refactor and add BIOYOND resources tests

unilabos/registry/resources/bioyond/bottle_carriers.yaml

@@ -0,0 +1,38 @@
+BIOYOND_PolymerStation_6VialCarrier:
+  category:
+    - bottle_carriers
+  class:
+    module: unilabos.resources.bioyond.bottle_carriers:BIOYOND_PolymerStation_6VialCarrier
+    type: pylabrobot
+  description: BIOYOND_PolymerStation_6VialCarrier
+  handles: [ ]
+  icon: ''
+  init_param_schema: { }
+  registry_type: resource
+  version: 1.0.0
+
+BIOYOND_PolymerStation_1BottleCarrier:
+  category:
+    - bottle_carriers
+  class:
+    module: unilabos.resources.bioyond.bottle_carriers:BIOYOND_PolymerStation_1BottleCarrier
+    type: pylabrobot
+  description: BIOYOND_PolymerStation_1BottleCarrier
+  handles: [ ]
+  icon: ''
+  init_param_schema: { }
+  registry_type: resource
+  version: 1.0.0
+
+BIOYOND_PolymerStation_1FlaskCarrier:
+  category:
+    - bottle_carriers
+  class:
+    module: unilabos.resources.bioyond.bottle_carriers:BIOYOND_PolymerStation_1FlaskCarrier
+    type: pylabrobot
+  description: BIOYOND_PolymerStation_1FlaskCarrier
+  handles: [ ]
+  icon: ''
+  init_param_schema: { }
+  registry_type: resource
+  version: 1.0.0

unilabos/resources/bioyond/bottle_carrier.py

@@ -1,78 +0,0 @@
-from unilabos.resources.bottle_carrier import Bottle, BottleCarrier
-from pylabrobot.resources import create_homogeneous_resources, Coordinate, ResourceHolder
-
-
-# 命名约定：试剂瓶-Bottle，烧杯-Beaker，烧瓶-Flask，小瓶-Vial
-
-def BIOYOND_Electrolyte_6VialCarrier(name: str) -> BottleCarrier:
-    """6瓶载架 - 2x3布局"""
-
-    # 载架尺寸 (mm)
-    carrier_size_x = 127.8
-    carrier_size_y = 85.5
-    carrier_size_z = 50.0
-
-    # 瓶位尺寸
-    bottle_diameter = 30.0
-    bottle_spacing_x = 42.0  # X方向间距
-    bottle_spacing_y = 35.0  # Y方向间距
-
-    # 计算起始位置 (居中排列)
-    start_x = (carrier_size_x - (3 - 1) * bottle_spacing_x - bottle_diameter) / 2
-    start_y = (carrier_size_y - (2 - 1) * bottle_spacing_y - bottle_diameter) / 2
-
-    # 创建6个位置坐标 (2行 x 3列)
-    locations = []
-    for row in range(2):
-        for col in range(3):
-            x = start_x + col * bottle_spacing_x
-            y = start_y + row * bottle_spacing_y
-            z = 5.0  # 架位底部
-            locations.append(Coordinate(x, y, z))
-
-    return BottleCarrier(
-        name=name,
-        size_x=carrier_size_x,
-        size_y=carrier_size_y,
-        size_z=carrier_size_z,
-        sites=create_homogeneous_resources(
-            klass=ResourceHolder,
-            locations=locations,
-            resource_size_x=bottle_diameter,
-            resource_size_y=bottle_diameter,
-            name_prefix=name,
-        ),
-        model="BIOYOND_Electrolyte_6VialCarrier",
-    )
-
-
-def BIOYOND_Electrolyte_1BottleCarrier(name: str) -> BottleCarrier:
-    """1瓶载架 - 单个中央位置"""
-
-    # 载架尺寸 (mm)
-    carrier_size_x = 127.8
-    carrier_size_y = 85.5
-    carrier_size_z = 100.0
-
-    # 烧杯尺寸
-    beaker_diameter = 80.0
-
-    # 计算中央位置
-    center_x = (carrier_size_x - beaker_diameter) / 2
-    center_y = (carrier_size_y - beaker_diameter) / 2
-    center_z = 5.0
-
-    return BottleCarrier(
-        name=name,
-        size_x=carrier_size_x,
-        size_y=carrier_size_y,
-        size_z=carrier_size_z,
-        sites=create_homogeneous_resources(
-            klass=ResourceHolder,
-            locations=[Coordinate(center_x, center_y, center_z)],
-            resource_size_x=beaker_diameter,
-            resource_size_y=beaker_diameter,
-            name_prefix=name,
-        ),
-        model="BIOYOND_Electrolyte_1BottleCarrier",
-    )

