add bioyond studio draft

unilabos/devices/workstation/bioyond_studio/experiment.py

@@ -0,0 +1,398 @@
+# experiment_workflow.py
+"""
+实验流程主程序
+"""
+
+import json
+from bioyond_rpc import BioyondV1RPC
+from config import API_CONFIG, WORKFLOW_MAPPINGS
+
+
+def run_experiment():
+    """运行实验流程"""
+    
+    # 初始化Bioyond客户端
+    config = {
+        **API_CONFIG,
+        "workflow_mappings": WORKFLOW_MAPPINGS
+    }
+    
+    Bioyond = BioyondV1RPC(config)
+    
+    print("\n============= 多工作流参数测试（简化接口+材料缓存）=============")
+    
+    # 显示可用的材料名称（前20个）
+    available_materials = Bioyond.get_available_materials()
+    print(f"可用材料名称（前20个）: {available_materials[:20]}")
+    print(f"总共有 {len(available_materials)} 个材料可用\n")
+    
+    # 1. 反应器放入
+    print("1. 添加反应器放入工作流，带参数...")
+    Bioyond.reactor_taken_in(
+        assign_material_name="BTDA-DD", 
+        cutoff="10000", 
+        temperature="-10"
+    )
+    
+    # 2. 液体投料-烧杯 (第一个)
+    print("2. 添加液体投料-烧杯，带参数...")
+    Bioyond.liquid_feeding_beaker(
+        volume="34768.7", 
+        assign_material_name="ODA",
+        time="0", 
+        torque_variation="1", 
+        titrationType="1", 
+        temperature=-10
+    )
+    
+    # 3. 液体投料-烧杯 (第二个)
+    print("3. 添加液体投料-烧杯，带参数...")
+    Bioyond.liquid_feeding_beaker(
+        volume="34080.9", 
+        assign_material_name="MPDA",
+        time="5", 
+        torque_variation="2", 
+        titrationType="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", 
+        assign_material_name="SIDA", 
+        titration_type="1", 
+        time="0", 
+        torque_variation="1", 
+        temperature=-10
+    )
+    
+    # 5. 液体投料溶剂
+    print("5. 添加液体投料溶剂，带参数...")
+    Bioyond.liquid_feeding_solvents(
+        assign_material_name="NMP",
+        volume="19000", 
+        titration_type="1", 
+        time="5", 
+        torque_variation="2", 
+        temperature=-10
+    )
+    
+    # 6-8. 固体进料小瓶 (三个)
+    print("6. 添加固体进料小瓶，带参数...")
+    Bioyond.solid_feeding_vials(
+        material_id="3", 
+        time="180", 
+        torque_variation="2",
+        assign_material_name="BTDA-1", 
+        temperature=-10.00
+    )
+    
+    print("7. 添加固体进料小瓶，带参数...")
+    Bioyond.solid_feeding_vials(
+        material_id="3", 
+        time="180", 
+        torque_variation="2",
+        assign_material_name="BTDA-2", 
+        temperature=25.00
+    )
+    
+    print("8. 添加固体进料小瓶，带参数...")
+    Bioyond.solid_feeding_vials(
+        material_id="3", 
+        time="480", 
+        torque_variation="2",
+        assign_material_name="BTDA-3", 
+        temperature=25.00
+    )
+    
+    # 液体投料滴定（第一个）
+    print("9. 添加液体投料滴定，带参数...")  # ODPA
+    Bioyond.liquid_feeding_titration(
+        volume_formula="1000", 
+        assign_material_name="BTDA-DD",
+        titration_type="1", 
+        time="360", 
+        torque_variation="2", 
+        temperature="25.00"
+    )
+    
+    # 液体投料滴定（第二个）
+    print("10. 添加液体投料滴定，带参数...")  # ODPA
+    Bioyond.liquid_feeding_titration(
+        volume_formula="500", 
+        assign_material_name="BTDA-DD",
+        titration_type="1", 
+        time="360", 
+        torque_variation="2", 
+        temperature="25.00"
+    )
+
+    # 液体投料滴定（第三个）
+    print("11. 添加液体投料滴定，带参数...")  # ODPA
+    Bioyond.liquid_feeding_titration(
+        volume_formula="500", 
+        assign_material_name="BTDA-DD",
+        titration_type="1", 
+        time="360", 
+        torque_variation="2", 
+        temperature="25.00"
+    )
+    
+    print("12. 添加液体投料滴定，带参数...")  # ODPA
+    Bioyond.liquid_feeding_titration(
+        volume_formula="500", 
+        assign_material_name="BTDA-DD",
+        titration_type="1", 
+        time="360", 
+        torque_variation="2", 
+        temperature="25.00"
+    )
+    
+    print("13. 添加液体投料滴定，带参数...")  # ODPA
+    Bioyond.liquid_feeding_titration(
+        volume_formula="500", 
+        assign_material_name="BTDA-DD",
+        titration_type="1", 
+        time="360", 
+        torque_variation="2", 
+        temperature="25.00"
+    )
+    
+    print("14. 添加液体投料滴定，带参数...")  # ODPA
+    Bioyond.liquid_feeding_titration(
+        volume_formula="500", 
+        assign_material_name="BTDA-DD",
+        titration_type="1", 
+        time="360", 
+        torque_variation="2", 
+        temperature="25.00"
+    )
+
+
+
+    print("15. 添加液体投料溶剂，带参数...")
