Merge remote-tracking branch 'origin/dev' into feature/organic-extraction

unilabos/app/main.py

@@ -1,6 +1,7 @@
 import argparse
 import asyncio
 import os
+import platform
 import shutil
 import signal
 import sys
@@ -358,7 +359,7 @@ def main():
     if BasicConfig.test_mode:
         print_status("启用测试模式：所有动作将模拟执行，不调用真实硬件", "warning")
     BasicConfig.communication_protocol = "websocket"
-    machine_name = os.popen("hostname").read().strip()
+    machine_name = platform.node()
     machine_name = "".join([c if c.isalnum() or c == "_" else "_" for c in machine_name])
     BasicConfig.machine_name = machine_name
     BasicConfig.vis_2d_enable = args_dict["2d_vis"]

unilabos/app/web/client.py

@@ -3,7 +3,7 @@ HTTP客户端模块
 
 提供与远程服务器通信的客户端功能，只有host需要用
 """
-
+import gzip
 import json
 import os
 from typing import List, Dict, Any, Optional
@@ -290,10 +290,17 @@ class HTTPClient:
         Returns:
             Response: API响应对象
         """
+        compressed_body = gzip.compress(
+            json.dumps(registry_data, ensure_ascii=False, default=str).encode("utf-8")
+        )
         response = requests.post(
             f"{self.remote_addr}/lab/resource",
-            json=registry_data,
-            headers={"Authorization": f"Lab {self.auth}"},
+            data=compressed_body,
+            headers={
+                "Authorization": f"Lab {self.auth}",
+                "Content-Type": "application/json",
+                "Content-Encoding": "gzip",
+            },
             timeout=30,
         )
         if response.status_code not in [200, 201]:

unilabos/app/ws_client.py

@@ -466,6 +466,7 @@ class MessageProcessor:
                 async with websockets.connect(
                     self.websocket_url,
                     ssl=ssl_context,
+                    open_timeout=20,
                     ping_interval=WSConfig.ping_interval,
                     ping_timeout=10,
                     additional_headers={
@@ -497,6 +498,18 @@ class MessageProcessor:
             except websockets.exceptions.ConnectionClosed:
                 logger.warning("[MessageProcessor] Connection closed")
                 self.connected = False
+            except TimeoutError:
+                logger.warning(
+                    f"[MessageProcessor] Connection timeout (attempt {self.reconnect_count + 1}), "
+                    f"server may be temporarily unavailable"
+                )
+                self.connected = False
+            except websockets.exceptions.InvalidStatus as e:
+                logger.warning(
+                    f"[MessageProcessor] Server returned unexpected HTTP status {e.response.status_code}, "
+                    f"WebSocket endpoint may not be ready yet"
+                )
+                self.connected = False
             except Exception as e:
                 logger.error(f"[MessageProcessor] Connection error: {str(e)}")
                 logger.error(traceback.format_exc())
@@ -505,18 +518,19 @@ class MessageProcessor:
                 self.websocket = None
 
             # 重连逻辑
-            if self.is_running and self.reconnect_count < WSConfig.max_reconnect_attempts:
+            if not self.is_running:
+                break
+            if self.reconnect_count < WSConfig.max_reconnect_attempts:
                 self.reconnect_count += 1
+                backoff = min(WSConfig.reconnect_interval * (2 ** (self.reconnect_count - 1)), 60)
                 logger.info(
-                    f"[MessageProcessor] Reconnecting in {WSConfig.reconnect_interval}s "
+                    f"[MessageProcessor] Reconnecting in {backoff}s "
                     f"(attempt {self.reconnect_count}/{WSConfig.max_reconnect_attempts})"
                 )
-                await asyncio.sleep(WSConfig.reconnect_interval)
-            elif self.reconnect_count >= WSConfig.max_reconnect_attempts:
+                await asyncio.sleep(backoff)
+            else:
                 logger.error("[MessageProcessor] Max reconnection attempts reached")
                 break
-            else:
-                self.reconnect_count -= 1
 
     async def _message_handler(self):
         """处理接收到的消息"""

