modify bioyond/plr converter, bioyond resource registry, and tests

unilabos/resources/bioyond/bottle_carriers.py

@@ -1,7 +1,13 @@
 from pylabrobot.resources import create_homogeneous_resources, Coordinate, ResourceHolder, create_ordered_items_2d
 
 from unilabos.resources.itemized_carrier import Bottle, BottleCarrier
-from unilabos.resources.bioyond.bottles import BIOYOND_PolymerStation_Solid_Vial, BIOYOND_PolymerStation_Solution_Beaker, BIOYOND_PolymerStation_Reagent_Bottle
+from unilabos.resources.bioyond.bottles import (
+    BIOYOND_PolymerStation_Solid_Stock,
+    BIOYOND_PolymerStation_Solid_Vial,
+    BIOYOND_PolymerStation_Liquid_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
 
 
@@ -92,6 +98,57 @@ def BIOYOND_Electrolyte_1BottleCarrier(name: str) -> BottleCarrier:
     return carrier
 
 
+def BIOYOND_PolymerStation_6StockCarrier(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 = 20.0
+    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
+
+    sites = create_ordered_items_2d(
+        klass=ResourceHolder,
+        num_items_x=3,
+        num_items_y=2,
+        dx=start_x,
+        dy=start_y,
+        dz=5.0,
+        item_dx=bottle_spacing_x,
+        item_dy=bottle_spacing_y,
+
+        size_x=bottle_diameter,
+        size_y=bottle_diameter,
+        size_z=carrier_size_z,
+    )
+    for k, v in sites.items():
+        v.name = f"{name}_{v.name}"
+
+    carrier = BottleCarrier(
+        name=name,
+        size_x=carrier_size_x,
+        size_y=carrier_size_y,
+        size_z=carrier_size_z,
+        sites=sites,
+        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_Stock(f"{name}_vial_{ordering[i]}")
+    return carrier
+
+
 def BIOYOND_PolymerStation_6VialCarrier(name: str) -> BottleCarrier:
     """6瓶载架 - 2x3布局"""
 
@@ -138,8 +195,10 @@ def BIOYOND_PolymerStation_6VialCarrier(name: str) -> BottleCarrier:
     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]}")
+    for i in range(3):
+        carrier[i] = BIOYOND_PolymerStation_Solid_Vial(f"{name}_solidvial_{ordering[i]}")
+    for i in range(3, 6):
+        carrier[i] = BIOYOND_PolymerStation_Liquid_Vial(f"{name}_liquidvial_{ordering[i]}")
     return carrier
 
 

unilabos/resources/bioyond/bottles.py

@@ -2,12 +2,30 @@ from unilabos.resources.itemized_carrier import Bottle, BottleCarrier
 # 工厂函数
 
 
-def BIOYOND_PolymerStation_Solid_Vial(
+def BIOYOND_PolymerStation_Solid_Stock(
     name: str,
     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(
+        name=name,
+        diameter=diameter,
+        height=height,
+        max_volume=max_volume,
+        barcode=barcode,
+        model="BIOYOND_PolymerStation_Solid_Stock",
+    )
+
+
+def BIOYOND_PolymerStation_Solid_Vial(
+    name: str,
+    diameter: float = 25.0,
+    height: float = 60.0,
+    max_volume: float = 30000.0,  # 30mL
+    barcode: str = None,
 ) -> Bottle:
     """创建粉末瓶"""
     return Bottle(
@@ -20,6 +38,24 @@ def BIOYOND_PolymerStation_Solid_Vial(
     )
 