+    Bioyond.liquid_feeding_solvents(
+        assign_material_name="PGME",
+        volume="16894.6", 
+        titration_type="1", 
+        time="360", 
+        torque_variation="2", 
+        temperature=25.00
+    )
+    
+    # 16. 反应器取出
+    print("16. 添加反应器取出工作流...")
+    Bioyond.reactor_taken_out()
+    
+    # 显示当前工作流序列
+    sequence = Bioyond.get_workflow_sequence()
+    print("\n当前工作流执行顺序:")
+    print(sequence)
+    
+    # 执行process_and_execute_workflow，合并工作流并创建任务
+    print("\n4. 执行process_and_execute_workflow...")
+    
+    result = Bioyond.process_and_execute_workflow(
+        workflow_name="test3_86", 
+        task_name="实验3_86"
+    )
+    
+    # 显示执行结果
+    print("\n5. 执行结果:")
+    if isinstance(result, str):
+        try:
+            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')}")
+            else:
+                print(f"任务创建失败: {result_dict.get('error')}")
+        except:
+            print(f"结果解析失败: {result}")
+    else:
+        if result.get("success"):
+            print("任务创建成功!")
+            print(f"- 工作流: {result.get('workflow', {}).get('name')}")
+            print(f"- 工作流ID: {result.get('workflow', {}).get('id')}")
+            print(f"- 任务结果: {result.get('task')}")
+        else:
+            print(f"任务创建失败: {result.get('error')}")
+    
+    # 可选：启动调度器
+    # Bioyond.scheduler_start()
+    
+    return Bioyond
+
+
+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": "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": "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\"}"
+        }
+    ]
+    
+    # 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
+    }
+
+
+if __name__ == "__main__":
+    # 运行主实验流程
+    bioyond_client = run_experiment()
+    
+    # 可选：准备材料数据
+    # materials = prepare_materials(bioyond_client)
+    # print(f"\n准备的材料数据: {materials}")

unilabos/devices/workstation/bioyond_studio/station.py

@@ -0,0 +1,334 @@
+"""
+Bioyond工作站实现
+Bioyond Workstation Implementation
+
+集成Bioyond物料管理的工作站示例
+"""
+from typing import Dict, Any, List, Optional, Union
+import json
+
+from unilabos.devices.workstation.workstation_base import WorkstationBase, ResourceSynchronizer
+from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker
+from unilabos.utils.log import logger
+from unilabos.resources.graphio import resource_bioyond_to_plr
+
+
+class BioyondWorkstation(WorkstationBase):
+    """Bioyond工作站
+    
+    集成Bioyond物料管理的工作站实现
+    """
+    
+    def __init__(
+        self,
+        bioyond_config: Optional[Dict[str, Any]] = None,
+        deck: Optional[str, Any] = None,
+        *args,
+        **kwargs,
+    ):
+        # 设置Bioyond配置
+        self.bioyond_config = bioyond_config or {
+            "base_url": "http://localhost:8080",
+            "api_key": "",
+            "sync_interval": 30,
+            "timeout": 30
+        }
+        
+        # 设置默认deck配置
+        
+        # 初始化父类
+        super().__init__(
+            #桌子
+            deck=deck,
+            *args,
+            **kwargs,
+        )
+        
+        # TODO: self._ros_node里面拿属性
+        logger.info(f"Bioyond工作站初始化完成")
+
+    def _create_communication_module(self):
+        """创建Bioyond通信模块"""
+        # 暂时返回None，因为工作站基类没有强制要求通信模块
+        return None
+    
+    def _create_material_management_module(self) -> BioyondMaterialManagement:
+        """创建Bioyond物料管理模块"""
+        # 获取必要的属性，如果不存在则使用默认值
+        device_id = getattr(self, 'device_id', 'bioyond_workstation')
+        resource_tracker = getattr(self, 'resource_tracker', None)
+        children_config = getattr(self, '_children', {})
+        
+       
+    
+    def _register_supported_workflows(self):
+        """注册Bioyond支持的工作流"""
+        from unilabos.devices.workstation.workstation_base import WorkflowInfo
+        
