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4 Commits

Author SHA1 Message Date
Xuwznln
30037a077a correct return message 2025-10-17 03:03:08 +08:00
ZiWei
6972680099 Refactor Bioyond workstation and experiment workflow -fix (#111)
* refactor(bioyond_studio): 优化材料缓存加载和参数验证逻辑

改进材料缓存加载逻辑以支持多种材料类型和详细材料处理
更新工作流参数验证中的字段名从key/value改为Key/DisplayValue
移除未使用的merge_workflow_with_parameters方法
添加get_station_info方法获取工作站基础信息
清理实验文件中的注释代码和更新导入路径

* fix: 修复资源移除时的父资源检查问题

在BaseROS2DeviceNode中,移除资源前添加对父资源是否为None的检查,避免空指针异常
同时更新Bottle和BottleCarrier类以支持**kwargs参数
修正测试文件中Liquid_feeding_beaker的大小写拼写错误
2025-10-17 02:59:58 +08:00
Xuwznln
e728007bc5 cancel upload_registry 2025-10-17 02:34:59 +08:00
ZiWei
9c5ecda7cc Refactor Bioyond workstation and experiment workflow (#110)
Refactored the Bioyond workstation classes to improve parameter handling and workflow management. Updated experiment.py to use BioyondReactionStation with deck and material mappings, and enhanced workflow step parameter mapping and execution logic. Adjusted JSON experiment configs, improved workflow sequence handling, and added UUID assignment to PLR materials. Removed unused station_config and material cache logic, and added detailed docstrings and debug output for workflow methods.
2025-10-17 02:32:13 +08:00
8 changed files with 727 additions and 652 deletions

View File

@@ -10,7 +10,7 @@
"type": "device",
"class": "reaction_station.bioyond",
"config": {
"bioyond_config": {
"config": {
"api_key": "DE9BDDA0",
"api_host": "http://192.168.1.200:44402",
"workflow_mappings": {
@@ -19,8 +19,8 @@
"Solid_feeding_vials": "3a160877-87e7-7699-7bc6-ec72b05eb5e6",
"Liquid_feeding_vials(non-titration)": "3a167d99-6158-c6f0-15b5-eb030f7d8e47",
"Liquid_feeding_solvents": "3a160824-0665-01ed-285a-51ef817a9046",
"Liquid_feeding(titration)": "3a160824-0665-01ed-285a-51ef817a9046",
"Liquid_feeding_beaker": "3a16087e-124f-8ddb-8ec1-c2dff09ca784",
"Liquid_feeding(titration)": "3a16082a-96ac-0449-446a-4ed39f3365b6",
"liquid_feeding_beaker": "3a16087e-124f-8ddb-8ec1-c2dff09ca784",
"Drip_back": "3a162cf9-6aac-565a-ddd7-682ba1796a4a"
},
"material_type_mappings": {

View File

@@ -356,7 +356,7 @@ def main():
if BasicConfig.upload_registry:
# 设备注册到服务端 - 需要 ak 和 sk
if args_dict.get("ak") and args_dict.get("sk"):
if BasicConfig.ak and BasicConfig.sk:
print_status("开始注册设备到服务端...", "info")
try:
register_devices_and_resources(lab_registry)