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -55,6 +55,7 @@ from unilabos.devices.liquid_handling.liquid_handler_abstract import (
     TransferLiquidReturn,
 )
 from unilabos.registry.placeholder_type import ResourceSlot
+from unilabos.resources.resource_tracker import ResourceTreeSet
 from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
 
 
@@ -90,20 +91,103 @@ class PRCXI9300Deck(Deck):
     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, **kwargs):
+    # T1-T16 默认位置 (4列×4行)
+    _DEFAULT_SITE_POSITIONS = [
+        (0, 0, 0), (138, 0, 0), (276, 0, 0), (414, 0, 0),         # T1-T4
+        (0, 96, 0), (138, 96, 0), (276, 96, 0), (414, 96, 0),     # T5-T8
+        (0, 192, 0), (138, 192, 0), (276, 192, 0), (414, 192, 0), # T9-T12
+        (0, 288, 0), (138, 288, 0), (276, 288, 0), (414, 288, 0), # T13-T16
+    ]
+    _DEFAULT_SITE_SIZE = {"width": 128.0, "height": 86, "depth": 0}
+    _DEFAULT_CONTENT_TYPE = ["plate", "tip_rack", "plates", "tip_racks", "tube_rack", "adaptor"]
+
+    def __init__(self, name: str, size_x: float, size_y: float, size_z: float,
+                 sites: Optional[List[Dict[str, Any]]] = None, **kwargs):
         super().__init__(size_x, size_y, size_z, name)
-        self.slots = [None] * 16  # PRCXI 9300/9320 最大有 16 个槽位
-        self.slot_locations = [Coordinate(0, 0, 0)] * 16
+        if sites is not None:
+            self.sites: List[Dict[str, Any]] = [dict(s) for s in sites]
+        else:
+            self.sites = []
+            for i, (x, y, z) in enumerate(self._DEFAULT_SITE_POSITIONS):
+                self.sites.append({
+                    "label": f"T{i + 1}",
+                    "visible": True,
+                    "position": {"x": x, "y": y, "z": z},
+                    "size": dict(self._DEFAULT_SITE_SIZE),
+                    "content_type": list(self._DEFAULT_CONTENT_TYPE),
+                })
+        # _ordering: label -> None, 用于外部通过 list(keys()).index(site) 将 Tn 转换为 spot index
+        self._ordering = collections.OrderedDict(
+            (site["label"], None) for site in self.sites
+        )
+
+    def _get_site_location(self, idx: int) -> Coordinate:
+        pos = self.sites[idx]["position"]
+        return Coordinate(pos["x"], pos["y"], pos["z"])
+
+    def _get_site_resource(self, idx: int) -> Optional[Resource]:
+        site_loc = self._get_site_location(idx)
+        for child in self.children:
+            if child.location == site_loc:
+                return child
+        return None
+
+    def assign_child_resource(
+        self,
+        resource: Resource,
+        location: Optional[Coordinate] = None,
+        reassign: bool = True,
+        spot: Optional[int] = None,
+    ):
+        idx = spot
+        if spot is not None:
+            idx = spot
+        else:
+            for i, site in enumerate(self.sites):
+                site_loc = self._get_site_location(i)
+                if site.get("label") == resource.name:
+                    idx = i
+                    break
+                if location is not None and site_loc == location:
+                    idx = i
+                    break
+
+        if idx is None:
+            for i in range(len(self.sites)):
+                if self._get_site_resource(i) is None:
+                    idx = i
+                    break
+
+        if idx is None:
+            raise ValueError(f"No available site on deck '{self.name}' for resource '{resource.name}'")
+
+        if not reassign and self._get_site_resource(idx) is not None:
+            raise ValueError(f"Site {idx} ('{self.sites[idx]['label']}') is already occupied")
+
+        loc = self._get_site_location(idx)
+        super().assign_child_resource(resource, location=loc, reassign=reassign)
 
     def assign_child_at_slot(self, resource: Resource, slot: int, reassign: bool = False) -> None:
-        if self.slots[slot - 1] is not None and not reassign:
-            raise ValueError(f"Spot {slot} is already occupied")
+        self.assign_child_resource(resource, spot=slot - 1, reassign=reassign)
 
