no opcua installation on macos

fix possible crash

fix deck & host_node

set liquid with tube

add test_resource_schema

fix test resource schema

registry update & workflow update

add test mode

support description & tags upload

fix config load

fix log

add registry name & add always free

correct config organic synthesis

Adapt to new scheduler, sampels, and edge upload format (#230)

* add sample_material

* adapt to new samples sys

* fix pump transfer. fix resource update when protocol & ros callback

* Adapt to new scheduler.

Feat/samples (#229)

* add sample_material

* adapt to new samples sys

adapt to new samples sys

adapt to new edge format

workflow upload & prcxi transfer liquid

lh liquid

speed up registry load

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

fix upload workflow json

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -1,15 +1,11 @@
 from __future__ import annotations
 
-import asyncio
 import time
 import traceback
 from collections import Counter
 from typing import List, Sequence, Optional, Literal, Union, Iterator, Dict, Any, Callable, Set, cast
 
-from typing_extensions import TypedDict
 from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, LiquidHandlerChatterboxBackend, Strictness
-from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
-from unilabos.devices.liquid_handling.laiyu.backend.laiyu_v_backend import UniLiquidHandlerLaiyuBackend
 from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod
 from pylabrobot.liquid_handling.standard import GripDirection
 from pylabrobot.resources import (
@@ -25,28 +21,40 @@ from pylabrobot.resources import (
     ResourceHolder,
     Lid,
     Trash,
-    Tip,
+    Tip, TubeRack,
 )
+from typing_extensions import TypedDict
 
+from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
 from unilabos.registry.placeholder_type import ResourceSlot
-from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
-from unilabos.resources.resource_tracker import ResourceTreeSet
+from unilabos.resources.resource_tracker import (
+    ResourceTreeSet,
+    ResourceDict,
+    EXTRA_SAMPLE_UUID,
+    EXTRA_UNILABOS_SAMPLE_UUID,
+)
+from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, ROS2DeviceNode
 
 
 class SimpleReturn(TypedDict):
-    samples: list
-    volumes: list
+    samples: List[List[ResourceDict]]
+    volumes: List[float]
 
 
 class SetLiquidReturn(TypedDict):
-    wells: list
-    volumes: list
+    wells: List[List[ResourceDict]]
+    volumes: List[float]
 
 
 class SetLiquidFromPlateReturn(TypedDict):
-    plate: list
-    wells: list
-    volumes: list
+    plate: List[List[ResourceDict]]
+    wells: List[List[ResourceDict]]
+    volumes: List[float]
+
+
+class TransferLiquidReturn(TypedDict):
+    sources: List[List[ResourceDict]]
+    targets: List[List[ResourceDict]]
 
 
 class LiquidHandlerMiddleware(LiquidHandler):
@@ -228,12 +236,11 @@ class LiquidHandlerMiddleware(LiquidHandler):
         res_samples = []
         res_volumes = []
         for resource, volume, channel in zip(resources, vols, use_channels):
-            res_samples.append(
-                {"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)}
-            )
+            sample_uuid_value = resource.unilabos_extra.get(EXTRA_SAMPLE_UUID, None)
+            res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: sample_uuid_value})
             res_volumes.append(volume)
             self.pending_liquids_dict[channel] = {
-                "sample_uuid": resource.unilabos_extra.get("sample_uuid", None),
+                EXTRA_SAMPLE_UUID: sample_uuid_value,
                 "volume": volume,
             }
         return SimpleReturn(samples=res_samples, volumes=res_volumes)
@@ -275,10 +282,10 @@ class LiquidHandlerMiddleware(LiquidHandler):
         res_samples = []
         res_volumes = []
         for resource, volume, channel in zip(resources, vols, use_channels):
-            res_uuid = self.pending_liquids_dict[channel]["sample_uuid"]
+            res_uuid = self.pending_liquids_dict[channel][EXTRA_SAMPLE_UUID]
             self.pending_liquids_dict[channel]["volume"] -= volume
-            resource.unilabos_extra["sample_uuid"] = res_uuid
-            res_samples.append({"name": resource.name, "sample_uuid": res_uuid})
+            resource.unilabos_extra[EXTRA_SAMPLE_UUID] = res_uuid
+            res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: res_uuid})
             res_volumes.append(volume)
 
         return SimpleReturn(samples=res_samples, volumes=res_volumes)
@@ -682,16 +689,20 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
             wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), volumes=res_volumes  # type: ignore
         )
 
-    @classmethod
     def set_liquid_from_plate(
-        cls, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float]
+        self, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float]
     ) -> SetLiquidFromPlateReturn:
         """Set the liquid in wells of a plate by well names (e.g., A1, A2, B3).
 