View File

@@ -334,8 +334,8 @@ class BioyondV1RPC(BaseRequest):
for j, param in enumerate(params):
if not isinstance(param, dict):
workflow_errors.append(f"步骤 {step_id} 模块 {module_name} 参数 {j} 必须是字典类型")
elif "key" not in param or "value" not in param:
workflow_errors.append(f"步骤 {step_id} 模块 {module_name} 参数 {j} 必须包含 key 和 value")
elif "Key" not in param or "DisplayValue" not in param:
workflow_errors.append(f"步骤 {step_id} 模块 {module_name} 参数 {j} 必须包含 Key 和 DisplayValue")
if workflow_errors:
validation_errors.append({
@@ -703,20 +703,35 @@ class BioyondV1RPC(BaseRequest):
"""预加载材料列表到缓存中"""
try:
print("正在加载材料列表缓存...")
stock_query = '{"typeMode": 2, "includeDetail": true}'
stock_result = self.stock_material(stock_query)
# 加载所有类型的材料:耗材(0)、样品(1)、试剂(2)
material_types = [1, 2]
for type_mode in material_types:
print(f"正在加载类型 {type_mode} 的材料...")
stock_query = f'{{"typeMode": {type_mode}, "includeDetail": true}}'
stock_result = self.stock_material(stock_query)
if isinstance(stock_result, str):
stock_data = json.loads(stock_result)
else:
stock_data = stock_result
if isinstance(stock_result, str):
stock_data = json.loads(stock_result)
else:
stock_data = stock_result
materials = stock_data
for material in materials:
material_name = material.get("name")
material_id = material.get("id")
if material_name and material_id:
self.material_cache[material_name] = material_id
materials = stock_data
for material in materials:
material_name = material.get("name")
material_id = material.get("id")
if material_name and material_id:
self.material_cache[material_name] = material_id
# 处理样品板等容器中的detail材料
detail_materials = material.get("detail", [])
for detail_material in detail_materials:
detail_name = detail_material.get("name")
detail_id = detail_material.get("detailMaterialId")
if detail_name and detail_id:
self.material_cache[detail_name] = detail_id
print(f"加载detail材料: {detail_name} -> ID: {detail_id}")
print(f"材料列表缓存加载完成,共加载 {len(self.material_cache)} 个材料")

