mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2025-12-14 13:14:39 +00:00
7c440d10ab
* Fix ResourceTreeSet load error * Raise error when using unsupported type to create ResourceTreeSet * Fix children key error * Fix children key error * Fix workstation resource not tracking * Fix workstation deck & children resource dupe * Fix workstation deck & children resource dupe * Fix multiple resource error * Fix resource tree update * Fix resource tree update * Force confirm uuid * Tip more error log * Refactor Bioyond workstation and experiment workflow (#105) 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. * Fix resource get. Fix resource parent not found. Mapping uuid for all resources. * mount parent uuid * Add logging configuration based on BasicConfig in main function * fix workstation node error * fix workstation node error * Update boot example * temp fix for resource get * temp fix for resource get * provide error info when cant find plr type * pack repo info * fix to plr type error * fix to plr type error * Update regular container method * support no size init * fix comprehensive_station.json * fix comprehensive_station.json * fix type conversion * fix state loading for regular container * Update deploy-docs.yml * Update deploy-docs.yml --------- Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>
569 lines
19 KiB
Python
569 lines
19 KiB
Python
"""
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Bioyond工作站实现
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Bioyond Workstation Implementation
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集成Bioyond物料管理的工作站示例
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"""
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import traceback
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from datetime import datetime
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from typing import Dict, Any, List, Optional, Union
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import json
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from unilabos.devices.workstation.workstation_base import WorkstationBase, ResourceSynchronizer
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from unilabos.devices.workstation.bioyond_studio.bioyond_rpc import BioyondV1RPC
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from unilabos.registry.placeholder_type import ResourceSlot, DeviceSlot
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from unilabos.resources.warehouse import WareHouse
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from unilabos.utils.log import logger
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from unilabos.resources.graphio import resource_bioyond_to_plr, resource_plr_to_bioyond
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from unilabos.ros.nodes.base_device_node import ROS2DeviceNode, BaseROS2DeviceNode
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from unilabos.ros.nodes.presets.workstation import ROS2WorkstationNode
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from pylabrobot.resources.resource import Resource as ResourcePLR
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from unilabos.devices.workstation.bioyond_studio.config import (
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API_CONFIG, WORKFLOW_MAPPINGS, MATERIAL_TYPE_MAPPINGS, WAREHOUSE_MAPPING
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)
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class BioyondResourceSynchronizer(ResourceSynchronizer):
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"""Bioyond资源同步器
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负责与Bioyond系统进行物料数据的同步
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"""
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def __init__(self, workstation: 'BioyondWorkstation'):
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super().__init__(workstation)
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self.bioyond_api_client = None
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self.sync_interval = 60 # 默认60秒同步一次
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self.last_sync_time = 0
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self.initialize()
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def initialize(self) -> bool:
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"""初始化Bioyond资源同步器"""
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try:
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self.bioyond_api_client = self.workstation.hardware_interface
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if self.bioyond_api_client is None:
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logger.error("Bioyond API客户端未初始化")
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return False
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# 设置同步间隔
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self.sync_interval = self.workstation.bioyond_config.get("sync_interval", 600)
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logger.info("Bioyond资源同步器初始化完成")
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return True
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except Exception as e:
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logger.error(f"Bioyond资源同步器初始化失败: {e}")
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return False
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def sync_from_external(self) -> bool:
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"""从Bioyond系统同步物料数据"""
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try:
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if self.bioyond_api_client is None:
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logger.error("Bioyond API客户端未初始化")
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return False
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bioyond_data = self.bioyond_api_client.stock_material('{"typeMode": 2, "includeDetail": true}')
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if not bioyond_data:
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logger.warning("从Bioyond获取的物料数据为空")
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return False
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# 转换为UniLab格式