         如果 liquid_names 和 volumes 为空，但 plate 和 well_names 不为空，直接返回 plate 和 wells。
         """
+        assert issubclass(plate.__class__, Plate) or issubclass(plate.__class__, TubeRack) , f"plate must be a Plate, now: {type(plate)}"
+        plate: Union[Plate, TubeRack]
         # 根据 well_names 获取对应的 Well 对象
-        wells = [plate.get_well(name) for name in well_names]
+        if issubclass(plate.__class__, Plate):
+            wells = [plate.get_well(name) for name in well_names]
+        elif issubclass(plate.__class__, TubeRack):
+            wells = [plate.get_tube(name) for name in well_names]
         res_volumes = []
 
         # 如果 liquid_names 和 volumes 都为空，直接返回
@@ -706,6 +717,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
             well.set_liquids([(liquid_name, volume)])  # type: ignore
             res_volumes.append(volume)
 
+        task = ROS2DeviceNode.run_async_func(self._ros_node.update_resource, True, **{"resources": wells})
+        submit_time = time.time()
+        while not task.done():
+            if time.time() - submit_time > 10:
+                self._ros_node.lab_logger().info(f"set_liquid_from_plate {plate} 超时")
+                break
+            time.sleep(0.01)
+
         return SetLiquidFromPlateReturn(
             plate=ResourceTreeSet.from_plr_resources([plate], known_newly_created=False).dump(),  # type: ignore
             wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(),  # type: ignore
@@ -1111,7 +1130,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
         mix_liquid_height: Optional[float] = None,
         delays: Optional[List[int]] = None,
         none_keys: List[str] = [],
-    ):
+    ) -> TransferLiquidReturn:
         """Transfer liquid with automatic mode detection.
 
         Supports three transfer modes:
@@ -1251,6 +1270,11 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                 "Supported modes: 1->N, N->1, or N->N."
             )
 
+        return TransferLiquidReturn(
+            sources=ResourceTreeSet.from_plr_resources(list(sources), known_newly_created=False).dump(),  # type: ignore
+            targets=ResourceTreeSet.from_plr_resources(list(targets), known_newly_created=False).dump(),  # type: ignore
+        )
+
     async def _transfer_one_to_one(
         self,
         sources: Sequence[Container],

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -52,6 +52,7 @@ from unilabos.devices.liquid_handling.liquid_handler_abstract import (
     SimpleReturn,
     SetLiquidReturn,
     SetLiquidFromPlateReturn,
+    TransferLiquidReturn,
 )
 from unilabos.registry.placeholder_type import ResourceSlot
 from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
@@ -90,7 +91,7 @@ class PRCXI9300Deck(Deck):
     """
 
     def __init__(self, name: str, size_x: float, size_y: float, size_z: float, **kwargs):
-        super().__init__(name, size_x, size_y, size_z)
+        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
 