 
+def BIOYOND_PolymerStation_Liquid_Vial(
+    name: str,
+    diameter: float = 25.0,
+    height: float = 60.0,
+    max_volume: float = 30000.0,  # 30mL
+    barcode: str = None,
+) -> Bottle:
+    """创建滴定液瓶"""
+    return Bottle(
+        name=name,
+        diameter=diameter,
+        height=height,
+        max_volume=max_volume,
+        barcode=barcode,
+        model="BIOYOND_PolymerStation_Liquid_Vial",
+    )
+
+
 def BIOYOND_PolymerStation_Solution_Beaker(
     name: str,
     diameter: float = 60.0,

unilabos/resources/graphio.py

@@ -614,6 +614,11 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: dict =
                 bottle.tracker.liquids = [
                     (detail["name"], float(detail.get("quantity", 0)) if detail.get("quantity") else 0)
                 ]
+        else:
+            bottle = plr_material[0] if plr_material.capacity > 0 else plr_material
+            bottle.tracker.liquids = [
+                (material["name"], float(material.get("quantity", 0)) if material.get("quantity") else 0)
+            ]
 
         plr_materials.append(plr_material)
 
@@ -633,6 +638,36 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: dict =
     return plr_materials
 
 
+def resource_plr_to_bioyond(plr_materials: list[ResourcePLR], type_mapping: dict = {}, warehouse_mapping: dict = {}) -> list[dict]:
+    bioyond_materials = []
+    for plr_material in plr_materials:
+        material = {
+            "name": plr_material.name,
+            "typeName": plr_material.__class__.__name__,
+            "code": plr_material.code,
+            "quantity": 0,
+            "detail": [],
+            "locations": [],
+        }
+        if hasattr(plr_material, "capacity") and plr_material.capacity > 1:
+            for idx in range(plr_material.capacity):
+                bottle = plr_material[idx]
+                detail = {
+                    "x": (idx // (plr_material.num_items_x * plr_material.num_items_y)) + 1,
+                    "y": ((idx % (plr_material.num_items_x * plr_material.num_items_y)) // plr_material.num_items_x) + 1,
+                    "z": (idx % plr_material.num_items_x) + 1,
+                    "code": bottle.code if hasattr(bottle, "code") else "",
+                    "quantity": sum(qty for _, qty in bottle.tracker.liquids) if hasattr(bottle, "tracker") else 0,
+                }
+                material["detail"].append(detail)
+            material["quantity"] = 1.0
+        else:
+            bottle = plr_material[0] if plr_material.capacity > 0 else plr_material
+            material["quantity"] = sum(qty for _, qty in bottle.tracker.liquids) if hasattr(plr_material, "tracker") else 0
+        bioyond_materials.append(material)
+    return bioyond_materials
+
+
 def initialize_resource(resource_config: dict, resource_type: Any = None) -> Union[list[dict], ResourcePLR]:
     """Initializes a resource based on its configuration.
 

unilabos/resources/itemized_carrier.py

@@ -5,15 +5,19 @@ Automated Liquid Handling Station Resource Classes - Simplified Version
 
 from __future__ import annotations
 
-from typing import Dict, Optional
+from typing import Dict, List, Optional, TypeVar, Union, Sequence, Tuple
+
+import pylabrobot
 
-from pylabrobot.resources.coordinate import Coordinate
-from pylabrobot.resources.container import Container
-from pylabrobot.resources.resource_holder import ResourceHolder
 from pylabrobot.resources import Resource as ResourcePLR
+from pylabrobot.resources import Well, ResourceHolder
+from pylabrobot.resources.coordinate import Coordinate
 
 
-class Bottle(Container):
+LETTERS = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+
+
+class Bottle(Well):
     """瓶子类 - 简化版，不追踪瓶盖"""
 
     def __init__(
@@ -37,6 +41,8 @@ class Bottle(Container):
             max_volume=max_volume,
             category=category,
             model=model,
+            bottom_type="flat",
+            cross_section_type="circle"
         )
         self.diameter = diameter
         self.height = height
@@ -50,13 +56,6 @@ class Bottle(Container):
             "barcode": self.barcode,
         }
 
-
-from string import ascii_uppercase as LETTERS
-from typing import Dict, List, Optional, Type, TypeVar, Union, Sequence, Tuple
-
-import pylabrobot
-from pylabrobot.resources.resource_holder import ResourceHolder
-
 T = TypeVar("T", bound=ResourceHolder)
 
 S = TypeVar("S", bound=ResourceHolder)