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unilab_resources = resource_bioyond_to_plr(
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bioyond_data,
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type_mapping=self.workstation.bioyond_config["material_type_mappings"],
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deck=self.workstation.deck
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)
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logger.info(f"从Bioyond同步了 {len(unilab_resources)} 个资源")
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return True
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except Exception as e:
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logger.error(f"从Bioyond同步物料数据失败: {e}")
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traceback.print_exc()
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return False
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def sync_to_external(self, resource: Any) -> bool:
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"""将本地物料数据变更同步到Bioyond系统"""
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try:
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if self.bioyond_api_client is None:
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logger.error("Bioyond API客户端未初始化")
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return False
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bioyond_material = resource_plr_to_bioyond(
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[resource],
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type_mapping=self.workstation.bioyond_config["material_type_mappings"],
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warehouse_mapping=self.workstation.bioyond_config["warehouse_mapping"]
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)[0]
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location_info = bioyond_material.pop("locations")
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material_id = self.bioyond_api_client.add_material(bioyond_material)
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response = self.bioyond_api_client.material_inbound(material_id, location_info[0]["id"])
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if not response:
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return {
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"status": "error",
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"message": "Failed to inbound material"
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}
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except:
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pass
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def handle_external_change(self, change_info: Dict[str, Any]) -> bool:
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"""处理Bioyond系统的变更通知"""
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try:
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# 这里可以实现对Bioyond变更的处理逻辑
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logger.info(f"处理Bioyond变更通知: {change_info}")
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return True
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except Exception as e:
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logger.error(f"处理Bioyond变更通知失败: {e}")
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return False
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class BioyondWorkstation(WorkstationBase):
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"""Bioyond工作站
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集成Bioyond物料管理的工作站实现
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"""
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def __init__(
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self,
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bioyond_config: Optional[Dict[str, Any]] = None,
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deck: Optional[Any] = None,
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*args,
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**kwargs,
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):
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# 初始化父类
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super().__init__(
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# 桌子
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deck=deck,
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*args,
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**kwargs,
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)
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# 检查 deck 是否为 None，防止 AttributeError
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if self.deck is None:
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logger.error("❌ Deck 配置为空，请检查配置文件中的 deck 参数")
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raise ValueError("Deck 配置不能为空，请在配置文件中添加正确的 deck 配置")
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# 初始化 warehouses 属性
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self.deck.warehouses = {}
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for resource in self.deck.children:
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if isinstance(resource, WareHouse):
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self.deck.warehouses[resource.name] = resource
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# 创建通信模块
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self._create_communication_module(bioyond_config)
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self.resource_synchronizer = BioyondResourceSynchronizer(self)
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self.resource_synchronizer.sync_from_external()
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# TODO: self._ros_node里面拿属性
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# 工作流加载
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self.is_running = False
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self.workflow_mappings = {}
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self.workflow_sequence = []
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self.pending_task_params = []