View File

@@ -3,8 +3,8 @@
"""
import json
from reaction_station import BioyondReactionStation
from config import API_CONFIG, WORKFLOW_MAPPINGS, DECK_CONFIG, MATERIAL_TYPE_MAPPINGS
from unilabos.devices.workstation.bioyond_studio.reaction_station import BioyondReactionStation
from unilabos.devices.workstation.bioyond_studio.config import API_CONFIG, WORKFLOW_MAPPINGS, DECK_CONFIG, MATERIAL_TYPE_MAPPINGS
def run_experiment():
@@ -45,7 +45,7 @@ def run_experiment():
assign_material_name="ODA",
time="0",
torque_variation="1",
titrationType="1",
titration_type="1",
temperature=-10
)
@@ -56,14 +56,14 @@ def run_experiment():
assign_material_name="MPDA",
time="5",
torque_variation="2",
titrationType="1",
titration_type="1",
temperature=0
)
# 4. 液体投料-小瓶非滴定
print("4. 添加液体投料-小瓶非滴定,带参数...")
Bioyond.liquid_feeding_vials_non_titration(
volumeFormula="639.5",
volume_formula="639.5",
assign_material_name="SIDA",
titration_type="1",
time="0",
@@ -91,7 +91,7 @@ def run_experiment():
assign_material_name="BTDA1",
temperature=-10.00
)
#二杆样品版90
print("7. 添加固体进料小瓶,带参数...")
Bioyond.solid_feeding_vials(
material_id="3",
@@ -100,7 +100,7 @@ def run_experiment():
assign_material_name="BTDA2",
temperature=25.00
)
#二杆样品版90
print("8. 添加固体进料小瓶,带参数...")
Bioyond.solid_feeding_vials(
material_id="3",
@@ -196,8 +196,8 @@ def run_experiment():
print("\n4. 执行process_and_execute_workflow...")
result = Bioyond.process_and_execute_workflow(
workflow_name="test3_8",
task_name="实验3_8"
workflow_name="test3",
task_name="实验3"
)
# 显示执行结果
@@ -207,9 +207,9 @@ def run_experiment():
result_dict = json.loads(result)
if result_dict.get("success"):
print("任务创建成功!")
print(f"- 工作流: {result_dict.get('workflow', {}).get('name')}")
print(f"- 工作流ID: {result_dict.get('workflow', {}).get('id')}")
print(f"- 任务结果: {result_dict.get('task')}")
# print(f"- 工作流: {result_dict.get('workflow', {}).get('name')}")
# print(f"- 工作流ID: {result_dict.get('workflow', {}).get('id')}")
# print(f"- 任务结果: {result_dict.get('task')}")
else:
print(f"任务创建失败: {result_dict.get('error')}")
except:
@@ -229,166 +229,166 @@ def run_experiment():
return Bioyond
def prepare_materials(bioyond):
"""准备实验材料(可选)"""
# def prepare_materials(bioyond):
# """准备实验材料(可选)"""
# 样品板材料数据定义
material_data_yp_1 = {
"typeId": "3a142339-80de-8f25-6093-1b1b1b6c322e",
"name": "样品板-1",
"unit": "",
"quantity": 1,
"details": [
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BPDA-DD-1",
"quantity": 1,
"x": 1,
"y": 1,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "PEPA",
"quantity": 1,
"x": 1,
"y": 2,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BPDA-DD-2",
"quantity": 1,
"x": 1,
"y": 3,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BPDA-1",
"quantity": 1,
"x": 2,
"y": 1,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "PMDA",
"quantity": 1,
"x": 2,
"y": 2,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BPDA-2",
"quantity": 1,
"x": 2,
"y": 3,
"Parameters": "{\"molecular\": 1}"
}
],
"Parameters": "{}"
}
# # 样品板材料数据定义
# material_data_yp_1 = {
# "typeId": "3a142339-80de-8f25-6093-1b1b1b6c322e",
# "name": "样品板-1",
# "unit": "个",
# "quantity": 1,
# "details": [
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BPDA-DD-1",
# "quantity": 1,
# "x": 1,
# "y": 1,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "PEPA",
# "quantity": 1,
# "x": 1,
# "y": 2,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BPDA-DD-2",
# "quantity": 1,
# "x": 1,
# "y": 3,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BPDA-1",
# "quantity": 1,
# "x": 2,
# "y": 1,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "PMDA",
# "quantity": 1,
# "x": 2,
# "y": 2,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BPDA-2",
# "quantity": 1,
# "x": 2,
# "y": 3,
# "Parameters": "{\"molecular\": 1}"
# }
# ],
# "Parameters": "{}"
# }
material_data_yp_2 = {
