bioyond_HR (#133)

* feat: Enhance Bioyond synchronization and resource management

- Implemented synchronization for all material types (consumables, samples, reagents) from Bioyond, logging detailed information for each type.
- Improved error handling and logging during synchronization processes.
- Added functionality to save Bioyond material IDs in UniLab resources for future updates.
- Enhanced the `sync_to_external` method to handle material movements correctly, including querying and creating materials in Bioyond.
- Updated warehouse configurations to support new storage types and improved layout for better resource management.
- Introduced new resource types such as reactors and tip boxes, with detailed specifications.
- Modified warehouse factory to support column offsets for naming conventions (e.g., A05-D08).
- Improved resource tracking by merging extra attributes instead of overwriting them.
- Added a new method for updating resources in Bioyond, ensuring better synchronization of resource changes.

* feat: 添加TipBox和Reactor的配置到bottles.yaml

* fix: 修复液体投料方法中的volume参数处理逻辑
This commit is contained in:
ZiWei
2025-10-29 12:10:05 +08:00
committed by GitHub
parent 545ea45024
commit d0884cdbd8
9 changed files with 388 additions and 45 deletions

View File

@@ -24,13 +24,42 @@
"Drip_back": "3a162cf9-6aac-565a-ddd7-682ba1796a4a"
},
"material_type_mappings": {
"烧杯": ["BIOYOND_PolymerStation_1FlaskCarrier", "3a14196b-24f2-ca49-9081-0cab8021bf1a"],
"试剂瓶": ["BIOYOND_PolymerStation_1BottleCarrier", ""],
"样品板": ["BIOYOND_PolymerStation_6StockCarrier", "3a14196e-b7a0-a5da-1931-35f3000281e9"],
"分装板": ["BIOYOND_PolymerStation_6VialCarrier", "3a14196e-5dfe-6e21-0c79-fe2036d052c4"],
"样品瓶": ["BIOYOND_PolymerStation_Solid_Stock", "3a14196a-cf7d-8aea-48d8-b9662c7dba94"],
"90%分装小瓶": ["BIOYOND_PolymerStation_Solid_Vial", "3a14196c-cdcf-088d-dc7d-5cf38f0ad9ea"],
"10%分装小瓶": ["BIOYOND_PolymerStation_Liquid_Vial", "3a14196c-76be-2279-4e22-7310d69aed68"]
"烧杯": [
"BIOYOND_PolymerStation_1FlaskCarrier",
"3a14196b-24f2-ca49-9081-0cab8021bf1a"
],
"试剂瓶": [
"BIOYOND_PolymerStation_1BottleCarrier",
""
],
"样品板": [
"BIOYOND_PolymerStation_6StockCarrier",
"3a14196e-b7a0-a5da-1931-35f3000281e9"
],
"分装板": [
"BIOYOND_PolymerStation_6VialCarrier",
"3a14196e-5dfe-6e21-0c79-fe2036d052c4"
],
"样品瓶": [
"BIOYOND_PolymerStation_Solid_Stock",
"3a14196a-cf7d-8aea-48d8-b9662c7dba94"
],
"90%分装小瓶": [
"BIOYOND_PolymerStation_Solid_Vial",
"3a14196c-cdcf-088d-dc7d-5cf38f0ad9ea"
],
"10%分装小瓶": [
"BIOYOND_PolymerStation_Liquid_Vial",
"3a14196c-76be-2279-4e22-7310d69aed68"
],
"枪头盒": [
"BIOYOND_PolymerStation_TipBox",
""
],
"反应器": [
"BIOYOND_PolymerStation_Reactor",
""
]
}
},
"deck": {
@@ -46,8 +75,7 @@
{
"id": "Bioyond_Deck",
"name": "Bioyond_Deck",
"children": [
],
"children": [],
"parent": "reaction_station_bioyond",
"type": "deck",
"class": "BIOYOND_PolymerReactionStation_Deck",

