Merge branch 'pr/169' into workstation_YB_merge_dev_ready_260113

unilabos/resources/bioyond/bottles.py

@@ -193,3 +193,20 @@ def BIOYOND_PolymerStation_Flask(
         barcode=barcode,
         model="BIOYOND_PolymerStation_Flask",
     )
+
+def BIOYOND_PolymerStation_Measurement_Vial(
+    name: str,
+    diameter: float = 25.0,
+    height: float = 60.0,
+    max_volume: float = 20000.0,  # 20mL
+    barcode: str = None,
+) -> Bottle:
+    """创建测量小瓶"""
+    return Bottle(
+        name=name,
+        diameter=diameter,
+        height=height,
+        max_volume=max_volume,
+        barcode=barcode,
+        model="BIOYOND_PolymerStation_Measurement_Vial",
+    )

unilabos/resources/bioyond/decks.py

@@ -51,20 +51,17 @@ class BIOYOND_PolymerReactionStation_Deck(Deck):
             "测量小瓶仓库(测密度)": bioyond_warehouse_density_vial("测量小瓶仓库(测密度)"),  # A01～B03
         }
         self.warehouse_locations = {
-            "堆栈1左": Coordinate(0.0, 430.0, 0.0),  # 左侧位置
-            "堆栈1右": Coordinate(2500.0, 430.0, 0.0),  # 右侧位置
-            "站内试剂存放堆栈": Coordinate(640.0, 480.0, 0.0),
+            "堆栈1左": Coordinate(-200.0, 450.0, 0.0),  # 左侧位置
+            "堆栈1右": Coordinate(2350.0, 450.0, 0.0),  # 右侧位置
+            "站内试剂存放堆栈": Coordinate(730.0, 390.0, 0.0),
             # "移液站内10%分装液体准备仓库": Coordinate(1200.0, 600.0, 0.0),
             "站内Tip盒堆栈": Coordinate(300.0, 150.0, 0.0),
-            "测量小瓶仓库(测密度)": Coordinate(922.0, 552.0, 0.0),
+            "测量小瓶仓库(测密度)": Coordinate(940.0, 530.0, 0.0),
         }
-        self.warehouses["站内试剂存放堆栈"].rotation = Rotation(z=90)
-        self.warehouses["测量小瓶仓库(测密度)"].rotation = Rotation(z=270)
 
         for warehouse_name, warehouse in self.warehouses.items():
             self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
 
-
 class BIOYOND_PolymerPreparationStation_Deck(Deck):
     def __init__(
         self,
@@ -148,6 +145,7 @@ class BIOYOND_YB_Deck(Deck):
 
         for warehouse_name, warehouse in self.warehouses.items():
             self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
+
 def YB_Deck(name: str) -> Deck:
     by=BIOYOND_YB_Deck(name=name)
     by.setup()

unilabos/resources/bioyond/warehouses.py

@@ -46,41 +46,55 @@ def bioyond_warehouse_1x4x4_right(name: str) -> WareHouse:
     )
 
 def bioyond_warehouse_density_vial(name: str) -> WareHouse:
-    """创建测量小瓶仓库(测密度) A01～B03"""
+    """创建测量小瓶仓库(测密度) - 竖向排列2列3行
+    布局（从下到上，从左到右）：
+    | A03 | B03 |  ← 顶部
+    | A02 | B02 |  ← 中部
+    | A01 | B01 |  ← 底部
+    """
     return warehouse_factory(
         name=name,
-        num_items_x=3,  # 3列（01-03）
-        num_items_y=2,  # 2行（A-B）
+        num_items_x=2,  # 2列（A, B）
+        num_items_y=3,  # 3行（01-03，从下到上）
         num_items_z=1,  # 1层
         dx=10.0,
         dy=10.0,
         dz=10.0,
-        item_dx=40.0,
-        item_dy=40.0,
+        item_dx=40.0,  # 列间距（A到B的横向距离）
+        item_dy=40.0,  # 行间距（01到02到03的竖向距离）
         item_dz=50.0,
-        # 用更小的 resource_size 来表现 "小点的孔位"
+        # ⭐ 竖向warehouse：槽位尺寸也是竖向的（小瓶已经是正方形，无需调整）
         resource_size_x=30.0,
         resource_size_y=30.0,
         resource_size_z=12.0,
         category="warehouse",
         col_offset=0,
-        layout="row-major",
+        layout="vertical-col-major",  # ⭐ 竖向warehouse专用布局
     )
 