-        self.slots[slot - 1] = resource
-        super().assign_child_resource(resource, location=self.slot_locations[slot - 1])
+    def serialize(self) -> dict:
+        data = super().serialize()
+        sites_out = []
+        for i, site in enumerate(self.sites):
+            occupied = self._get_site_resource(i)
+            sites_out.append({
+                "label": site["label"],
+                "visible": site.get("visible", True),
+                "occupied_by": occupied.name if occupied is not None else None,
+                "position": site["position"],
+                "size": site["size"],
+                "content_type": site["content_type"],
+            })
+        data["sites"] = sites_out
+        return data
 
 
-class PRCXI9300Container(Plate):
+class PRCXI9300Container(Container):
     """PRCXI 9300 的专用 Container 类，继承自 Plate，用于槽位定位和未知模块。
 
     该类定义了 PRCXI 9300 的工作台布局和槽位信息。
@@ -116,11 +200,10 @@ class PRCXI9300Container(Plate):
         size_y: float,
         size_z: float,
         category: str,
-        ordering: collections.OrderedDict,
         model: Optional[str] = None,
         **kwargs,
     ):
-        super().__init__(name, size_x, size_y, size_z, category=category, ordering=ordering, model=model)
+        super().__init__(name, size_x, size_y, size_z, category=category, model=model)
         self._unilabos_state = {}
 
     def load_state(self, state: Dict[str, Any]) -> None:
@@ -567,14 +650,14 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         tablets_info = []
         count = 0
         for child in deck.children:
-            if child.children:
-                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"]
-                        )
+            # 如果放其他类型的物料，是不可以的
+            if hasattr(child, "_unilabos_state") and "Material" in child._unilabos_state:
+                number = int(child.name.replace("T", ""))
+                tablets_info.append(
+                    WorkTablets(
+                        Number=number, Code=f"T{number}", Material=child._unilabos_state["Material"]
                     )
+                )
         if is_9320:
             print("当前设备是9320")
         # 始终初始化 step_mode 属性

unilabos/registry/registry.py

@@ -175,7 +175,8 @@ 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",
+                                    "class_name": "unilabos_class",  # 当前实验室物料的class name
+                                    "slot_on_deck": "unilabos_resource_slot:parent",  # 勾选的parent的config中的sites的name，展示name，参数对应slot（index）
                                 },
                             },
                             "test_latency": {

unilabos/resources/container.py

@@ -1,10 +1,6 @@
-import json
 from typing import Dict, Any
 
 from pylabrobot.resources import Container
-from unilabos_msgs.msg import Resource
-
-from unilabos.ros.msgs.message_converter import convert_from_ros_msg
 
 
 class RegularContainer(Container):
@@ -16,12 +12,12 @@ class RegularContainer(Container):
             kwargs["size_y"] = 0
         if "size_z" not in kwargs:
             kwargs["size_z"] = 0
+
         self.kwargs = kwargs
-        self.state = {}
         super().__init__(*args, category="container", **kwargs)
 
     def load_state(self, state: Dict[str, Any]):
-        self.state = state
+        super().load_state(state)
 
 
 def get_regular_container(name="container"):
@@ -29,7 +25,6 @@ def get_regular_container(name="container"):
     r.category = "container"
     return r
 
-#
 # class RegularContainer(object):
 #     # 第一个参数必须是id传入
 #     # noinspection PyShadowingBuiltins
@@ -89,4 +84,4 @@ def get_regular_container(name="container"):
 #         return to_dict
 #
 #     def __str__(self):
-#         return f"{self.id}"
+#         return f"{self.id}"

unilabos/resources/graphio.py

@@ -76,7 +76,7 @@ def canonicalize_nodes_data(
             if sample_id:
                 logger.error(f"{node}的sample_id参数已弃用，sample_id: {sample_id}")
         for k in list(node.keys()):
-            if k not in ["id", "uuid", "name", "description", "schema", "model", "icon", "parent_uuid", "parent", "type", "class", "position", "config", "data", "children", "pose"]:
+            if k not in ["id", "uuid", "name", "description", "schema", "model", "icon", "parent_uuid", "parent", "type", "class", "position", "config", "data", "children", "pose", "extra"]:
                 v = node.pop(k)
                 node["config"][k] = v
     if outer_host_node_id is not None:

unilabos/resources/resource_tracker.py

@@ -16,6 +16,7 @@ if TYPE_CHECKING:
 