"typeId": "3a142339-80de-8f25-6093-1b1b1b6c322e",
"name": "样品板-2",
"unit": "",
"quantity": 1,
"details": [
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BPDA-DD",
"quantity": 1,
"x": 1,
"y": 1,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "SIDA",
"quantity": 1,
"x": 1,
"y": 2,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BTDA-1",
"quantity": 1,
"x": 2,
"y": 1,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BTDA-2",
"quantity": 1,
"x": 2,
"y": 2,
"Parameters": "{\"molecular\": 1}"
},
{
"typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
"name": "BTDA-3",
"quantity": 1,
"x": 2,
"y": 3,
"Parameters": "{\"molecular\": 1}"
}
],
"Parameters": "{}"
}
# material_data_yp_2 = {
# "typeId": "3a142339-80de-8f25-6093-1b1b1b6c322e",
# "name": "样品板-2",
# "unit": "个",
# "quantity": 1,
# "details": [
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BPDA-DD",
# "quantity": 1,
# "x": 1,
# "y": 1,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "SIDA",
# "quantity": 1,
# "x": 1,
# "y": 2,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BTDA-1",
# "quantity": 1,
# "x": 2,
# "y": 1,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BTDA-2",
# "quantity": 1,
# "x": 2,
# "y": 2,
# "Parameters": "{\"molecular\": 1}"
# },
# {
# "typeId": "3a14233a-84a3-088d-6676-7cb4acd57c64",
# "name": "BTDA-3",
# "quantity": 1,
# "x": 2,
# "y": 3,
# "Parameters": "{\"molecular\": 1}"
# }
# ],
# "Parameters": "{}"
# }
# 烧杯材料数据定义
beaker_materials = [
{
"typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
"name": "PDA-1",
"unit": "微升",
"quantity": 1,
"parameters": "{\"DeviceMaterialType\":\"NMP\"}"
},
{
"typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
"name": "TFDB",
"unit": "微升",
"quantity": 1,
"parameters": "{\"DeviceMaterialType\":\"NMP\"}"
},
{
"typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
"name": "ODA",
"unit": "微升",
"quantity": 1,
"parameters": "{\"DeviceMaterialType\":\"NMP\"}"
},
{
"typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
"name": "MPDA",
"unit": "微升",
"quantity": 1,
"parameters": "{\"DeviceMaterialType\":\"NMP\"}"
},
{
"typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
"name": "PDA-2",
"unit": "微升",
"quantity": 1,
"parameters": "{\"DeviceMaterialType\":\"NMP\"}"
}
]
# # 烧杯材料数据定义
# beaker_materials = [
# {
# "typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
# "name": "PDA-1",
# "unit": "微升",
# "quantity": 1,
# "parameters": "{\"DeviceMaterialType\":\"NMP\"}"
# },
# {
# "typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
# "name": "TFDB",
# "unit": "微升",
# "quantity": 1,
# "parameters": "{\"DeviceMaterialType\":\"NMP\"}"
# },
# {
# "typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
# "name": "ODA",
# "unit": "微升",
# "quantity": 1,
# "parameters": "{\"DeviceMaterialType\":\"NMP\"}"
# },
# {
# "typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
# "name": "MPDA",
# "unit": "微升",
# "quantity": 1,
# "parameters": "{\"DeviceMaterialType\":\"NMP\"}"
# },
# {
# "typeId": "3a14233b-f0a9-ba84-eaa9-0d4718b361b6",
# "name": "PDA-2",
# "unit": "微升",
# "quantity": 1,
# "parameters": "{\"DeviceMaterialType\":\"NMP\"}"
# }
# ]
# 如果需要可以在这里调用add_material方法添加材料
# 例如:
# result = bioyond.add_material(json.dumps(material_data_yp_1))
# print(f"添加材料结果: {result}")
# # 如果需要可以在这里调用add_material方法添加材料
# # 例如:
# # result = bioyond.add_material(json.dumps(material_data_yp_1))
# # print(f"添加材料结果: {result}")
return {
"sample_plates": [material_data_yp_1, material_data_yp_2],
"beakers": beaker_materials
}
# return {
# "sample_plates": [material_data_yp_1, material_data_yp_2],
# "beakers": beaker_materials
# }
if __name__ == "__main__":