 def bioyond_warehouse_reagent_storage(name: str) -> WareHouse:
-    """创建BioYond站内试剂存放堆栈（A01～A02, 1行×2列）"""
+    """创建BioYond站内试剂存放堆栈 - 竖向排列1列2行
+    布局（竖向，从下到上）：
+    | A02 |  ← 顶部
+    | A01 |  ← 底部
+    """
     return warehouse_factory(
         name=name,
-        num_items_x=2,  # 2列（01-02）
-        num_items_y=1,  # 1行（A）
+        num_items_x=1,  # 1列
+        num_items_y=2,  # 2行（01-02，从下到上）
         num_items_z=1,  # 1层
         dx=10.0,
         dy=10.0,
         dz=10.0,
-        item_dx=137.0,
-        item_dy=96.0,
+        item_dx=96.0,   # 列间距（这里只有1列，不重要）
+        item_dy=137.0,  # 行间距（A01到A02的竖向距离）
         item_dz=120.0,
+        # ⭐ 竖向warehouse：交换槽位尺寸，使槽位框也是竖向的
+        resource_size_x=86.0,   # 原来的 resource_size_y
+        resource_size_y=127.0,  # 原来的 resource_size_x
+        resource_size_z=25.0,
         category="warehouse",
+        layout="vertical-col-major",  # ⭐ 竖向warehouse专用布局
     )
 
 def bioyond_warehouse_tipbox_storage(name: str) -> WareHouse:

unilabos/resources/container.py

@@ -27,7 +27,7 @@ class RegularContainer(Container):
 def get_regular_container(name="container"):
     r = RegularContainer(name=name)
     r.category = "container"
-    return RegularContainer(name=name)
+    return r
 
 #
 # class RegularContainer(object):

unilabos/resources/graphio.py

@@ -779,6 +779,22 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
             if not locations:
                 logger.debug(f"[物料位置] {unique_name} 没有location信息，跳过warehouse放置")
 
+            # ⭐ 预先检查：如果物料的任何location在竖向warehouse中，提前交换尺寸
+            # 这样可以避免多个location时尺寸不一致的问题
+            needs_size_swap = False
+            for loc in locations:
+                wh_name_check = loc.get("whName")
+                if wh_name_check in ["站内试剂存放堆栈", "测量小瓶仓库(测密度)"]:
+                    needs_size_swap = True
+                    break
+
+            if needs_size_swap and hasattr(plr_material, 'size_x') and hasattr(plr_material, 'size_y'):
+                original_x = plr_material.size_x
+                original_y = plr_material.size_y
+                plr_material.size_x = original_y
+                plr_material.size_y = original_x
+                logger.debug(f"   物料 {unique_name} 将放入竖向warehouse，预先交换尺寸: {original_x}×{original_y} → {plr_material.size_x}×{plr_material.size_y}")
+
             for loc in locations:
                 wh_name = loc.get("whName")
                 logger.debug(f"[物料位置] {unique_name} 尝试放置到 warehouse: {wh_name} (Bioyond坐标: x={loc.get('x')}, y={loc.get('y')}, z={loc.get('z')})")
@@ -800,7 +816,6 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
                     logger.debug(f"[Warehouse匹配] 找到warehouse: {wh_name} (容量: {warehouse.capacity}, 行×列: {warehouse.num_items_x}×{warehouse.num_items_y})")
 
                     # Bioyond坐标映射 (重要！): x→行(1=A,2=B...), y→列(1=01,2=02...), z→层(通常=1)
-                    # PyLabRobot warehouse是列优先存储: A01,B01,C01,D01, A02,B02,C02,D02, ...
                     x = loc.get("x", 1)  # 行号 (1-based: 1=A, 2=B, 3=C, 4=D)
                     y = loc.get("y", 1)  # 列号 (1-based: 1=01, 2=02, 3=03...)
                     z = loc.get("z", 1)  # 层号 (1-based, 通常为1)
@@ -809,12 +824,23 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
                     if wh_name == "堆栈1右":
                         y = y - 4  # 将5-8映射到1-4
 