 
 EXTRA_CLASS = "unilabos_resource_class"
+FRONTEND_POSE_EXTRA = "unilabos_frontend_pose_extra"
 EXTRA_SAMPLE_UUID = "sample_uuid"
 EXTRA_UNILABOS_SAMPLE_UUID = "unilabos_sample_uuid"
 
@@ -100,6 +101,7 @@ class ResourceDictPosition(BaseModel):
     cross_section_type: Literal["rectangle", "circle", "rounded_rectangle"] = Field(
         description="Cross section type", default="rectangle"
     )
+    extra: Optional[Dict[str, Any]] = Field(description="Extra data", default=None)
 
 
 class ResourceDictType(TypedDict):
@@ -412,6 +414,15 @@ class ResourceTreeSet(object):
                 "tip": "tip",  # 添加 tip 类型支持
                 "tube": "tube",
                 "bottle_carrier": "bottle_carrier",
+                "material_hole": "material_hole",
+                "container": "container",
+                "material_plate": "material_plate",
+                "electrode_sheet": "electrode_sheet",
+                "warehouse": "warehouse",
+                "magazine_holder": "magazine_holder",
+                "resource_group": "resource_group",
+                "trash": "trash",
+                "plate_adapter": "plate_adapter",
             }
             if source in replace_info:
                 return replace_info[source]
@@ -455,6 +466,7 @@ class ResourceTreeSet(object):
                 "position3d": raw_pos,
                 "rotation": d["rotation"],
                 "cross_section_type": d.get("cross_section_type", "rectangle"),
+                "extra": extra.get(FRONTEND_POSE_EXTRA)
             }
 
             # 先构建当前节点的字典（不包含children）
@@ -540,6 +552,7 @@ 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][FRONTEND_POSE_EXTRA] = node.res_content.pose.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)
@@ -608,7 +621,7 @@ class ResourceTreeSet(object):
                 plr_resources.append(plr_resource)
 
             except Exception as e:
-                logger.error(f"转换 PLR 资源失败: {e}")
+                logger.error(f"转换 PLR 资源失败: {e} {str(plr_dict)[:1000]}")
                 import traceback
 
                 logger.error(f"堆栈: {traceback.format_exc()}")
@@ -828,14 +841,27 @@ class ResourceTreeSet(object):
                                 f"从远端同步了 {added_count} 个物料子树"
                             )
                     else:
-                        # 情况2: 二级是物料（不是 device）
-                        if remote_child_name not in local_children_map:
-                            # 引入整个子树
-                            remote_child.res_content.parent = local_device.res_content
-                            local_device.children.append(remote_child)
-                            logger.info(f"Device '{remote_root_id}': 从远端同步物料子树 '{remote_child_name}'")
-                        else:
-                            logger.info(f"物料 '{remote_root_id}/{remote_child_name}' 已存在，跳过")
+                        # 二级物料已存在，比较三级子节点是否缺失
+                        local_material = local_children_map[remote_child_name]
+                        local_material_children_map = {child.res_content.name: child for child in
+                                                       local_material.children}
+                        added_count = 0
+                        for remote_sub in remote_child.children:
+                            remote_sub_name = remote_sub.res_content.name
+                            if remote_sub_name not in local_material_children_map:
+                                remote_sub.res_content.parent = local_material.res_content
+                                local_material.children.append(remote_sub)
+                                added_count += 1
+                            else:
+                                logger.info(
+                                    f"物料 '{remote_root_id}/{remote_child_name}/{remote_sub_name}' "
+                                    f"已存在，跳过"
+                                )
+                        if added_count > 0:
+                            logger.info(
+                                f"物料 '{remote_root_id}/{remote_child_name}': "
+                                f"从远端同步了 {added_count} 个子物料"
+                            )
             else:
                 # 情况1: 一级节点是物料（不是 device）
                 # 检查是否已存在

