot -> create_resource node_id
+
+    protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
+
+    # ==================== 第一步：按 slot 去重创建 create_resource 节点 ====================
+    # 收集所有唯一的 slot
+    slots_info = {}  # slot -> {labware, res_id}
+    for labware_id, item in labware_info.items():
+        slot = str(item.get("slot", ""))
+        if slot and slot not in slots_info:
+            res_id = f"plate_slot_{slot}"
+            slots_info[slot] = {
+                "labware": item.get("labware", ""),
+                "res_id": res_id,
+            }
+
+    # 为每个唯一的 slot 创建 create_resource 节点
+    res_index = 0
+    last_create_resource_id = None
+    for slot, info in slots_info.items():
+        node_id = str(uuid.uuid4())
+        res_id = info["res_id"]
+
+        res_index += 1
+        G.add_node(
+            node_id,
+            template_name="create_resource",
+            resource_name="host_node",
+            name=f"Plate {res_index}",
+            description=f"Create plate on slot {slot}",
+            lab_node_type="Labware",
+            footer="create_resource-host_node",
+            param={
+                "res_id": res_id,
+                "device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
+                "class_name": CREATE_RESOURCE_DEFAULTS["class_name"],
+                "parent": CREATE_RESOURCE_DEFAULTS["parent_template"].format(slot=slot),
+                "bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
+                "slot_on_deck": slot,
+            },
+        )
+        slot_to_create_resource[slot] = node_id
+
+        # create_resource 之间通过 ready 串联
+        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 ====================
+    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():
+        # 跳过 Tip/Rack 类型
+        if "Rack" in str(labware_id) or "Tip" in str(labware_id):
+            continue
+        if item.get("type") == "hardware":
+            continue
+
+        slot = str(item.get("slot", ""))
+        wells = item.get("well", [])
+        if not wells or not slot:
+            continue
+
+        # res_id 不能有空格
+        res_id = str(labware_id).replace(" ", "_")
+        well_count = len(wells)
+
+        node_id = str(uuid.uuid4())
+        set_liquid_index += 1
+
+        G.add_node(
+            node_id,
+            template_name="set_liquid_from_plate",
+            resource_name="liquid_handler.prcxi",
+            name=f"SetLiquid {set_liquid_index}",
+            description=f"Set liquid: {labware_id}",
+            lab_node_type="Reagent",
+            footer="set_liquid_from_plate-liquid_handler.prcxi",
+            param={
+                "plate": [],  # 通过连接传递
+                "well_names": wells,  # 孔位名数组，如 ["A1", "A3", "A5"]
+                "liquid_names": [res_id] * well_count,
+                "volumes": [DEFAULT_LIQUID_VOLUME] * well_count,
+            },
+        )
+
+        # ready 连接：上一个节点 -> set_liquid_from_plate
+        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
+        create_res_node_id = slot_to_create_resource.get(slot)
+        if create_res_node_id:
+            G.add_edge(create_res_node_id, node_id, source_port="labware", target_port="input_plate")
+
+        # 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"
+
+    last_control_node_id = last_set_liquid_id
+
+    # 端口名称映射：JSON 字段名 -> 实际 handle key
+    INPUT_PORT_MAPPING = {
+        "sources": "sources_identifier",
+        "targets": "targets_identifier",
+        "vessel": "vessel",
+        "to_vessel": "to_vessel",
+        "from_vessel": "from_vessel",
+        "reagent": "reagent",
+        "solvent": "solvent",
+        "compound": "compound",
+    }
+
+    OUTPUT_PORT_MAPPING = {
+        "sources": "sources_out",  # 输出端口是 xxx_out
+        "targets": "targets_out",  # 输出端口是 xxx_out
+        "vessel": "vessel_out",
+        "to_vessel": "to_vessel_out",
+        "from_vessel": "from_vessel_out",
+        "filtrate_vessel": "filtrate_out",
+        "reagent": "reagent",
+        "solvent": "solvent",
+        "compound": "compound",
+    }
+
+    # 需要根据 wells 数量扩展的参数列表（复数形式）
+    EXPAND_BY_WELLS_PARAMS = ["asp_vols", "dis_vols", "asp_flow_rates", "dis_flow_rates"]
+
+    # 处理协议步骤
+    for step in protocol_steps:
+        node_id = str(uuid.uuid4())
+        params = step.get("param", {}).copy()  # 复制一份，避免修改原数据
+        connected_params = set()  # 记录被连接的参数
+        warnings = []  # 收集警告信息
+
+        # 参数重命名：单数 -> 复数
+        for old_name, new_name in PARAM_RENAME_MAPPING.items():
+            if old_name in params:
+                params[new_name] = params.pop(old_name)
+
+        # 处理输入连接
+        for param_key, target_port in INPUT_PORT_MAPPING.items():
+            resource_name = params.get(param_key)
+            if resource_name and resource_name in resource_last_writer:
+                source_node, source_port = resource_last_writer[resource_name].split(":")
+                G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
+                connected_params.add(param_key)
+            elif resource_name and resource_name not in resource_last_writer:
+                # 资源名在 labware_info 中不存在
+                warnings.append(f"{param_key}={resource_name} 未找到")
+
+        # 获取 targets 对应的 wells 数量，用于扩展参数
+        targets_name = params.get("targets")
+        sources_name = params.get("sources")
+        targets_wells_count = 1
+        sources_wells_count = 1
+
+        if targets_name and targets_name in labware_info:
+            target_wells = labware_info[targets_name].get("well", [])
+            targets_wells_count = len(target_wells) if target_wells else 1
+        elif targets_name:
+            warnings.append(f"targets={targets_name} 未在 reagent 中定义")
+
+        if sources_name and sources_name in labware_info:
+            source_wells = labware_info[sources_name].get("well", [])
+            sources_wells_count = len(source_wells) if source_wells else 1
+        elif sources_name:
+            warnings.append(f"sources={sources_name} 未在 reagent 中定义")
+
+        # 检查 sources 和 targets 的 wells 数量是否匹配
+        if targets_wells_count != sources_wells_count and targets_name and sources_name:
+            warnings.append(f"wells 数量不匹配: sources={sources_wells_count}, targets={targets_wells_count}")
+
+        # 使用 targets 的 wells 数量来扩展参数
+        wells_count = targets_wells_count
+
+        # 扩展单值参数为数组（根据 targets 的 wells 数量）
+        for expand_param in EXPAND_BY_WELLS_PARAMS:
+            if expand_param in params:
+                value = params[expand_param]
+                # 如果是单个值，扩展为数组
+                if not isinstance(value, list):
+                    params[expand_param] = [value] * wells_count
+                # 如果已经是数组但长度不对，记录警告
+                elif len(value) != wells_count:
+                    warnings.append(f"{expand_param} 数量({len(value)})与 wells({wells_count})不匹配")
+
+        # 如果 sources/targets 已通过连接传递，将参数值改为空数组
+        for param_key in connected_params:
+            if param_key in params:
+                params[param_key] = []
+
+        # 更新 step 的 param 和 footer
+        step_copy = step.copy()
+        step_copy["param"] = params
+
+        # 如果有警告，修改 footer 添加警告标记（警告放前面）
+        if warnings:
+            original_footer = step.get("footer", "")
+            step_copy["footer"] = f"[WARN: {'; '.join(warnings)}] {original_footer}"
+
+        G.add_node(node_id, **step_copy)
+
+        # 控制流
+        if last_control_node_id is not None:
+            G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
+        last_control_node_id = node_id
+
+        # 处理输出：更新 resource_last_writer
+        for param_key, output_port in OUTPUT_PORT_MAPPING.items():
+            resource_name = step.get("param", {}).get(param_key)  # 使用原始参数值
+            if resource_name:
+                resource_last_writer[resource_name] = f"{node_id}:{output_port}"
+
+    return G
+
+
+def draw_protocol_graph(protocol_graph: WorkflowGraph, output_path: str):
+    """
+    (辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图，用于可视化。
+    """
+    if not protocol_graph:
+        print("Cannot draw graph: Graph object is empty.")
+        return
+
+    G = nx.DiGraph()
+
+    for node_id, attrs in protocol_graph.nodes.items():
+        label = attrs.get("description", attrs.get("template_name", node_id[:8]))
+        G.add_node(node_id, label=label, **attrs)
+
+    for edge in protocol_graph.edges:
+        G.add_edge(edge["source"], edge["target"])
+
+    plt.figure(figsize=(20, 15))
+    try:
+        pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
+    except Exception:
+        pos = nx.shell_layout(G)  # Fallback layout
+
+    node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
+    nx.draw(
+        G,
+        pos,
+        with_labels=False,
+        node_size=2500,
+        node_color="skyblue",
+        node_shape="o",
+        edge_color="gray",
+        width=1.5,
+        arrowsize=15,
+    )
+    nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
+
+    plt.title("Chemical Protocol Workflow Graph", size=15)
+    plt.savefig(output_path, dpi=300, bbox_inches="tight")
+    plt.close()
+    print(f"  - Visualization saved to '{output_path}'")
+
+
+COMPASS = {"n", "e", "s", "w", "ne", "nw", "se", "sw", "c"}
+
+
+def _is_compass(port: str) -> bool:
+    return isinstance(port, str) and port.lower() in COMPASS
+
+
+def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
+    """
+    使用 Graphviz 端口语法绘制协议工作流图。
+    - 若边上的 source_port/target_port 是 compass（n/e/s/w/...），直接用 compass。
+    - 否则自动为节点创建 record 形状并定义命名端口 <portname>。
+    最终由 PyGraphviz 渲染并输出到 output_path（后缀决定格式，如 .png/.svg/.pdf）。
+    """
+    if not protocol_graph:
+        print("Cannot draw graph: Graph object is empty.")