unilabos/resources/bioyond/bottle_carriers.py

@@ -0,0 +1,213 @@
+from pylabrobot.resources import create_homogeneous_resources, Coordinate, ResourceHolder
+
+from unilabos.resources.bottle_carrier import Bottle, BottleCarrier
+from unilabos.resources.bioyond.bottles import BIOYOND_PolymerStation_Solid_Vial, BIOYOND_PolymerStation_Solution_Beaker, BIOYOND_PolymerStation_Reagent_Bottle
+# 命名约定：试剂瓶-Bottle，烧杯-Beaker，烧瓶-Flask，小瓶-Vial
+
+
+def BIOYOND_Electrolyte_6VialCarrier(name: str) -> BottleCarrier:
+    """6瓶载架 - 2x3布局"""
+
+    # 载架尺寸 (mm)
+    carrier_size_x = 127.8
+    carrier_size_y = 85.5
+    carrier_size_z = 50.0
+
+    # 瓶位尺寸
+    bottle_diameter = 30.0
+    bottle_spacing_x = 42.0  # X方向间距
+    bottle_spacing_y = 35.0  # Y方向间距
+
+    # 计算起始位置 (居中排列)
+    start_x = (carrier_size_x - (3 - 1) * bottle_spacing_x - bottle_diameter) / 2
+    start_y = (carrier_size_y - (2 - 1) * bottle_spacing_y - bottle_diameter) / 2
+
+    # 创建6个位置坐标 (2行 x 3列)
+    locations = []
+    for row in range(2):
+        for col in range(3):
+            x = start_x + col * bottle_spacing_x
+            y = start_y + row * bottle_spacing_y
+            z = 5.0  # 架位底部
+            locations.append(Coordinate(x, y, z))
+
+    carrier = BottleCarrier(
+        name=name,
+        size_x=carrier_size_x,
+        size_y=carrier_size_y,
+        size_z=carrier_size_z,
+        sites=create_homogeneous_resources(
+            klass=ResourceHolder,
+            locations=locations,
+            resource_size_x=bottle_diameter,
+            resource_size_y=bottle_diameter,
+            name_prefix=name,
+        ),
+        model="BIOYOND_Electrolyte_6VialCarrier",
+    )
+    carrier.num_items_x = 3
+    carrier.num_items_y = 2
+    carrier.num_items_z = 1
+    for i in range(6):
+        carrier[i] = BIOYOND_PolymerStation_Solid_Vial(f"{name}_vial_{i+1}")
+    return carrier
+
+
+def BIOYOND_Electrolyte_1BottleCarrier(name: str) -> BottleCarrier:
+    """1瓶载架 - 单个中央位置"""
+
+    # 载架尺寸 (mm)
+    carrier_size_x = 127.8
+    carrier_size_y = 85.5
+    carrier_size_z = 100.0
+
+    # 烧杯尺寸
+    beaker_diameter = 80.0
+
+    # 计算中央位置
+    center_x = (carrier_size_x - beaker_diameter) / 2
+    center_y = (carrier_size_y - beaker_diameter) / 2
+    center_z = 5.0
+
+    carrier = BottleCarrier(
+        name=name,
+        size_x=carrier_size_x,
+        size_y=carrier_size_y,
+        size_z=carrier_size_z,
+        sites=create_homogeneous_resources(
+            klass=ResourceHolder,
+            locations=[Coordinate(center_x, center_y, center_z)],
+            resource_size_x=beaker_diameter,
+            resource_size_y=beaker_diameter,
+            name_prefix=name,
+        ),
+        model="BIOYOND_Electrolyte_1BottleCarrier",
+    )
+    carrier.num_items_x = 1
+    carrier.num_items_y = 1
+    carrier.num_items_z = 1
+    carrier[0] = BIOYOND_PolymerStation_Solution_Beaker(f"{name}_beaker_1")
+    return carrier
+
+
+def BIOYOND_PolymerStation_6VialCarrier(name: str) -> BottleCarrier:
+    """6瓶载架 - 2x3布局"""
+
+    # 载架尺寸 (mm)
+    carrier_size_x = 127.8
+    carrier_size_y = 85.5
+    carrier_size_z = 50.0
+
+    # 瓶位尺寸
+    bottle_diameter = 30.0
+    bottle_spacing_x = 42.0  # X方向间距
+    bottle_spacing_y = 35.0  # Y方向间距
+
+    # 计算起始位置 (居中排列)
+    start_x = (carrier_size_x - (3 - 1) * bottle_spacing_x - bottle_diameter) / 2