View File

@@ -233,7 +233,7 @@ class BioyondV1RPC(BaseRequest):
return response.get("data", {})
def material_outbound(self, material_id: str, location_name: str, quantity: int) -> dict:
"""指定库位出库物料"""
"""指定库位出库物料(通过库位名称)"""
location_id = LOCATION_MAPPING.get(location_name, location_name)
params = {
@@ -251,7 +251,36 @@ class BioyondV1RPC(BaseRequest):
})
if not response or response['code'] != 1:
return {}
return None
return response
def material_outbound_by_id(self, material_id: str, location_id: str, quantity: int) -> dict:
"""指定库位出库物料直接使用location_id
Args:
material_id: 物料ID
location_id: 库位ID不是库位名称是UUID
quantity: 数量
Returns:
dict: API响应失败返回None
"""
params = {
"materialId": material_id,
"locationId": location_id,
"quantity": quantity
}
response = self.post(
url=f'{self.host}/api/lims/storage/outbound',
params={
"apiKey": self.api_key,
"requestTime": self.get_current_time_iso8601(),
"data": params
})
if not response or response['code'] != 1:
return None
return response
# ==================== 工作流查询相关接口 ====================

View File

@@ -48,3 +48,25 @@ BIOYOND_PolymerStation_Solution_Beaker:
icon: ''
init_param_schema: {}
version: 1.0.0
BIOYOND_PolymerStation_TipBox:
category:
- bottles
- tip_boxes
class:
module: unilabos.resources.bioyond.bottles:BIOYOND_PolymerStation_TipBox
type: pylabrobot
handles: []
icon: ''
init_param_schema: {}
version: 1.0.0
BIOYOND_PolymerStation_Reactor:
category:
- bottles
- reactors
class:
module: unilabos.resources.bioyond.bottles:BIOYOND_PolymerStation_Reactor
type: pylabrobot
handles: []
icon: ''
init_param_schema: {}
version: 1.0.0

View File

@@ -90,3 +90,89 @@ def BIOYOND_PolymerStation_Reagent_Bottle(
barcode=barcode,
model="BIOYOND_PolymerStation_Reagent_Bottle",
)
def BIOYOND_PolymerStation_Reactor(
name: str,
diameter: float = 30.0,
height: float = 80.0,
max_volume: float = 50000.0, # 50mL
barcode: str = None,
) -> Bottle:
"""创建反应器"""
return Bottle(
name=name,
diameter=diameter,
height=height,
max_volume=max_volume,
barcode=barcode,
model="BIOYOND_PolymerStation_Reactor",
)
def BIOYOND_PolymerStation_TipBox(
name: str,
size_x: float = 127.76, # 枪头盒宽度
size_y: float = 85.48, # 枪头盒长度
size_z: float = 100.0, # 枪头盒高度
barcode: str = None,
):
"""创建4×6枪头盒 (24个枪头)
Args:
name: 枪头盒名称
size_x: 枪头盒宽度 (mm)
size_y: 枪头盒长度 (mm)
size_z: 枪头盒高度 (mm)
barcode: 条形码
Returns:
TipBoxCarrier: 包含24个枪头孔位的枪头盒
"""
from pylabrobot.resources import Container, Coordinate
# 创建枪头盒容器
tip_box = Container(
name=name,
size_x=size_x,
size_y=size_y,
size_z=size_z,
category="tip_rack",
model="BIOYOND_PolymerStation_TipBox_4x6",
)
# 设置自定义属性
tip_box.barcode = barcode
tip_box.tip_count = 24 # 4行×6列
tip_box.num_items_x = 6 # 6列
tip_box.num_items_y = 4 # 4行
# 创建24个枪头孔位 (4行×6列)
# 假设孔位间距为 9mm
tip_spacing_x = 9.0 # 列间距
tip_spacing_y = 9.0 # 行间距
start_x = 14.38 # 第一个孔位的x偏移
start_y = 11.24 # 第一个孔位的y偏移
for row in range(4): # A, B, C, D
for col in range(6): # 1-6
spot_name = f"{chr(65 + row)}{col + 1}" # A1, A2, ..., D6
x = start_x + col * tip_spacing_x
y = start_y + row * tip_spacing_y
# 创建枪头孔位容器
tip_spot = Container(
name=spot_name,
size_x=8.0, # 单个枪头孔位大小
size_y=8.0,
size_z=size_z - 10.0, # 略低于盒子高度
category="tip_spot",
)
# 添加到枪头盒
tip_box.assign_child_resource(
tip_spot,
location=Coordinate(x=x, y=y, z=0)
)
return tip_box