+        return
+
+    # 1) 先用 networkx 搭建有向图，保留端口属性
+    G = nx.DiGraph()
+    for node_id, attrs in protocol_graph.nodes.items():
+        label = attrs.get("description", attrs.get("template_name", node_id[:8]))
+        # 保留一个干净的“中心标签”，用于放在 record 的中间槽
+        G.add_node(node_id, _core_label=str(label), **{k: v for k, v in attrs.items() if k not in ("label",)})
+
+    edges_data = []
+    in_ports_by_node = {}  # 收集命名输入端口
+    out_ports_by_node = {}  # 收集命名输出端口
+
+    for edge in protocol_graph.edges:
+        u = edge["source"]
+        v = edge["target"]
+        sp = edge.get("source_handle_key") or edge.get("source_port")
+        tp = edge.get("target_handle_key") or edge.get("target_port")
+
+        # 记录到图里（保留原始端口信息）
+        G.add_edge(u, v, source_handle_key=sp, target_handle_key=tp)
+        edges_data.append((u, v, sp, tp))
+
+        # 如果不是 compass，就按“命名端口”先归类，等会儿给节点造 record
+        if sp and not _is_compass(sp):
+            out_ports_by_node.setdefault(u, set()).add(str(sp))
+        if tp and not _is_compass(tp):
+            in_ports_by_node.setdefault(v, set()).add(str(tp))
+
+    # 2) 转为 AGraph，使用 Graphviz 渲染
+    A = to_agraph(G)
+    A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
+    A.node_attr.update(
+        shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica"
+    )
+    A.edge_attr.update(arrowsize="0.8", color="#666666")
+
+    # 3) 为需要命名端口的节点设置 record 形状与 label
+    #    左列 = 输入端口；中间 = 核心标签；右列 = 输出端口
+    for n in A.nodes():
+        node = A.get_node(n)
+        core = G.nodes[n].get("_core_label", n)
+
+        in_ports = sorted(in_ports_by_node.get(n, []))
+        out_ports = sorted(out_ports_by_node.get(n, []))
+
+        # 如果该节点涉及命名端口，则用 record；否则保留原 box
+        if in_ports or out_ports:
+
+            def port_fields(ports):
+                if not ports:
+                    return " "  # 必须留一个空槽占位
+                # 每个端口一个小格子，<p> name
+                return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
+
+            left = port_fields(in_ports)
+            right = port_fields(out_ports)
+
+            # 三栏：左(入) | 中(节点名) | 右(出)
+            record_label = f"{{ {left} | {core} | {right} }}"
+            node.attr.update(shape="record", label=record_label)
+        else:
+            # 没有命名端口：普通盒子，显示核心标签
+            node.attr.update(label=str(core))
+
+    # 4) 给边设置 headport / tailport
+    #    - 若端口为 compass：直接用 compass（e.g., headport="e"）
+    #    - 若端口为命名端口：使用在 record 中定义的 <port> 名（同名即可）
+    for u, v, sp, tp in edges_data:
+        e = A.get_edge(u, v)
+
+        # Graphviz 属性：tail 是源，head 是目标
+        if sp:
+            if _is_compass(sp):
+                e.attr["tailport"] = sp.lower()
+            else:
+                # 与 record label 中 <port> 名一致；特殊字符已在 label 中做了清洗
+                e.attr["tailport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(sp))
+
+        if tp:
+            if _is_compass(tp):
+                e.attr["headport"] = tp.lower()
+            else:
+                e.attr["headport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(tp))
+
+        # 可选：若想让边更贴边缘，可设置 constraint/spline 等
+        # e.attr["arrowhead"] = "vee"
+
+    # 5) 输出
+    A.draw(output_path, prog="dot")
+    print(f"  - Port-aware workflow rendered to '{output_path}'")
+
+
+# ---------------- Registry Adapter ----------------
+
+
+class RegistryAdapter:
+    """根据 module 的类名（冒号右侧）反查 registry 的 resource_name（原 device_class），并抽取参数顺序"""
+
+    def __init__(self, device_registry: Dict[str, Any]):
+        self.device_registry = device_registry or {}
+        self.module_class_to_resource = self._build_module_class_index()
+
+    def _build_module_class_index(self) -> Dict[str, str]:
+        idx = {}
+        for resource_name, info in self.device_registry.items():
+            module = info.get("module")
+            if isinstance(module, str) and ":" in module:
+                cls = module.split(":")[-1]
+                idx[cls] = resource_name
+                idx[cls.lower()] = resource_name
+        return idx
+
+    def resolve_resource_by_classname(self, class_name: str) -> Optional[str]:
+        if not class_name:
+            return None