+    start_y = (carrier_size_y - (2 - 1) * bottle_spacing_y - bottle_diameter) / 2
+
+    # 创建6个位置坐标 (2行 x 3列)
+    locations = []
+    for row in range(2):
+        for col in range(3):
+            x = start_x + col * bottle_spacing_x
+            y = start_y + row * bottle_spacing_y
+            z = 5.0  # 架位底部
+            locations.append(Coordinate(x, y, z))
+
+    carrier = BottleCarrier(
+        name=name,
+        size_x=carrier_size_x,
+        size_y=carrier_size_y,
+        size_z=carrier_size_z,
+        sites=create_homogeneous_resources(
+            klass=ResourceHolder,
+            locations=locations,
+            resource_size_x=bottle_diameter,
+            resource_size_y=bottle_diameter,
+            name_prefix=name,
+        ),
+        model="BIOYOND_PolymerStation_6VialCarrier",
+    )
+    carrier.num_items_x = 3
+    carrier.num_items_y = 2
+    carrier.num_items_z = 1
+    ordering = ["A1", "A2", "A3", "B1", "B2", "B3"]  # 自定义顺序
+    for i in range(6):
+        carrier[i] = BIOYOND_PolymerStation_Solid_Vial(f"{name}_vial_{ordering[i]}")
+    return carrier
+
+
+def BIOYOND_PolymerStation_1BottleCarrier(name: str) -> BottleCarrier:
+    """1瓶载架 - 单个中央位置"""
+
+    # 载架尺寸 (mm)
+    carrier_size_x = 127.8
+    carrier_size_y = 85.5
+    carrier_size_z = 20.0
+
+    # 烧杯尺寸
+    beaker_diameter = 60.0
+
+    # 计算中央位置
+    center_x = (carrier_size_x - beaker_diameter) / 2
+    center_y = (carrier_size_y - beaker_diameter) / 2
+    center_z = 5.0
+
+    carrier = BottleCarrier(
+        name=name,
+        size_x=carrier_size_x,
+        size_y=carrier_size_y,
+        size_z=carrier_size_z,
+        sites=create_homogeneous_resources(
+            klass=ResourceHolder,
+            locations=[Coordinate(center_x, center_y, center_z)],
+            resource_size_x=beaker_diameter,
+            resource_size_y=beaker_diameter,
+            name_prefix=name,
+        ),
+        model="BIOYOND_PolymerStation_1BottleCarrier",
+    )
+    carrier.num_items_x = 1
+    carrier.num_items_y = 1
+    carrier.num_items_z = 1
+    carrier[0] = BIOYOND_PolymerStation_Reagent_Bottle(f"{name}_flask_1")
+    return carrier
+
+
+def BIOYOND_PolymerStation_1FlaskCarrier(name: str) -> BottleCarrier:
+    """1瓶载架 - 单个中央位置"""
+
+    # 载架尺寸 (mm)
+    carrier_size_x = 127.8
+    carrier_size_y = 85.5
+    carrier_size_z = 20.0
+
+    # 烧杯尺寸
+    beaker_diameter = 70.0
+
+    # 计算中央位置
+    center_x = (carrier_size_x - beaker_diameter) / 2
+    center_y = (carrier_size_y - beaker_diameter) / 2
+    center_z = 5.0
+
+    carrier = BottleCarrier(
+        name=name,
+        size_x=carrier_size_x,
+        size_y=carrier_size_y,
+        size_z=carrier_size_z,
+        sites=create_homogeneous_resources(
+            klass=ResourceHolder,
+            locations=[Coordinate(center_x, center_y, center_z)],
+            resource_size_x=beaker_diameter,
+            resource_size_y=beaker_diameter,
+            name_prefix=name,
+        ),
+        model="BIOYOND_PolymerStation_1FlaskCarrier",
+    )
+    carrier.num_items_x = 1
+    carrier.num_items_y = 1
+    carrier.num_items_z = 1
+    carrier[0] = BIOYOND_PolymerStation_Reagent_Bottle(f"{name}_bottle_1")
+    return carrier

unilabos/resources/bioyond/bottles.py

@@ -2,11 +2,12 @@ from unilabos.resources.bottle_carrier import Bottle, BottleCarrier
 # 工厂函数
 