View File

@@ -1,7 +1,22 @@
from os import name
from pylabrobot.resources import Deck, Coordinate, Rotation
from unilabos.resources.bioyond.warehouses import bioyond_warehouse_1x4x4, bioyond_warehouse_1x4x2, bioyond_warehouse_liquid_and_lid_handling, bioyond_warehouse_1x2x2, bioyond_warehouse_1x3x3, bioyond_warehouse_10x1x1, bioyond_warehouse_3x3x1, bioyond_warehouse_3x3x1_2, bioyond_warehouse_5x1x1
from unilabos.resources.bioyond.warehouses import (
bioyond_warehouse_1x4x4,
bioyond_warehouse_1x4x4_right, # 新增:右侧仓库 (A05D08)
bioyond_warehouse_1x4x2,
bioyond_warehouse_liquid_and_lid_handling,
bioyond_warehouse_1x2x2,
bioyond_warehouse_1x3x3,
bioyond_warehouse_10x1x1,
bioyond_warehouse_3x3x1,
bioyond_warehouse_3x3x1_2,
bioyond_warehouse_5x1x1,
bioyond_warehouse_1x8x4,
bioyond_warehouse_reagent_storage,
bioyond_warehouse_liquid_preparation,
bioyond_warehouse_tipbox_storage, # 新增Tip盒堆栈
)
class BIOYOND_PolymerReactionStation_Deck(Deck):
@@ -20,15 +35,22 @@ class BIOYOND_PolymerReactionStation_Deck(Deck):
def setup(self) -> None:
# 添加仓库
# 说明: 堆栈1物理上分为左右两部分
# - 堆栈1左: A01D04 (4行×4列, 位于反应站左侧)
# - 堆栈1右: A05D08 (4行×4列, 位于反应站右侧)
self.warehouses = {
"堆栈1": bioyond_warehouse_1x4x4("堆栈1"),
"堆栈2": bioyond_warehouse_1x4x4("堆栈2"),
"站内试剂存放堆栈": bioyond_warehouse_liquid_and_lid_handling("站内试剂存放堆栈"),
"堆栈1": bioyond_warehouse_1x4x4("堆栈1"), # 左侧堆栈: A01D04
"堆栈1右": bioyond_warehouse_1x4x4_right("堆栈1右"), # 右侧堆栈: A05D08
"站内试剂存放堆栈": bioyond_warehouse_reagent_storage("站内试剂存放堆栈"), # A01A02
"移液站内10%分装液体准备仓库": bioyond_warehouse_liquid_preparation("移液站内10%分装液体准备仓库"), # A01B04
"站内Tip盒堆栈": bioyond_warehouse_tipbox_storage("站内Tip盒堆栈"), # A01B03, 存放枪头盒
}
self.warehouse_locations = {
"堆栈1": Coordinate(0.0, 430.0, 0.0),
"堆栈2": Coordinate(2550.0, 430.0, 0.0),
"站内试剂存放堆栈": Coordinate(800.0, 475.0, 0.0),
"堆栈1": 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(1100.0, 475.0, 0.0),
"移液站内10%分装液体准备仓库": Coordinate(1500.0, 300.0, 0.0),
"站内Tip盒堆栈": Coordinate(1800.0, 300.0, 0.0), # TODO: 根据实际位置调整坐标
}
self.warehouses["站内试剂存放堆栈"].rotation = Rotation(z=90)