+        return self.module_class_to_resource.get(class_name) or self.module_class_to_resource.get(class_name.lower())
+
+    def get_device_module(self, resource_name: Optional[str]) -> Optional[str]:
+        if not resource_name:
+            return None
+        return self.device_registry.get(resource_name, {}).get("module")
+
+    def get_actions(self, resource_name: Optional[str]) -> Dict[str, Any]:
+        if not resource_name:
+            return {}
+        return (self.device_registry.get(resource_name, {}).get("class", {}).get("action_value_mappings", {})) or {}
+
+    def get_action_schema(self, resource_name: Optional[str], template_name: str) -> Optional[Json]:
+        return (self.get_actions(resource_name).get(template_name) or {}).get("schema")
+
+    def get_action_goal_default(self, resource_name: Optional[str], template_name: str) -> Json:
+        return (self.get_actions(resource_name).get(template_name) or {}).get("goal_default", {}) or {}
+
+    def get_action_input_keys(self, resource_name: Optional[str], template_name: str) -> List[str]:
+        schema = self.get_action_schema(resource_name, template_name) or {}
+        goal = (schema.get("properties") or {}).get("goal") or {}
+        props = goal.get("properties") or {}
+        required = goal.get("required") or []
+        return list(dict.fromkeys(required + list(props.keys())))

unilabos/workflow/convert_from_json.py

@@ -0,0 +1,315 @@
+"""
+JSON 工作流转换模块
+
+将 workflow/reagent 格式的 JSON 转换为统一工作流格式。
+
+输入格式:
+{
+    "workflow": [
+        {"action": "...", "action_args": {...}},
+        ...
+    ],
+    "reagent": {
+        "reagent_name": {"slot": int, "well": [...], "labware": "..."},
+        ...
+    }
+}
+"""
+
+import json
+from os import PathLike
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Tuple, Union
+
+from unilabos.workflow.common import WorkflowGraph, build_protocol_graph
+from unilabos.registry.registry import lab_registry
+
+
+# ==================== 字段映射配置 ====================
+
+# action 到 resource_name 的映射
+ACTION_RESOURCE_MAPPING: Dict[str, str] = {
+    # 生物实验操作
+    "transfer_liquid": "liquid_handler.prcxi",
+    "transfer": "liquid_handler.prcxi",
+    "incubation": "incubator.prcxi",
+    "move_labware": "labware_mover.prcxi",
+    "oscillation": "shaker.prcxi",
+    # 有机化学操作
+    "HeatChillToTemp": "heatchill.chemputer",
+    "StopHeatChill": "heatchill.chemputer",
+    "StartHeatChill": "heatchill.chemputer",
+    "HeatChill": "heatchill.chemputer",
+    "Dissolve": "stirrer.chemputer",
+    "Transfer": "liquid_handler.chemputer",
+    "Evaporate": "rotavap.chemputer",
+    "Recrystallize": "reactor.chemputer",
+    "Filter": "filter.chemputer",
+    "Dry": "dryer.chemputer",
+    "Add": "liquid_handler.chemputer",
+}
+
+# action_args 字段到 parameters 字段的映射
+# 格式: {"old_key": "new_key"}, 仅映射需要重命名的字段
+ARGS_FIELD_MAPPING: Dict[str, str] = {
+    # 如果需要字段重命名，在这里配置
+    # "old_field_name": "new_field_name",
+}
+
+# 默认工作站名称
+DEFAULT_WORKSTATION = "PRCXI"
+
+
+# ==================== 核心转换函数 ====================
+
+
+def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]:
+    """
+    从 registry 获取指定设备和动作的 handles 配置
+
+    Args:
+        resource_name: 设备资源名称，如 "liquid_handler.prcxi"
+        template_name: 动作模板名称，如 "transfer_liquid"
+
+    Returns:
+        包含 source 和 target handler_keys 的字典:
+        {"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]}
+    """
+    result = {"source": [], "target": []}
+
+    device_info = lab_registry.device_type_registry.get(resource_name, {})
+    if not device_info:
+        return result
+
+    action_mappings = device_info.get("class", {}).get("action_value_mappings", {})
+    action_config = action_mappings.get(template_name, {})
+    handles = action_config.get("handles", {})
+
+    if isinstance(handles, dict):
+        for handle in handles.get("input", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["source"].append(handler_key)
+        for handle in handles.get("output", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["target"].append(handler_key)
+
+    return result
+
+
+def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]:
+    """
+    校验工作流图中所有边的句柄配置是否正确
+
+    Args:
+        graph: 工作流图对象
+
+    Returns:
+        (is_valid, errors): 是否有效，错误信息列表
+    """
+    errors = []
+    nodes = graph.nodes
+
+    for edge in graph.edges:
+        left_uuid = edge.get("source")
+        right_uuid = edge.get("target")
+        right_source_conn_key = edge.get("target_handle_key", "")
+        left_target_conn_key = edge.get("source_handle_key", "")
+
+        left_node = nodes.get(left_uuid, {})
+        right_node = nodes.get(right_uuid, {})
+
+        left_res_name = left_node.get("resource_name", "")
+        left_template_name = left_node.get("template_name", "")
+        right_res_name = right_node.get("resource_name", "")
+        right_template_name = right_node.get("template_name", "")
+
+        left_node_handles = get_action_handles(left_res_name, left_template_name)
+        target_valid_keys = left_node_handles.get("target", [])
+        target_valid_keys.append("ready")
+
+        right_node_handles = get_action_handles(right_res_name, right_template_name)
+        source_valid_keys = right_node_handles.get("source", [])
+        source_valid_keys.append("ready")
+
+        # 验证目标节点（right）的输入端口
+        if not right_source_conn_key:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(f"目标节点 '{node_name}' 的输入端口 (target_handle_key) 为空，应设置为: {source_valid_keys}")
+        elif right_source_conn_key not in source_valid_keys:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(
+                f"目标节点 '{node_name}' 的输入端口 '{right_source_conn_key}' 不存在，支持的输入端口: {source_valid_keys}"
+            )
+
+        # 验证源节点（left）的输出端口
+        if not left_target_conn_key:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(f"源节点 '{node_name}' 的输出端口 (source_handle_key) 为空，应设置为: {target_valid_keys}")
+        elif left_target_conn_key not in target_valid_keys:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(
+                f"源节点 '{node_name}' 的输出端口 '{left_target_conn_key}' 不存在，支持的输出端口: {target_valid_keys}"
+            )
+
+    return len(errors) == 0, errors
+
+
+def normalize_workflow_steps(workflow: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+    """
+    将 workflow 格式的步骤数据规范化
+
+    输入格式:
+        [{"action": "...", "action_args": {...}}, ...]
+
+    输出格式:
+        [{"action": "...", "parameters": {...}, "step_number": int}, ...]
+
+    Args:
+        workflow: workflow 数组
+
+    Returns:
+        规范化后的步骤列表
+    """
+    normalized = []
+    for idx, step in enumerate(workflow):
+        action = step.get("action")
+        if not action:
+            continue
+
+        # 获取参数: action_args
+        raw_params = step.get("action_args", {})
+        params = {}
+
+        # 应用字段映射
+        for key, value in raw_params.items():
+            mapped_key = ARGS_FIELD_MAPPING.get(key, key)
+            params[mapped_key] = value
+
+        step_dict = {
+            "action": action,
+            "parameters": params,
+            "step_number": idx + 1,
+        }
+
+        # 保留描述字段
+        if "description" in step:
+            step_dict["description"] = step["description"]
+
+        normalized.append(step_dict)
+
+    return normalized
+
+
+def convert_from_json(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = DEFAULT_WORKSTATION,
+    validate: bool = True,
+) -> WorkflowGraph:
+    """
+    从 JSON 数据或文件转换为 WorkflowGraph
+
+    JSON 格式:
+        {"workflow": [...], "reagent": {...}}
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+        validate: 是否校验句柄配置，默认 True
+
+    Returns:
+        WorkflowGraph: 构建好的工作流图
+
+    Raises:
+        ValueError: 不支持的 JSON 格式
+        FileNotFoundError: 文件不存在
+        json.JSONDecodeError: JSON 解析失败
+    """
+    # 处理输入数据
+    if isinstance(data, (str, PathLike)):
+        path = Path(data)
+        if path.exists():
+            with path.open("r", encoding="utf-8") as fp:
+                json_data = json.load(fp)
+        elif isinstance(data, str):
+            json_data = json.loads(data)
+        else:
+            raise FileNotFoundError(f"文件不存在: {data}")
+    elif isinstance(data, dict):
+        json_data = data
+    else:
+        raise TypeError(f"不支持的数据类型: {type(data)}")