View File

@@ -245,79 +245,7 @@ class BioyondWorkstation(WorkstationBase):
}
# ==================== 工作流合并与参数设置 API ====================
def merge_workflow_with_parameters(self, json_str: str) -> dict:
"""合并工作流并设置参数"""
try:
# 解析输入的 JSON 数据
data = json.loads(json_str)
# 构造 API 请求参数
params = {
"name": data.get("name", ""),
"workflows": data.get("workflows", [])
}
# 验证必要参数
if not params["name"]:
return {
"code": 0,
"message": "工作流名称不能为空",
"timestamp": int(datetime.now().timestamp() * 1000)
}
if not params["workflows"]:
return {
"code": 0,
"message": "工作流列表不能为空",
"timestamp": int(datetime.now().timestamp() * 1000)
}
except json.JSONDecodeError as e:
return {
"code": 0,
"message": f"JSON 解析错误: {str(e)}",
"timestamp": int(datetime.now().timestamp() * 1000)
}
except Exception as e:
return {
"code": 0,
"message": f"参数处理错误: {str(e)}",
"timestamp": int(datetime.now().timestamp() * 1000)
}
# 发送 POST 请求到 Bioyond API
try:
response = self.hardware_interface.post(
url=f'{self.hardware_interface.host}/api/lims/workflow/merge-workflow-with-parameters',
params={
"apiKey": self.hardware_interface.api_key,
"requestTime": self.hardware_interface.get_current_time_iso8601(),
"data": params,
})
# 处理响应
if not response:
return {
"code": 0,
"message": "API 请求失败,未收到响应",
"timestamp": int(datetime.now().timestamp() * 1000)
}
# 返回完整的响应结果
return {
"code": response.get("code", 0),
"message": response.get("message", ""),
"timestamp": response.get("timestamp", int(datetime.now().timestamp() * 1000))
}
except Exception as e:
return {
"code": 0,
"message": f"API 请求异常: {str(e)}",
"timestamp": int(datetime.now().timestamp() * 1000)
}
def append_to_workflow_sequence(self, web_workflow_name: str) -> bool:
# 检查是否为JSON格式的字符串
actual_workflow_name = web_workflow_name
@@ -391,6 +319,23 @@ class BioyondWorkstation(WorkstationBase):
# ==================== 基础物料管理接口 ====================
# ============ 工作站状态管理 ============
def get_station_info(self) -> Dict[str, Any]:
"""获取工作站基础信息
Returns:
Dict[str, Any]: 工作站基础信息包括设备ID、状态等
"""
return {
"device_id": getattr(self._ros_node, 'device_id', 'unknown'),
"station_type": "BioyondWorkstation",
"workflow_status": self.current_workflow_status.value if hasattr(self, 'current_workflow_status') else "unknown",
"is_busy": getattr(self, 'is_busy', False),
"deck_info": {
"name": self.deck.name if self.deck and hasattr(self.deck, 'name') else "unknown",
"children_count": len(self.deck.children) if self.deck and hasattr(self.deck, 'children') else 0
} if self.deck else None,
"hardware_interface": type(self.hardware_interface).__name__ if self.hardware_interface else None
}
def get_workstation_status(self) -> Dict[str, Any]:
"""获取工作站状态

View File

@@ -32,6 +32,7 @@ class Bottle(Well):
barcode: Optional[str] = "",
category: str = "container",
model: Optional[str] = None,
**kwargs,
):
super().__init__(
name=name,
@@ -427,6 +428,7 @@ class BottleCarrier(ItemizedCarrier):
sites: Optional[Dict[Union[int, str], ResourceHolder]] = None,
category: str = "bottle_carrier",
model: Optional[str] = None,
**kwargs,
):
super().__init__(
name=name,

View File

@@ -582,6 +582,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
- update: 更新现有资源
- remove: 从资源树中移除资源
"""
from pylabrobot.resources.resource import Resource as ResourcePLR
try:
data = json.loads(req.command)
results = []
@@ -662,22 +663,23 @@ class BaseROS2DeviceNode(Node, Generic[T]):
)
found_plr_resources = []
other_plr_resources = []
for res_list in found_resources:
for res in res_list:
if issubclass(res.__class__, ResourcePLR):
found_plr_resources.append(res)
for found_resource in found_resources:
for resource in found_resource:
if issubclass(resource.__class__, ResourcePLR):
found_plr_resources.append(resource)
else:
other_plr_resources.append(res)
other_plr_resources.append(resource)
func = getattr(self.driver_instance, "resource_tree_remove", None)
if callable(func):
func(found_plr_resources)
for plr_resource in found_plr_resources:
plr_resource.parent.unassign_child_resource(plr_resource)
if plr_resource.parent is not None:
plr_resource.parent.unassign_child_resource(plr_resource)
self.resource_tracker.remove_resource(plr_resource)
self.lab_logger().info(f"移除物料 {plr_resource} 及其子节点")
for res in other_plr_resources:
self.resource_tracker.remove_resource(res)
self.lab_logger().info(f"移除物料 {res} 及其子节点")
for other_plr_resource in other_plr_resources:
self.resource_tracker.remove_resource(other_plr_resource)
self.lab_logger().info(f"移除物料 {other_plr_resource} 及其子节点")
results.append({"success": True, "action": "remove"})
except Exception as e:
error_msg = f"Error processing {action} operation: {str(e)}"