View File

@@ -2,7 +2,7 @@ from unilabos.resources.warehouse import WareHouse, warehouse_factory
def bioyond_warehouse_1x4x4(name: str) -> WareHouse:
"""创建BioYond 4x1x4仓库"""
"""创建BioYond 4x4x1仓库 (左侧堆栈: A01D04)"""
return warehouse_factory(
name=name,
num_items_x=4,
@@ -15,6 +15,25 @@ def bioyond_warehouse_1x4x4(name: str) -> WareHouse:
item_dy=106.0,
item_dz=130.0,
category="warehouse",
col_offset=0, # 从01开始: A01, A02, A03, A04
)
def bioyond_warehouse_1x4x4_right(name: str) -> WareHouse:
"""创建BioYond 4x4x1仓库 (右侧堆栈: A05D08)"""
return warehouse_factory(
name=name,
num_items_x=4,
num_items_y=4,
num_items_z=1,
dx=10.0,
dy=10.0,
dz=10.0,
item_dx=147.0,
item_dy=106.0,
item_dz=130.0,
category="warehouse",
col_offset=4, # 从05开始: A05, A06, A07, A08
)
@@ -159,3 +178,71 @@ def bioyond_warehouse_liquid_and_lid_handling(name: str) -> WareHouse:
category="warehouse",
removed_positions=None
)
def bioyond_warehouse_1x8x4(name: str) -> WareHouse:
"""创建BioYond 8x4x1反应站堆栈A01D08"""
return warehouse_factory(
name=name,
num_items_x=8, # 8列01-08
num_items_y=4, # 4行A-D
num_items_z=1, # 1层
dx=10.0,
dy=10.0,
dz=10.0,
item_dx=147.0,
item_dy=106.0,
item_dz=130.0,
category="warehouse",
)
def bioyond_warehouse_reagent_storage(name: str) -> WareHouse:
"""创建BioYond站内试剂存放堆栈A01A02, 1行×2列"""
return warehouse_factory(
name=name,
num_items_x=2, # 2列01-02
num_items_y=1, # 1行A
num_items_z=1, # 1层
dx=10.0,
dy=10.0,
dz=10.0,
item_dx=137.0,
item_dy=96.0,
item_dz=120.0,
category="warehouse",
)
def bioyond_warehouse_liquid_preparation(name: str) -> WareHouse:
"""创建BioYond移液站内10%分装液体准备仓库A01B04"""
return warehouse_factory(
name=name,
num_items_x=4, # 4列01-04
num_items_y=2, # 2行A-B
num_items_z=1, # 1层
dx=10.0,
dy=10.0,
dz=10.0,
item_dx=137.0,
item_dy=96.0,
item_dz=120.0,
category="warehouse",
)
def bioyond_warehouse_tipbox_storage(name: str) -> WareHouse:
"""创建BioYond站内Tip盒堆栈A01B03用于存放枪头盒"""
return warehouse_factory(
name=name,
num_items_x=3, # 3列01-03
num_items_y=2, # 2行A-B
num_items_z=1, # 1层
dx=10.0,
dy=10.0,
dz=10.0,
item_dx=137.0,
item_dy=96.0,
item_dz=120.0,
category="warehouse",
)