+
+    # 校验格式
+    if "workflow" not in json_data or "reagent" not in json_data:
+        raise ValueError(
+            "不支持的 JSON 格式。请使用标准格式:\n"
+            '{"workflow": [{"action": "...", "action_args": {...}}, ...], '
+            '"reagent": {"name": {"slot": int, "well": [...], "labware": "..."}, ...}}'
+        )
+
+    # 提取数据
+    workflow = json_data["workflow"]
+    reagent = json_data["reagent"]
+
+    # 规范化步骤数据
+    protocol_steps = normalize_workflow_steps(workflow)
+
+    # reagent 已经是字典格式，直接使用
+    labware_info = reagent
+
+    # 构建工作流图
+    graph = build_protocol_graph(
+        labware_info=labware_info,
+        protocol_steps=protocol_steps,
+        workstation_name=workstation_name,
+        action_resource_mapping=ACTION_RESOURCE_MAPPING,
+    )
+
+    # 校验句柄配置
+    if validate:
+        is_valid, errors = validate_workflow_handles(graph)
+        if not is_valid:
+            import warnings
+
+            for error in errors:
+                warnings.warn(f"句柄校验警告: {error}")
+
+    return graph
+
+
+def convert_json_to_node_link(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = DEFAULT_WORKSTATION,
+) -> Dict[str, Any]:
+    """
+    将 JSON 数据转换为 node-link 格式的字典
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        Dict: node-link 格式的工作流数据
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_node_link_dict()
+
+
+def convert_json_to_workflow_list(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = DEFAULT_WORKSTATION,
+) -> List[Dict[str, Any]]:
+    """
+    将 JSON 数据转换为工作流列表格式
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        List: 工作流节点列表
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_dict()

unilabos/workflow/legacy/convert_from_json_legacy.py

@@ -0,0 +1,356 @@
+"""
+JSON 工作流转换模块
+
+提供从多种 JSON 格式转换为统一工作流格式的功能。
+支持的格式：
+1. workflow/reagent 格式
+2. steps_info/labware_info 格式
+"""
+
+import json
+from os import PathLike
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Set, Tuple, Union
+
+from unilabos.workflow.common import WorkflowGraph, build_protocol_graph
+from unilabos.registry.registry import lab_registry
+
+
+def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]:
+    """
+    从 registry 获取指定设备和动作的 handles 配置
+
+    Args:
+        resource_name: 设备资源名称，如 "liquid_handler.prcxi"
+        template_name: 动作模板名称，如 "transfer_liquid"
+
+    Returns:
+        包含 source 和 target handler_keys 的字典:
+        {"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]}
+    """
+    result = {"source": [], "target": []}
+
+    device_info = lab_registry.device_type_registry.get(resource_name, {})
+    if not device_info:
+        return result
+
+    action_mappings = device_info.get("class", {}).get("action_value_mappings", {})
+    action_config = action_mappings.get(template_name, {})
+    handles = action_config.get("handles", {})
+
+    if isinstance(handles, dict):
+        # 处理 input handles (作为 target)
+        for handle in handles.get("input", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["source"].append(handler_key)
+        # 处理 output handles (作为 source)
+        for handle in handles.get("output", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["target"].append(handler_key)
+
+    return result
+
+
+def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]:
+    """
+    校验工作流图中所有边的句柄配置是否正确
+
+    Args:
+        graph: 工作流图对象
+
+    Returns:
+        (is_valid, errors): 是否有效，错误信息列表
+    """
+    errors = []
+    nodes = graph.nodes
+
+    for edge in graph.edges:
+        left_uuid = edge.get("source")
+        right_uuid = edge.get("target")
+        # target_handle_key是target, right的输入节点（入节点）
+        # source_handle_key是source, left的输出节点（出节点）
+        right_source_conn_key = edge.get("target_handle_key", "")
+        left_target_conn_key = edge.get("source_handle_key", "")
+
+        # 获取源节点和目标节点信息
+        left_node = nodes.get(left_uuid, {})
+        right_node = nodes.get(right_uuid, {})
+
+        left_res_name = left_node.get("resource_name", "")
+        left_template_name = left_node.get("template_name", "")
+        right_res_name = right_node.get("resource_name", "")
+        right_template_name = right_node.get("template_name", "")