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if "workflow_mappings" in bioyond_config:
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self._set_workflow_mappings(bioyond_config["workflow_mappings"])
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logger.info(f"Bioyond工作站初始化完成")
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def post_init(self, ros_node: ROS2WorkstationNode):
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self._ros_node = ros_node
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ROS2DeviceNode.run_async_func(self._ros_node.update_resource, True, **{
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"resources": [self.deck]
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})
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def transfer_resource_to_another(self, resource: List[ResourceSlot], mount_resource: List[ResourceSlot], sites: List[str], mount_device_id: DeviceSlot):
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ROS2DeviceNode.run_async_func(self._ros_node.transfer_resource_to_another, True, **{
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"plr_resources": resource,
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"target_device_id": mount_device_id,
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"target_resources": mount_resource,
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"sites": sites,
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})
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def _create_communication_module(self, config: Optional[Dict[str, Any]] = None) -> None:
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"""创建Bioyond通信模块"""
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self.bioyond_config = config or {
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**API_CONFIG,
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"workflow_mappings": WORKFLOW_MAPPINGS,
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"material_type_mappings": MATERIAL_TYPE_MAPPINGS,
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"warehouse_mapping": WAREHOUSE_MAPPING
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}
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self.hardware_interface = BioyondV1RPC(self.bioyond_config)
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def resource_tree_add(self, resources: List[ResourcePLR]) -> None:
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"""添加资源到资源树并更新ROS节点
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Args:
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resources (List[ResourcePLR]): 要添加的资源列表
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"""
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self.resource_synchronizer.sync_to_external(resources)
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@property
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def bioyond_status(self) -> Dict[str, Any]:
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"""获取 Bioyond 系统状态信息
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这个属性被 ROS 节点用来发布设备状态
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Returns:
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Dict[str, Any]: Bioyond 系统的状态信息
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"""
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try:
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# 基础状态信息
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status = {
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}
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# 如果有反应站接口，获取调度器状态
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if self.hardware_interface:
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try:
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scheduler_status = self.hardware_interface.scheduler_status()
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status["scheduler"] = scheduler_status
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except Exception as e:
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logger.warning(f"获取调度器状态失败: {e}")
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status["scheduler"] = {"error": str(e)}
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# 添加物料缓存信息
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if self.hardware_interface:
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try:
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available_materials = self.hardware_interface.get_available_materials()
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status["material_cache_count"] = len(available_materials)
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except Exception as e:
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logger.warning(f"获取物料缓存失败: {e}")
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status["material_cache_count"] = 0
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return status
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except Exception as e:
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logger.error(f"获取Bioyond状态失败: {e}")
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return {
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"status": "error",
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"message": str(e),
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"station_type": getattr(self, 'station_type', 'unknown'),
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"station_name": getattr(self, 'station_name', 'unknown')
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}
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# ==================== 工作流合并与参数设置 API ====================
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def merge_workflow_with_parameters(self, json_str: str) -> dict:
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"""合并工作流并设置参数"""
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try:
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# 解析输入的 JSON 数据
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data = json.loads(json_str)
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# 构造 API 请求参数
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params = {