@@ -154,25 +155,29 @@ class PRCXI9300Plate(Plate):
         **kwargs,
     ):
         # 如果 ordered_items 不为 None，直接使用
+        items = None
+        ordering_param = None
         if ordered_items is not None:
             items = ordered_items
         elif ordering is not None:
             # 检查 ordering 中的值是否是字符串（从 JSON 反序列化时的情况）
             # 如果是字符串，说明这是位置名称，需要让 Plate 自己创建 Well 对象
             # 我们只传递位置信息（键），不传递值，使用 ordering 参数
-            if ordering and isinstance(next(iter(ordering.values()), None), str):
-                # ordering 的值是字符串，只使用键（位置信息）创建新的 OrderedDict
-                # 传递 ordering 参数而不是 ordered_items，让 Plate 自己创建 Well 对象
-                items = None
-                # 使用 ordering 参数，只包含位置信息（键）
-                ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
+            if ordering:
+                values = list(ordering.values())
+                value = values[0]
+                if isinstance(value, str):
+                    # ordering 的值是字符串，只使用键（位置信息）创建新的 OrderedDict
+                    # 传递 ordering 参数而不是 ordered_items，让 Plate 自己创建 Well 对象
+                    items = None
+                    # 使用 ordering 参数，只包含位置信息（键）
+                    ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
+                elif value is None:
+                    ordering_param = ordering
             else:
                 # ordering 的值已经是对象，可以直接使用
                 items = ordering
                 ordering_param = None
-        else:
-            items = None
-            ordering_param = None
 
         # 根据情况传递不同的参数
         if items is not None:
@@ -243,14 +248,15 @@ class PRCXI9300TipRack(TipRack):
         if ordered_items is not None:
             items = ordered_items
         elif ordering is not None:
-            # 检查 ordering 中的值是否是字符串（从 JSON 反序列化时的情况）
-            # 如果是字符串，说明这是位置名称，需要让 TipRack 自己创建 Tip 对象
-            # 我们只传递位置信息（键），不传递值，使用 ordering 参数
-            if ordering and isinstance(next(iter(ordering.values()), None), str):
-                # ordering 的值是字符串，只使用键（位置信息）创建新的 OrderedDict
+            # 检查 ordering 中的值类型来决定如何处理：
+            # - 字符串值（从 JSON 反序列化）: 只用键创建 ordering_param
+            # - None 值（从第二次往返序列化）: 同样只用键创建 ordering_param
+            # - 对象值（已经是实际的 Resource 对象）: 直接作为 ordered_items 使用
+            first_val = next(iter(ordering.values()), None) if ordering else None
+            if not ordering or first_val is None or isinstance(first_val, str):
+                # ordering 的值是字符串或 None，只使用键（位置信息）创建新的 OrderedDict
                 # 传递 ordering 参数而不是 ordered_items，让 TipRack 自己创建 Tip 对象
                 items = None
-                # 使用 ordering 参数，只包含位置信息（键）
                 ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
             else:
                 # ordering 的值已经是对象，可以直接使用
@@ -392,14 +398,15 @@ class PRCXI9300TubeRack(TubeRack):
             items_to_pass = ordered_items
             ordering_param = None
         elif ordering is not None:
-            # 检查 ordering 中的值是否是字符串（从 JSON 反序列化时的情况）
-            # 如果是字符串，说明这是位置名称，需要让 TubeRack 自己创建 Tube 对象
-            # 我们只传递位置信息（键），不传递值，使用 ordering 参数
-            if ordering and isinstance(next(iter(ordering.values()), None), str):
-                # ordering 的值是字符串，只使用键（位置信息）创建新的 OrderedDict
+            # 检查 ordering 中的值类型来决定如何处理：
+            # - 字符串值（从 JSON 反序列化）: 只用键创建 ordering_param
+            # - None 值（从第二次往返序列化）: 同样只用键创建 ordering_param
+            # - 对象值（已经是实际的 Resource 对象）: 直接作为 ordered_items 使用
+            first_val = next(iter(ordering.values()), None) if ordering else None
+            if not ordering or first_val is None or isinstance(first_val, str):
+                # ordering 的值是字符串或 None，只使用键（位置信息）创建新的 OrderedDict
                 # 传递 ordering 参数而不是 ordered_items，让 TubeRack 自己创建 Tube 对象
                 items_to_pass = None
-                # 使用 ordering 参数，只包含位置信息（键）
                 ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
             else:
                 # ordering 的值已经是对象，可以直接使用
@@ -713,7 +720,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         mix_liquid_height: Optional[float] = None,
         delays: Optional[List[int]] = None,
         none_keys: List[str] = [],
-    ):
+    ) -> TransferLiquidReturn:
         return await super().transfer_liquid(
             sources,
             targets,