View File

@@ -580,6 +580,8 @@ def resource_plr_to_ulab(resource_plr: "ResourcePLR", parent_name: str = None, w
"trash": "trash",
"deck": "deck",
"tip_rack": "tip_rack",
"warehouse": "warehouse",
"container": "container",
}
if source in replace_info:
return replace_info[source]
@@ -632,9 +634,24 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
type_mapping.get(material.get("typeName"), ("RegularContainer", ""))[0] if type_mapping else "RegularContainer"
)
plr_material: ResourcePLR = initialize_resource(
plr_material_result = initialize_resource(
{"name": material["name"], "class": className}, resource_type=ResourcePLR
)
# initialize_resource 可能返回列表或单个对象
if isinstance(plr_material_result, list):
if len(plr_material_result) == 0:
logger.warning(f"物料 {material['name']} 初始化失败,跳过")
continue
plr_material = plr_material_result[0]
else:
plr_material = plr_material_result
# 确保 plr_material 是 ResourcePLR 实例
if not isinstance(plr_material, ResourcePLR):
logger.warning(f"物料 {material['name']} 不是有效的 ResourcePLR 实例,类型: {type(plr_material)}")
continue
plr_material.code = material.get("code", "") and material.get("barCode", "") or ""
plr_material.unilabos_uuid = str(uuid.uuid4())
@@ -659,25 +676,66 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
]
bottle.code = detail.get("code", "")
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)
]
# 只对有 capacity 属性的容器(液体容器)处理液体追踪
if hasattr(plr_material, 'capacity'):
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)
if deck and hasattr(deck, "warehouses"):
for loc in material.get("locations", []):
if hasattr(deck, "warehouses") and loc.get("whName") in deck.warehouses:
warehouse = deck.warehouses[loc["whName"]]
idx = (
(loc.get("y", 0) - 1) * warehouse.num_items_x * warehouse.num_items_y
+ (loc.get("x", 0) - 1) * warehouse.num_items_x
+ (loc.get("z", 0) - 1)
)
wh_name = loc.get("whName")
# 特殊处理: Bioyond的"堆栈1"需要映射到"堆栈1左"或"堆栈1右"
# 根据列号(x)判断: 1-4映射到左侧, 5-8映射到右侧
if wh_name == "堆栈1":
x_val = loc.get("x", 1)
if 1 <= x_val <= 4:
wh_name = "堆栈1左"
elif 5 <= x_val <= 8:
wh_name = "堆栈1右"
else:
logger.warning(f"物料 {material['name']} 的列号 x={x_val} 超出范围无法映射到堆栈1左或堆栈1右")
continue
if hasattr(deck, "warehouses") and wh_name in deck.warehouses:
warehouse = deck.warehouses[wh_name]
# 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)
# 如果是右侧堆栈,需要调整列号 (5→1, 6→2, 7→3, 8→4)
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}")
else:
# 多行warehouse: 使用列优先索引 (与Bioyond坐标系统一致)
# warehouse keys顺序: A01,B01,C01,D01, A02,B02,C02,D02, ...
# 索引计算: idx = (col-1) * num_rows + (row-1) + (layer-1) * (rows * cols)
row_idx = x - 1 # x表示行: 转为0-based
col_idx = y - 1 # y表示列: 转为0-based
layer_idx = z - 1 # 转为0-based
idx = layer_idx * (warehouse.num_items_x * warehouse.num_items_y) + col_idx * warehouse.num_items_y + row_idx
logger.debug(f"多行warehouse {wh_name}: x={x}(行),y={y}(列) → row={row_idx},col={col_idx} → idx={idx}")
if 0 <= idx < warehouse.capacity:
if warehouse[idx] is None or isinstance(warehouse[idx], ResourceHolder):
warehouse[idx] = plr_material
logger.debug(f"✅ 物料 {material['name']} 放置到 {wh_name}[{idx}] (Bioyond坐标: x={loc.get('x')}, y={loc.get('y')})")
else:
logger.warning(f"物料 {material['name']} 的索引 {idx} 超出仓库 {wh_name} 容量 {warehouse.capacity}")
return plr_materials
@@ -714,8 +772,8 @@ def resource_plr_to_bioyond(plr_resources: list[ResourcePLR], type_mapping: dict
bottle = resource[0] if resource.capacity > 0 else resource
material = {
"typeId": "3a14196b-24f2-ca49-9081-0cab8021bf1a",
"name": resource.get("name", ""),
"unit": "",
"name": resource.name if hasattr(resource, "name") else "",
"unit": "", # 修复Bioyond API 要求 unit 字段不能为空
"quantity": sum(qty for _, qty in bottle.tracker.liquids) if hasattr(bottle, "tracker") else 0,
"Parameters": "{}"
}
@@ -759,6 +817,8 @@ def initialize_resource(resource_config: dict, resource_type: Any = None) -> Uni
elif type(resource_class_config) == str:
# Allow special resource class names to be used
if resource_class_config not in lab_registry.resource_type_registry:
logger.warning(f"❌ 类 {resource_class_config} 不在 registry 中,返回原始配置")
logger.debug(f" 可用的类: {list(lab_registry.resource_type_registry.keys())[:10]}...")
return [resource_config]
# If the resource class is a string, look up the class in the
# resource_type_registry and import it

View File

@@ -23,6 +23,7 @@ def warehouse_factory(
empty: bool = False,
category: str = "warehouse",
model: Optional[str] = None,
col_offset: int = 0, # 新增列起始偏移量用于生成A05-D08等命名
):
# 创建16个板架位 (4层 x 4位置)
locations = []
@@ -44,7 +45,9 @@ def warehouse_factory(
name_prefix=name,
)
len_x, len_y = (num_items_x, num_items_y) if num_items_z == 1 else (num_items_y, num_items_z) if num_items_x == 1 else (num_items_x, num_items_z)
keys = [f"{LETTERS[j]}{i + 1}" for i in range(len_x) for j in range(len_y)]
# 应用列偏移量支持A05-D08等命名
# 使用列优先顺序生成keys (与Bioyond坐标系统一致): A01,B01,C01,D01, A02,B02,C02,D02, ...
keys = [f"{LETTERS[j]}{i + 1 + col_offset:02d}" for i in range(len_x) for j in range(len_y)]
sites = {i: site for i, site in zip(keys, _sites.values())}
return WareHouse(

View File

@@ -848,9 +848,15 @@ class DeviceNodeResourceTracker(object):
extra: extra字典值
"""
if isinstance(resource, dict):
resource["extra"] = extra
# ⭐ 修复合并extra而不是覆盖
current_extra = resource.get("extra", {})
current_extra.update(extra)
resource["extra"] = current_extra
else:
setattr(resource, "unilabos_extra", extra)
# ⭐ 修复合并unilabos_extra而不是覆盖
current_extra = getattr(resource, "unilabos_extra", {})
current_extra.update(extra)
setattr(resource, "unilabos_extra", current_extra)
def _traverse_and_process(self, resource, process_func) -> int:
"""