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"name": data.get("name", ""),
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"workflows": data.get("workflows", [])
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}
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# 验证必要参数
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if not params["name"]:
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return {
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"code": 0,
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"message": "工作流名称不能为空",
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"timestamp": int(datetime.now().timestamp() * 1000)
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}
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if not params["workflows"]:
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return {
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"code": 0,
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"message": "工作流列表不能为空",
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"timestamp": int(datetime.now().timestamp() * 1000)
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}
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except json.JSONDecodeError as e:
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return {
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"code": 0,
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"message": f"JSON 解析错误: {str(e)}",
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"timestamp": int(datetime.now().timestamp() * 1000)
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}
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except Exception as e:
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return {
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"code": 0,
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"message": f"参数处理错误: {str(e)}",
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"timestamp": int(datetime.now().timestamp() * 1000)
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}
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# 发送 POST 请求到 Bioyond API
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try:
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response = self.hardware_interface.post(
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url=f'{self.hardware_interface.host}/api/lims/workflow/merge-workflow-with-parameters',
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params={
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"apiKey": self.hardware_interface.api_key,
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"requestTime": self.hardware_interface.get_current_time_iso8601(),
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"data": params,
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})
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# 处理响应
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if not response:
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return {
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"code": 0,
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"message": "API 请求失败，未收到响应",
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"timestamp": int(datetime.now().timestamp() * 1000)
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}
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|
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# 返回完整的响应结果
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||
return {
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"code": response.get("code", 0),
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||
"message": response.get("message", ""),
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"timestamp": response.get("timestamp", int(datetime.now().timestamp() * 1000))
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}
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||
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||
except Exception as e:
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return {
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"code": 0,
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"message": f"API 请求异常: {str(e)}",
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"timestamp": int(datetime.now().timestamp() * 1000)
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}
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def append_to_workflow_sequence(self, web_workflow_name: str) -> bool:
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# 检查是否为JSON格式的字符串
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actual_workflow_name = web_workflow_name
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if web_workflow_name.startswith('{') and web_workflow_name.endswith('}'):
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try:
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data = json.loads(web_workflow_name)
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actual_workflow_name = data.get("web_workflow_name", web_workflow_name)
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print(f"解析JSON格式工作流名称: {web_workflow_name} -> {actual_workflow_name}")
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except json.JSONDecodeError:
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print(f"JSON解析失败，使用原始字符串: {web_workflow_name}")
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||
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workflow_id = self._get_workflow(actual_workflow_name)
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if workflow_id:
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self.workflow_sequence.append(workflow_id)
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print(f"添加工作流到执行顺序: {actual_workflow_name} -> {workflow_id}")
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return True
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||
return False
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||
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||
def set_workflow_sequence(self, json_str: str) -> List[str]:
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||
try:
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||