-                    # 特殊处理：对于1行×N列的横向warehouse（如站内试剂存放堆栈）
-                    # Bioyond的y坐标表示线性位置序号，而不是列号
-                    if warehouse.num_items_y == 1:
-                        # 1行warehouse: 直接用y作为线性索引
-                        idx = y - 1
-                        logger.debug(f"1行warehouse {wh_name}: y={y} → idx={idx}")
+                    # 特殊处理竖向warehouse（站内试剂存放堆栈、测量小瓶仓库）
+                    # 这些warehouse使用 vertical-col-major 布局
+                    if wh_name in ["站内试剂存放堆栈", "测量小瓶仓库(测密度)"]:
+                        # vertical-col-major 布局的坐标映射：
+                        # - Bioyond的x(1=A,2=B)对应warehouse的列(col, x方向)
+                        # - Bioyond的y(1=01,2=02,3=03)对应warehouse的行(row, y方向)，从下到上
+                        # vertical-col-major 中: row=0 对应底部，row=n-1 对应顶部
+                        # Bioyond y=1(01) 对应底部 → row=0, y=2(02) 对应中间 → row=1
+                        # 索引计算: idx = row * num_cols + col
+                        col_idx = x - 1  # Bioyond的x(A,B) → col索引(0,1)
+                        row_idx = y - 1  # Bioyond的y(01,02,03) → row索引(0,1,2)
+                        layer_idx = z - 1
+
+                        idx = layer_idx * (warehouse.num_items_x * warehouse.num_items_y) + row_idx * warehouse.num_items_x + col_idx
+                        logger.debug(f"🔍 竖向warehouse {wh_name}: Bioyond(x={x},y={y},z={z}) → warehouse(col={col_idx},row={row_idx},layer={layer_idx}) → idx={idx}, capacity={warehouse.capacity}")
+
+                    # 普通横向warehouse的处理
                     else:
                         # 多行warehouse: 根据 layout 使用不同的索引计算
                         row_idx = x - 1  # x表示行: 转为0-based
@@ -838,6 +864,7 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
 
                     if 0 <= idx < warehouse.capacity:
                         if warehouse[idx] is None or isinstance(warehouse[idx], ResourceHolder):
+                            # 物料尺寸已在放入warehouse前根据需要进行了交换
                             warehouse[idx] = plr_material
                             logger.debug(f"✅ 物料 {unique_name} 放置到 {wh_name}[{idx}] (Bioyond坐标: x={loc.get('x')}, y={loc.get('y')})")
                     else:
@@ -1011,11 +1038,24 @@ def resource_plr_to_bioyond(plr_resources: list[ResourcePLR], type_mapping: dict
                 logger.debug(f"  📭 [单瓶物料] {resource.name} 无液体，使用资源名: {material_name}")
 
             # 🎯 处理物料默认参数和单位
-            # 检查是否有该物料名称的默认参数配置
+            # 优先级: typeId参数 > 物料名称参数 > 默认值
             default_unit = "个"  # 默认单位
             material_parameters = {}
 
-            if material_name in material_params:
+            # 1️⃣ 首先检查是否有 typeId 对应的参数配置（从 material_params 中获取，key 格式为 "type:<typeId>"）
+            type_params_key = f"type:{type_id}"
+            if type_params_key in material_params:
+                params_config = material_params[type_params_key].copy()
+
+                # 提取 unit 字段（如果有）
+                if "unit" in params_config:
+                    default_unit = params_config.pop("unit")  # 从参数中移除，放到外层
+
+                # 剩余的字段放入 Parameters
+                material_parameters = params_config
+                logger.debug(f"  🔧 [物料参数-按typeId] 为 typeId={type_id[:8]}... 应用配置: unit={default_unit}, parameters={material_parameters}")
+            # 2️⃣ 其次检查是否有该物料名称的默认参数配置
+            elif material_name in material_params:
                 params_config = material_params[material_name].copy()
 
                 # 提取 unit 字段（如果有）
@@ -1024,7 +1064,7 @@ def resource_plr_to_bioyond(plr_resources: list[ResourcePLR], type_mapping: dict
 
                 # 剩余的字段放入 Parameters
                 material_parameters = params_config
-                logger.debug(f"  🔧 [物料参数] 为 {material_name} 应用配置: unit={default_unit}, parameters={material_parameters}")
+                logger.debug(f"  🔧 [物料参数-按名称] 为 {material_name} 应用配置: unit={default_unit}, parameters={material_parameters}")
 