unilabos/ros/nodes/base_device_node.py

@@ -915,8 +915,24 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         else []
                     )
                     if target_site is not None and sites is not None and site_names is not None:
-                        site_index = sites.index(original_instance)
-                        site_name = site_names[site_index]
+                        site_index = None
+                        try:
+                            # sites 可能是 Resource 列表或 dict 列表 (如 PRCXI9300Deck)
+                            # 只有itemized_carrier在使用，准备弃用
+                            site_index = sites.index(original_instance)
+                        except ValueError:
+                            # dict 类型的 sites: 通过name匹配
+                            for idx, site in enumerate(sites):
+                                if original_instance.name == site["occupied_by"]:
+                                    site_index = idx
+                                    break
+                                elif (original_instance.location.x == site["position"]["x"] and original_instance.location.y == site["position"]["y"] and original_instance.location.z == site["position"]["z"]):
+                                    site_index = idx
+                                    break
+                        if site_index is None:
+                            site_name = None
+                        else:
+                            site_name = site_names[site_index]
                         if site_name != target_site:
                             parent = self.transfer_to_new_resource(original_instance, tree, additional_add_params)
                             if parent is not None:
@@ -924,6 +940,14 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                                 parent_appended = True
 
                 # 加载状态
+                # noinspection PyProtectedMember
+                original_instance._size_x = plr_resource._size_x
+                # noinspection PyProtectedMember
+                original_instance._size_y = plr_resource._size_y
+                # noinspection PyProtectedMember
+                original_instance._size_z = plr_resource._size_z
+                # noinspection PyProtectedMember
+                original_instance._local_size_z = plr_resource._local_size_z
                 original_instance.location = plr_resource.location
                 original_instance.rotation = plr_resource.rotation
                 original_instance.barcode = plr_resource.barcode
@@ -984,7 +1008,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         ].call_async(
                             r
                         )  # type: ignore
-                        self.lab_logger().info(f"确认资源云端 Add 结果: {response.response}")
+                        self.lab_logger().trace(f"确认资源云端 Add 结果: {response.response}")
                         results.append(result)
                     elif action == "update":
                         if tree_set is None:
@@ -1010,7 +1034,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                             ].call_async(
                                 r
                             )  # type: ignore
-                            self.lab_logger().info(f"确认资源云端 Update 结果: {response.response}")
+                            self.lab_logger().trace(f"确认资源云端 Update 结果: {response.response}")
                         results.append(result)
                     elif action == "remove":
                         result = _handle_remove(resources_uuid)

unilabos/ros/nodes/presets/host_node.py

@@ -1195,7 +1195,7 @@ class HostNode(BaseROS2DeviceNode):
                 self.lab_logger().info(f"[Host Node-Resource] UUID映射: {len(uuid_mapping)} 个节点")
             # 还需要加入到资源图中，暂不实现，考虑资源图新的获取方式
             response.response = json.dumps(uuid_mapping)
-            self.lab_logger().info(f"[Host Node-Resource] Resource tree add completed, success: {success}")
+            self.lab_logger().info(f"[Host Node-Resource] Resource tree update completed, success: {success}")
 
     async def _resource_tree_update_callback(self, request: SerialCommand_Request, response: SerialCommand_Response):
         """

unilabos/workflow/common.py

@@ -26,7 +26,7 @@
     res_id: plate_slot_{slot}
     device_id: /PRCXI
     class_name: PRCXI_BioER_96_wellplate
-    parent: /PRCXI/PRCXI_Deck/T{slot}
+    parent: /PRCXI/PRCXI_Deck
     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
@@ -122,7 +122,7 @@ NODE_TYPE_DEFAULT = "ILab"  # 所有节点的默认类型
 # 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
+    "parent_template": "/PRCXI/PRCXI_Deck",
     "class_name": "PRCXI_BioER_96_wellplate",
 }
 
@@ -424,7 +424,7 @@ def build_protocol_graph(
                 "res_id": res_id,
                 "device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
                 "class_name": lw_type,
-                "parent": CREATE_RESOURCE_DEFAULTS["parent_template"].format(slot=slot),
+                "parent": CREATE_RESOURCE_DEFAULTS["parent_template"],
                 "bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
                 "slot_on_deck": slot,
             },