 
-def create_powder_bottle(
+def BIOYOND_PolymerStation_Solid_Vial(
     name: str,
-    diameter: float = 30.0,
-    height: float = 50.0,
-    max_volume: float = 50000.0,  # 50mL
+    diameter: float = 20.0,
+    height: float = 100.0,
+    max_volume: float = 30000.0,  # 30mL
+    barcode: str = None,
 ) -> Bottle:
     """创建粉末瓶"""
     return Bottle(
@@ -14,15 +15,17 @@ def create_powder_bottle(
         diameter=diameter,
         height=height,
         max_volume=max_volume,
-        category="powder_bottle",
+        barcode=barcode,
+        model="BIOYOND_PolymerStation_Solid_Vial",
     )
 
 
-def create_solution_beaker(
+def BIOYOND_PolymerStation_Solution_Beaker(
     name: str,
-    diameter: float = 80.0,
-    height: float = 100.0,
-    max_volume: float = 500000.0,  # 500mL
+    diameter: float = 60.0,
+    height: float = 70.0,
+    max_volume: float = 200000.0,  # 200mL
+    barcode: str = None,
 ) -> Bottle:
     """创建溶液烧杯"""
     return Bottle(
@@ -30,15 +33,17 @@ def create_solution_beaker(
         diameter=diameter,
         height=height,
         max_volume=max_volume,
-        category="solution_beaker",
+        barcode=barcode,
+        model="BIOYOND_PolymerStation_Solution_Beaker",
     )
 
 
-def create_reagent_bottle(
+def BIOYOND_PolymerStation_Reagent_Bottle(
     name: str,
-    diameter: float = 20.0,
-    height: float = 40.0,
-    max_volume: float = 15000.0,  # 15mL
+    diameter: float = 70.0,
+    height: float = 120.0,
+    max_volume: float = 500000.0,  # 500mL
+    barcode: str = None,
 ) -> Bottle:
     """创建试剂瓶"""
     return Bottle(
@@ -46,5 +51,6 @@ def create_reagent_bottle(
         diameter=diameter,
         height=height,
         max_volume=max_volume,
-        category="reagent_bottle",
-    )
+        barcode=barcode,
+        model="BIOYOND_PolymerStation_Reagent_Bottle",
+    )

unilabos/resources/bioyond/decks.py

@@ -0,0 +1,48 @@
+from pylabrobot.resources import Deck, Coordinate
+
+from unilabos.resources.bioyond.warehouses import bioyond_warehouse_1x4x4, bioyond_warehouse_1x4x2, bioyond_warehouse_liquid_and_lid_handling
+
+
+class BIOYOND_PolymerReactionStation_Deck(Deck):
+    def __init__(self, name: str = "PolymerReactionStation_Deck") -> None:
+        super().__init__(name=name, size_x=2700.0, size_y=1080.0, size_z=1500.0)
+
+    def setup(self) -> None:
+        # 添加仓库
+        self.warehouses = {
+            "io_warehouse_left": bioyond_warehouse_1x4x4("io_warehouse_left"),
+            "io_warehouse_right": bioyond_warehouse_1x4x4("io_warehouse_right"),
+            "liquid_and_lid_handling": bioyond_warehouse_liquid_and_lid_handling("liquid_and_lid_handling"),
+        }
+        self.warehouse_locations = {
+            "io_warehouse_left": Coordinate(0.0, 650.0, 0.0),
+            "io_warehouse_right": Coordinate(2550.0, 650.0, 0.0),
+            "liquid_and_lid_handling": Coordinate(800.0, 475.0, 0.0),
+        }
+
+        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, name: str = "PolymerPreparationStation_Deck") -> None:
+        super().__init__(name=name, size_x=2700.0, size_y=1080.0, size_z=1500.0)
+        self.warehouses = {}
+
+    def setup(self) -> None:
+        # 添加仓库
+        self.warehouses = {
+            "io_warehouse_left": bioyond_warehouse_1x4x4("io_warehouse_left"),
+            "io_warehouse_right": bioyond_warehouse_1x4x4("io_warehouse_right"),
+            "solutions": bioyond_warehouse_1x4x2("warehouse_solutions"),
+            "liquid_and_lid_handling": bioyond_warehouse_liquid_and_lid_handling("warehouse_liquid_and_lid_handling"),
+        }
+        self.warehouse_locations = {
+            "io_warehouse_left": Coordinate(0.0, 650.0, 0.0),
+            "io_warehouse_right": Coordinate(2550.0, 650.0, 0.0),
+            "solutions": Coordinate(1915.0, 900.0, 0.0),
+            "liquid_and_lid_handling": Coordinate(1330.0, 490.0, 0.0),
+        }
+
+        for warehouse_name, warehouse in self.warehouses.items():
+            self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])