             # 转换为 JSON 字符串
             parameters_json = json.dumps(material_parameters) if material_parameters else "{}"
@@ -1151,11 +1191,7 @@ def initialize_resource(resource_config: dict, resource_type: Any = None) -> Uni
         if resource_class_config["type"] == "pylabrobot":
             resource_plr = RESOURCE(name=resource_config["name"])
             if resource_type != ResourcePLR:
-                tree_sets = ResourceTreeSet.from_plr_resources([resource_plr])
-                # r = resource_plr_to_ulab(resource_plr=resource_plr, parent_name=resource_config.get("parent", None))
-                # # r = resource_plr_to_ulab(resource_plr=resource_plr)
-                # if resource_config.get("position") is not None:
-                #     r["position"] = resource_config["position"]
+                tree_sets = ResourceTreeSet.from_plr_resources([resource_plr], known_newly_created=True)
                 r = tree_sets.dump()
             else:
                 r = resource_plr

unilabos/resources/itemized_carrier.py

@@ -50,12 +50,45 @@ class Bottle(Well):
         self.barcode = barcode
 
     def serialize(self) -> dict:
+        # Pylabrobot expects barcode to be an object with serialize(), but here it is a str.
+        # We temporarily unset it to avoid AttributeError in super().serialize().
+        _barcode = self.barcode
+        self.barcode = None
+        try:
+            data = super().serialize()
+        finally:
+            self.barcode = _barcode
+
         return {
-            **super().serialize(),
+            **data,
             "diameter": self.diameter,
             "height": self.height,
         }
 
+    @classmethod
+    def deserialize(cls, data: dict, allow_marshal: bool = False):
+        # Extract barcode before calling parent deserialize to avoid type error
+        barcode_data = data.pop("barcode", None)
+
+        # Call parent deserialize
+        instance = super(Bottle, cls).deserialize(data, allow_marshal=allow_marshal)
+
+        # Set barcode as string (not as Barcode object)
+        if barcode_data:
+            if isinstance(barcode_data, str):
+                instance.barcode = barcode_data
+            elif isinstance(barcode_data, dict):
+                # If it's a dict (Barcode serialized format), extract the data field
+                instance.barcode = barcode_data.get("data", "")
+        else:
+            instance.barcode = ""
+
+        # Set additional attributes
+        instance.diameter = data.get("diameter", instance._size_x)
+        instance.height = data.get("height", instance._size_z)
+
+        return instance
+
 T = TypeVar("T", bound=ResourceHolder)
 
 S = TypeVar("S", bound=ResourceHolder)

unilabos/resources/resource_tracker.py

@@ -1,7 +1,7 @@
 import inspect
 import traceback
 import uuid
-from pydantic import BaseModel, field_serializer, field_validator
+from pydantic import BaseModel, field_serializer, field_validator, ValidationError
 from pydantic import Field
 from typing import List, Tuple, Any, Dict, Literal, Optional, cast, TYPE_CHECKING, Union
 
@@ -147,20 +147,24 @@ class ResourceDictInstance(object):
         if not content.get("extra"):  # MagicCode
             content["extra"] = {}
         if "position" in content:
-            pose = content.get("pose",{})
-            if "position" not in pose :
+            pose = content.get("pose", {})
+            if "position" not in pose:
                 if "position" in content["position"]:
                     pose["position"] = content["position"]["position"]
                 else:
                     pose["position"] = {"x": 0, "y": 0, "z": 0}
             if "size" not in pose:
                 pose["size"] = {
-                    "width": content["config"].get("size_x", 0), 
-                    "height": content["config"].get("size_y", 0), 
-                    "depth": content["config"].get("size_z", 0)
+                    "width": content["config"].get("size_x", 0),
+                    "height": content["config"].get("size_y", 0),
+                    "depth": content["config"].get("size_z", 0),
                 }
             content["pose"] = pose
-        return ResourceDictInstance(ResourceDict.model_validate(content))
+        try:
+            res_dict = ResourceDict.model_validate(content)
+            return ResourceDictInstance(res_dict)
+        except ValidationError as err:
+            raise err
 
     def get_plr_nested_dict(self) -> Dict[str, Any]:
         """获取资源实例的嵌套字典表示"""
@@ -322,7 +326,7 @@ class ResourceTreeSet(object):
             )
 