data = json.loads(json_str)
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||
web_workflow_names = data.get("web_workflow_names", [])
|
||
except:
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||
return []
|
||
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||
sequence = []
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||
for web_name in web_workflow_names:
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||
workflow_id = self._get_workflow(web_name)
|
||
if workflow_id:
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||
sequence.append(workflow_id)
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||
|
||
def get_all_workflows(self) -> Dict[str, str]:
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return self.workflow_mappings.copy()
|
||
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||
def _get_workflow(self, web_workflow_name: str) -> str:
|
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if web_workflow_name not in self.workflow_mappings:
|
||
print(f"未找到工作流映射配置: {web_workflow_name}")
|
||
return ""
|
||
workflow_id = self.workflow_mappings[web_workflow_name]
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||
print(f"获取工作流: {web_workflow_name} -> {workflow_id}")
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||
return workflow_id
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||
|
||
def _set_workflow_mappings(self, mappings: Dict[str, str]):
|
||
self.workflow_mappings = mappings
|
||
print(f"设置工作流映射配置: {mappings}")
|
||
|
||
def process_web_workflows(self, json_str: str) -> Dict[str, str]:
|
||
try:
|
||
data = json.loads(json_str)
|
||
web_workflow_list = data.get("web_workflow_list", [])
|
||
except json.JSONDecodeError:
|
||
print(f"无效的JSON字符串: {json_str}")
|
||
return {}
|
||
result = {}
|
||
|
||
self.workflow_sequence = []
|
||
for web_name in web_workflow_list:
|
||
workflow_id = self._get_workflow(web_name)
|
||
if workflow_id:
|
||
result[web_name] = workflow_id
|
||
self.workflow_sequence.append(workflow_id)
|
||
else:
|
||
print(f"无法获取工作流ID: {web_name}")
|
||
print(f"工作流执行顺序: {self.workflow_sequence}")
|
||
return result
|
||
|
||
def clear_workflows(self):
|
||
self.workflow_sequence = []
|
||
print("清空工作流执行顺序")
|
||
|
||
# ==================== 基础物料管理接口 ====================
|
||
|
||
# ============ 工作站状态管理 ============
|
||
|
||
def get_workstation_status(self) -> Dict[str, Any]:
|
||
"""获取工作站状态
|
||
|
||
Returns:
|
||
Dict[str, Any]: 工作站状态信息
|
||
"""
|
||
try:
|
||
# 获取基础工作站状态
|
||
base_status = {
|
||
"station_info": self.get_station_info(),
|
||
"bioyond_status": self.bioyond_status
|
||
}
|
||
|
||
# 如果有接口，获取设备列表
|
||
if self.hardware_interface:
|
||
try:
|
||
devices = self.hardware_interface.device_list()
|
||
base_status["devices"] = devices
|
||
except Exception as e:
|
||
logger.warning(f"获取设备列表失败: {e}")
|
||
base_status["devices"] = []
|
||
|
||
return {
|
||
"success": True,
|
||
"data": base_status,
|
||
"action": "get_workstation_status"
|
||
}
|
||
|
||
except Exception as e:
|
||
error_msg = f"获取工作站状态失败: {str(e)}"
|
||
logger.error(error_msg)
|
||
return {
|
||
"success": False,
|
||
"message": error_msg,
|
||
"action": "get_workstation_status"
|
||
}
|
||
|
||
def get_bioyond_status(self) -> Dict[str, Any]:
|
||
"""获取完整的 Bioyond 状态信息
|
||
|
||
这个方法提供了比 bioyond_status 属性更详细的状态信息，
|
||
包括错误处理和格式化的响应结构
|
||
|
||
Returns:
|
||
Dict[str, Any]: 格式化的 Bioyond 状态响应
|
||
"""
|
||
try:
|
||
status = self.bioyond_status
|
||
return {
|
||
"success": True,
|
||
"data": status,
|
||
"action": "get_bioyond_status"
|
||
}
|
||
|
||
except Exception as e:
|
||
error_msg = f"获取 Bioyond 状态失败: {str(e)}"
|
||
logger.error(error_msg)
|
||
return {
|
||
"success": False,
|
||
"message": error_msg,
|
||
"action": "get_bioyond_status"
|
||
}
|
||
|
||
def reset_workstation(self) -> Dict[str, Any]:
|
||
"""重置工作站
|
||
|
||
重置工作站到初始状态
|
||
|
||
Returns:
|
||
Dict[str, Any]: 操作结果
|
||
"""
|
||
try:
|
||
logger.info("开始重置工作站")
|
||
|
||
# 重置调度器
|
||
if self.hardware_interface:
|
||
self.hardware_interface.scheduler_reset()
|
||
|
||
# 刷新物料缓存
|
||
if self.hardware_interface:
|
||
self.hardware_interface.refresh_material_cache()
|
||
|
||
# 重新同步资源
|
||
if self.resource_synchronizer:
|
||
self.resource_synchronizer.sync_from_external()
|
||
|
||
logger.info("工作站重置完成")
|
||
return {
|
||
"success": True,
|
||
"message": "工作站重置成功",
|
||
"action": "reset_workstation"
|
||
}
|
||
|
||
except Exception as e:
|
||
error_msg = f"重置工作站失败: {str(e)}"
|
||
logger.error(error_msg)
|
||
return {
|
||
"success": False,
|
||
"message": error_msg,
|
||
"action": "reset_workstation"
|
||
}
|
||
|
||
def load_bioyond_data_from_file(self, file_path: str) -> bool:
|
||
"""从文件加载Bioyond数据（用于测试）"""
|
||
try:
|
||
with open(file_path, "r", encoding="utf-8") as f:
|
||
bioyond_data = json.load(f)
|
||
|
||
logger.info(f"从文件加载Bioyond数据: {file_path}")
|
||
|
||
# 转换为UniLab格式
|
||
unilab_resources = resource_bioyond_to_plr(
|
||
bioyond_data,
|
||
type_mapping=self.bioyond_config["material_type_mappings"],
|
||
deck=self.deck
|
||
)
|
||
|
||
logger.info(f"成功加载 {len(unilab_resources)} 个资源")
|
||
return True
|
||
|
||
except Exception as e:
|
||
logger.error(f"从文件加载Bioyond数据失败: {e}")
|
||
return False
|
||
|
||
|
||
# 使用示例
|
||
def create_bioyond_workstation_example():
|
||
"""创建Bioyond工作站示例"""
|
||
|
||
# 配置参数
|
||
device_id = "bioyond_workstation_001"
|
||
|
||
# 子资源配置
|
||
children = {
|
||
"plate_1": {
|
||
"name": "plate_1",
|
||
"type": "plate",
|
||
"position": {"x": 100, "y": 100, "z": 0},
|
||
"config": {
|
||
"size_x": 127.76,
|
||
"size_y": 85.48,
|
||
"size_z": 14.35,
|
||
"model": "Generic 96 Well Plate"
|
||
}
|
||
}
|
||
}
|
||
|
||
# Bioyond配置
|
||
bioyond_config = {
|
||
"base_url": "http://bioyond.example.com/api",
|
||
"api_key": "your_api_key_here",
|
||
"sync_interval": 60, # 60秒同步一次
|
||
"timeout": 30
|
||
}
|
||
|
||
# Deck配置
|
||
deck_config = {
|
||
"size_x": 1000.0,
|
||
"size_y": 1000.0,
|
||
"size_z": 100.0,
|
||
"model": "BioyondDeck"
|
||
}
|
||
|
||
# 创建工作站
|
||
workstation = BioyondWorkstation(
|
||
station_resource=deck_config,
|
||
bioyond_config=bioyond_config,
|
||
deck_config=deck_config,
|
||
)
|
||
|
||
return workstation
|
||
|
||
|
||
if __name__ == "__main__":
|
||
pass |