unilabos/resources/bioyond/warehouses.py

@@ -18,12 +18,12 @@ def bioyond_warehouse_1x4x4(name: str) -> WareHouse:
     )
 
 
-def bioyond_warehouse_1x3x2(name: str) -> WareHouse:
-    """创建BioYond 3x1x2仓库"""
+def bioyond_warehouse_1x4x2(name: str) -> WareHouse:
+    """创建BioYond 4x1x2仓库"""
     return WareHouse(
         name=name,
         num_items_x=1,
-        num_items_y=3,
+        num_items_y=4,
         num_items_z=2,
         dx=137.0,
         dy=96.0,

unilabos/resources/graphio.py

@@ -480,7 +480,43 @@ def resource_plr_to_ulab(resource_plr: "ResourcePLR", parent_name: str = None, w
     return r
 
 
-def initialize_resource(resource_config: dict) -> list[dict]:
+def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: dict = {}, location_id_mapping: dict = None) -> list[dict]:
+    """
+    将 bioyond 物料格式转换为 ulab 物料格式
+
+    Args:
+        bioyond_materials: bioyond 系统的物料查询结果列表
+        type_mapping: 物料类型映射字典，格式 {bioyond_type: plr_class_name}
+        location_id_mapping: 库位 ID 到名称的映射字典，格式 {location_id: location_name}
+
+    Returns:
+        pylabrobot 格式的物料列表
+    """
+    plr_materials = []
+
+    for material in bioyond_materials:
+        className = type_mapping.get(material.get("typeName"), "RegularContainer") if type_mapping else "RegularContainer"
+        
+        plr_material: ResourcePLR = initialize_resource({"name": material["name"], "class": className}, resource_type=ResourcePLR)
+        plr_material.code = material.get("code", "") and material.get("barCode", "") or ""
+
+        # 处理子物料（detail）
+        if material.get("detail") and len(material["detail"]) > 0:
+            child_ids = []
+            for detail in material["detail"]:
+                number = (detail.get("z", 0) - 1) * plr_material.num_items_x * plr_material.num_items_y + \
+                         (detail.get("x", 0) - 1) * plr_material.num_items_x + \
+                         (detail.get("y", 0) - 1)
+                bottle = plr_material[number].resource
+                bottle.code = detail.get("code", "")
+                bottle.tracker.liquids = [(detail["name"], float(detail.get("quantity", 0)) if detail.get("quantity") else 0)]
+                
+        plr_materials.append(plr_material)
+
+    return plr_materials
+
+
+def initialize_resource(resource_config: dict, resource_type: Any = None) -> Union[list[dict], ResourcePLR]:
     """Initializes a resource based on its configuration.
 
     If the config is detailed, then do nothing;
@@ -512,11 +548,14 @@ def initialize_resource(resource_config: dict) -> list[dict]:
 
         if resource_class_config["type"] == "pylabrobot":
             resource_plr = RESOURCE(name=resource_config["name"])
-            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"]
-            r = tree_to_list([r])
+            if resource_type != ResourcePLR:
+                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"]
+                r = tree_to_list([r])
+            else:
+                r = resource_plr
         elif resource_class_config["type"] == "unilabos":
             res_instance: RegularContainer = RESOURCE(id=resource_config["name"])
             res_instance.ulr_resource = convert_to_ros_msg(Resource, {k:v for k,v in resource_config.items() if k != "class"})

unilabos/resources/warehouse.py

@@ -24,6 +24,9 @@ class WareHouse(Carrier[ResourceHolder]):
         category: str = "warehouse",
         model: Optional[str] = None,
     ):
+        self.num_items_x = num_items_x
+        self.num_items_y = num_items_y
+        self.num_items_z = num_items_z
         # 创建16个板架位 (4层 x 4位置)
         locations = []