     @classmethod
-    def from_plr_resources(cls, resources: List["PLRResource"]) -> "ResourceTreeSet":
+    def from_plr_resources(cls, resources: List["PLRResource"], known_newly_created=False) -> "ResourceTreeSet":
         """
         从plr资源创建ResourceTreeSet
         """
@@ -339,6 +343,8 @@ class ResourceTreeSet(object):
             }
             if source in replace_info:
                 return replace_info[source]
+            elif source is None:
+                return ""
             else:
                 print("转换pylabrobot的时候，出现未知类型", source)
                 return source
@@ -349,7 +355,8 @@ class ResourceTreeSet(object):
             if not uid:
                 uid = str(uuid.uuid4())
                 res.unilabos_uuid = uid
-                logger.warning(f"{res}没有uuid，请设置后再传入，默认填充{uid}！\n{traceback.format_exc()}")
+                if not known_newly_created:
+                    logger.warning(f"{res}没有uuid，请设置后再传入，默认填充{uid}！\n{traceback.format_exc()}")
 
             # 获取unilabos_extra，默认为空字典
             extra = getattr(res, "unilabos_extra", {})
@@ -448,7 +455,13 @@ class ResourceTreeSet(object):
         from pylabrobot.utils.object_parsing import find_subclass
 
         # 类型映射
-        TYPE_MAP = {"plate": "Plate", "well": "Well", "deck": "Deck", "container": "RegularContainer", "tip_spot": "TipSpot"}
+        TYPE_MAP = {
+            "plate": "Plate",
+            "well": "Well",
+            "deck": "Deck",
+            "container": "RegularContainer",
+            "tip_spot": "TipSpot",
+        }
 
         def collect_node_data(node: ResourceDictInstance, name_to_uuid: dict, all_states: dict, name_to_extra: dict):
             """一次遍历收集 name_to_uuid, all_states 和 name_to_extra"""
@@ -608,6 +621,16 @@ class ResourceTreeSet(object):
         """
         return [tree.root_node for tree in self.trees]
 
+    @property
+    def root_nodes_uuid(self) -> List[ResourceDictInstance]:
+        """
+        获取所有树的根节点
+
+        Returns:
+            所有根节点的资源实例列表
+        """
+        return [tree.root_node.res_content.uuid for tree in self.trees]
+
     @property
     def all_nodes(self) -> List[ResourceDictInstance]:
         """
@@ -918,6 +941,33 @@ class DeviceNodeResourceTracker(object):
 
         return self._traverse_and_process(resource, process)
 
+    def loop_find_with_uuid(self, resource, target_uuid: str):
+        """
+        递归遍历资源树，根据 uuid 查找并返回对应的资源
+
+        Args:
+            resource: 资源对象（可以是list、dict或实例）
+            target_uuid: 要查找的uuid
+
+        Returns:
+            找到的资源对象，未找到则返回None
+        """
+        found_resource = None
+
+        def process(res):
+            nonlocal found_resource
+            if found_resource is not None:
+                return 0  # 已找到，跳过后续处理
+            current_uuid = self._get_resource_attr(res, "uuid", "unilabos_uuid")
+            if current_uuid and current_uuid == target_uuid:
+                found_resource = res
+                logger.trace(f"找到资源UUID: {target_uuid}")
+                return 1
+            return 0
+
+        self._traverse_and_process(resource, process)
+        return found_resource
+
     def loop_set_extra(self, resource, name_to_extra_map: Dict[str, dict]) -> int:
         """
         递归遍历资源树，根据 name 设置所有节点的 extra
@@ -1103,7 +1153,7 @@ class DeviceNodeResourceTracker(object):
         for key in keys_to_remove:
             self.resource2parent_resource.pop(key, None)
 
-        logger.debug(f"成功移除资源: {resource}")
+        logger.trace(f"[ResourceTracker] 成功移除资源: {resource}")
         return True
 
     def clear_resource(self):

unilabos/resources/warehouse.py

@@ -43,6 +43,10 @@ def warehouse_factory(
                 if layout == "row-major":
                     # 行优先：row=0(A行) 应该显示在上方，需要较小的 y 值
                     y = dy + row * item_dy
+                elif layout == "vertical-col-major":
+                    # 竖向warehouse: row=0 对应顶部（y小），row=n-1 对应底部（y大）
+                    # 但标签 01 应该在底部，所以使用反向映射
+                    y = dy + (num_items_y - row - 1) * item_dy
                 else:
                     # 列优先：保持原逻辑（row=0 对应较大的 y）
                     y = dy + (num_items_y - row - 1) * item_dy