+
+        # 获取源节点的 output handles
+        left_node_handles = get_action_handles(left_res_name, left_template_name)
+        target_valid_keys = left_node_handles.get("target", [])
+        target_valid_keys.append("ready")
+
+        # 获取目标节点的 input handles
+        right_node_handles = get_action_handles(right_res_name, right_template_name)
+        source_valid_keys = right_node_handles.get("source", [])
+        source_valid_keys.append("ready")
+
+        # 如果节点配置了 output handles，则 source_port 必须有效
+        if not right_source_conn_key:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(f"源节点 '{node_name}' 的 source_handle_key 为空，" f"应设置为: {source_valid_keys}")
+        elif right_source_conn_key not in source_valid_keys:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(
+                f"源节点 '{node_name}' 的 source 端点 '{right_source_conn_key}' 不存在，" f"支持的端点: {source_valid_keys}"
+            )
+
+        # 如果节点配置了 input handles，则 target_port 必须有效
+        if not left_target_conn_key:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(f"目标节点 '{node_name}' 的 target_handle_key 为空，" f"应设置为: {target_valid_keys}")
+        elif left_target_conn_key not in target_valid_keys:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(
+                f"目标节点 '{node_name}' 的 target 端点 '{left_target_conn_key}' 不存在，"
+                f"支持的端点: {target_valid_keys}"
+            )
+
+    return len(errors) == 0, errors
+
+
+# action 到 resource_name 的映射
+ACTION_RESOURCE_MAPPING: Dict[str, str] = {
+    # 生物实验操作
+    "transfer_liquid": "liquid_handler.prcxi",
+    "transfer": "liquid_handler.prcxi",
+    "incubation": "incubator.prcxi",
+    "move_labware": "labware_mover.prcxi",
+    "oscillation": "shaker.prcxi",
+    # 有机化学操作
+    "HeatChillToTemp": "heatchill.chemputer",
+    "StopHeatChill": "heatchill.chemputer",
+    "StartHeatChill": "heatchill.chemputer",
+    "HeatChill": "heatchill.chemputer",
+    "Dissolve": "stirrer.chemputer",
+    "Transfer": "liquid_handler.chemputer",
+    "Evaporate": "rotavap.chemputer",
+    "Recrystallize": "reactor.chemputer",
+    "Filter": "filter.chemputer",
+    "Dry": "dryer.chemputer",
+    "Add": "liquid_handler.chemputer",
+}
+
+
+def normalize_steps(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+    """
+    将不同格式的步骤数据规范化为统一格式
+
+    支持的输入格式：
+    - action + parameters
+    - action + action_args
+    - operation + parameters
+
+    Args:
+        data: 原始步骤数据列表
+
+    Returns:
+        规范化后的步骤列表，格式为 [{"action": str, "parameters": dict, "description": str?, "step_number": int?}, ...]
+    """
+    normalized = []
+    for idx, step in enumerate(data):
+        # 获取动作名称（支持 action 或 operation 字段）
+        action = step.get("action") or step.get("operation")
+        if not action:
+            continue
+
+        # 获取参数（支持 parameters 或 action_args 字段）
+        raw_params = step.get("parameters") or step.get("action_args") or {}
+        params = dict(raw_params)
+
+        # 规范化 source/target -> sources/targets
+        if "source" in raw_params and "sources" not in raw_params:
+            params["sources"] = raw_params["source"]
+        if "target" in raw_params and "targets" not in raw_params:
+            params["targets"] = raw_params["target"]
+
+        # 获取描述（支持 description 或 purpose 字段）
+        description = step.get("description") or step.get("purpose")
+
+        # 获取步骤编号（优先使用原始数据中的 step_number，否则使用索引+1）
+        step_number = step.get("step_number", idx + 1)
+
+        step_dict = {"action": action, "parameters": params, "step_number": step_number}
+        if description:
+            step_dict["description"] = description
+
+        normalized.append(step_dict)
+
+    return normalized
+
+
+def normalize_labware(data: List[Dict[str, Any]]) -> Dict[str, Dict[str, Any]]:
+    """
+    将不同格式的 labware 数据规范化为统一的字典格式
+
+    支持的输入格式：
+    - reagent_name + material_name + positions
+    - name + labware + slot
+
+    Args:
+        data: 原始 labware 数据列表
+
+    Returns:
+        规范化后的 labware 字典，格式为 {name: {"slot": int, "labware": str, "well": list, "type": str, "role": str, "name": str}, ...}
+    """
+    labware = {}
+    for item in data:
+        # 获取 key 名称（优先使用 reagent_name，其次是 material_name 或 name）
+        reagent_name = item.get("reagent_name")
+        key = reagent_name or item.get("material_name") or item.get("name")
+        if not key:
+            continue
+
+        key = str(key)
+
+        # 处理重复 key，自动添加后缀
+        idx = 1
+        original_key = key
+        while key in labware:
+            idx += 1
+            key = f"{original_key}_{idx}"
+
+        labware[key] = {
+            "slot": item.get("positions") or item.get("slot"),
+            "labware": item.get("material_name") or item.get("labware"),
+            "well": item.get("well", []),
+            "type": item.get("type", "reagent"),
+            "role": item.get("role", ""),
+            "name": key,
+        }
+
+    return labware
+
+
+def convert_from_json(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = "PRCXi",
+    validate: bool = True,
+) -> WorkflowGraph:
+    """
+    从 JSON 数据或文件转换为 WorkflowGraph
+
+    支持的 JSON 格式：
+    1. {"workflow": [...], "reagent": {...}} - 直接格式
+    2. {"steps_info": [...], "labware_info": [...]} - 需要规范化的格式
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+        validate: 是否校验句柄配置，默认 True
+
+    Returns:
+        WorkflowGraph: 构建好的工作流图
+
+    Raises:
+        ValueError: 不支持的 JSON 格式 或 句柄校验失败
+        FileNotFoundError: 文件不存在
+        json.JSONDecodeError: JSON 解析失败
+    """
+    # 处理输入数据
+    if isinstance(data, (str, PathLike)):
+        path = Path(data)
+        if path.exists():
+            with path.open("r", encoding="utf-8") as fp:
+                json_data = json.load(fp)
+        elif isinstance(data, str):
+            # 尝试作为 JSON 字符串解析
+            json_data = json.loads(data)
+        else:
+            raise FileNotFoundError(f"文件不存在: {data}")
+    elif isinstance(data, dict):
+        json_data = data
+    else:
+        raise TypeError(f"不支持的数据类型: {type(data)}")
+
+    # 根据格式解析数据
+    if "workflow" in json_data and "reagent" in json_data:
+        # 格式1: workflow/reagent（已经是规范格式）
+        protocol_steps = json_data["workflow"]
+        labware_info = json_data["reagent"]
+    elif "steps_info" in json_data and "labware_info" in json_data:
+        # 格式2: steps_info/labware_info（需要规范化）
+        protocol_steps = normalize_steps(json_data["steps_info"])
+        labware_info = normalize_labware(json_data["labware_info"])
+    elif "steps" in json_data and "labware" in json_data:
+        # 格式3: steps/labware（另一种常见格式）
+        protocol_steps = normalize_steps(json_data["steps"])
+        if isinstance(json_data["labware"], list):
+            labware_info = normalize_labware(json_data["labware"])
+        else:
+            labware_info = json_data["labware"]
+    else:
+        raise ValueError(
+            "不支持的 JSON 格式。支持的格式：\n"
+            "1. {'workflow': [...], 'reagent': {...}}\n"
+            "2. {'steps_info': [...], 'labware_info': [...]}\n"
+            "3. {'steps': [...], 'labware': [...]}"
+        )
+
+    # 构建工作流图
+    graph = build_protocol_graph(
+        labware_info=labware_info,
+        protocol_steps=protocol_steps,
+        workstation_name=workstation_name,
+        action_resource_mapping=ACTION_RESOURCE_MAPPING,
+    )
+
+    # 校验句柄配置
+    if validate:
+        is_valid, errors = validate_workflow_handles(graph)
+        if not is_valid:
+            import warnings
+
+            for error in errors:
+                warnings.warn(f"句柄校验警告: {error}")
+
+    return graph
+
+
+def convert_json_to_node_link(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = "PRCXi",
+) -> Dict[str, Any]:
+    """
+    将 JSON 数据转换为 node-link 格式的字典
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        Dict: node-link 格式的工作流数据
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_node_link_dict()
+
+
+def convert_json_to_workflow_list(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = "PRCXi",
+) -> List[Dict[str, Any]]:
+    """
+    将 JSON 数据转换为工作流列表格式
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        List: 工作流节点列表
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_dict()
+
+
+# 为了向后兼容，保留下划线前缀的别名
+_normalize_steps = normalize_steps
+_normalize_labware = normalize_labware