+        # Bioyond物料同步工作流
+        self.supported_workflows["bioyond_sync"] = WorkflowInfo(
+            name="bioyond_sync",
+            description="从Bioyond系统同步物料",
+            parameters={
+                "sync_type": {"type": "string", "default": "full", "options": ["full", "incremental"]},
+                "force_sync": {"type": "boolean", "default": False}
+            }
+        )
+        
+        # Bioyond物料更新工作流
+        self.supported_workflows["bioyond_update"] = WorkflowInfo(
+            name="bioyond_update",
+            description="将本地物料变更同步到Bioyond",
+            parameters={
+                "material_ids": {"type": "list", "default": []},
+                "sync_all": {"type": "boolean", "default": True}
+            }
+        )
+        
+        logger.info(f"注册了 {len(self.supported_workflows)} 个Bioyond工作流")
+    
+    async def execute_bioyond_sync_workflow(self, parameters: Dict[str, Any]) -> Dict[str, Any]:
+        """执行Bioyond同步工作流"""
+        try:
+            sync_type = parameters.get("sync_type", "full")
+            force_sync = parameters.get("force_sync", False)
+            
+            logger.info(f"开始执行Bioyond同步工作流: {sync_type}")
+            
+            # 获取物料管理模块
+            material_manager = self.material_management
+            
+            if sync_type == "full":
+                # 全量同步
+                success = await material_manager.sync_from_bioyond()
+            else:
+                # 增量同步（这里可以实现增量同步逻辑）
+                success = await material_manager.sync_from_bioyond()
+            
+            if success:
+                result = {
+                    "status": "success",
+                    "message": f"Bioyond同步完成: {sync_type}",
+                    "synced_resources": len(material_manager.plr_resources)
+                }
+            else:
+                result = {
+                    "status": "failed",
+                    "message": "Bioyond同步失败"
+                }
+            
+            logger.info(f"Bioyond同步工作流执行完成: {result['status']}")
+            return result
+            
+        except Exception as e:
+            logger.error(f"Bioyond同步工作流执行失败: {e}")
+            return {
+                "status": "error",
+                "message": str(e)
+            }
+    
+    async def execute_bioyond_update_workflow(self, parameters: Dict[str, Any]) -> Dict[str, Any]:
+        """执行Bioyond更新工作流"""
+        try:
+            material_ids = parameters.get("material_ids", [])
+            sync_all = parameters.get("sync_all", True)
+            
+            logger.info(f"开始执行Bioyond更新工作流: sync_all={sync_all}")
+            
+            # 获取物料管理模块
+            material_manager = self.material_management
+            
+            if sync_all:
+                # 同步所有物料
+                success_count = 0
+                for resource in material_manager.plr_resources.values():
+                    success = await material_manager.sync_to_bioyond(resource)
+                    if success:
+                        success_count += 1
+            else:
+                # 同步指定物料
+                success_count = 0
+                for material_id in material_ids:
+                    resource = material_manager.find_material_by_id(material_id)
+                    if resource:
+                        success = await material_manager.sync_to_bioyond(resource)
+                        if success:
+                            success_count += 1
+            
+            result = {
+                "status": "success",
+                "message": f"Bioyond更新完成",
+                "updated_resources": success_count,
+                "total_resources": len(material_ids) if not sync_all else len(material_manager.plr_resources)
+            }
+            
+            logger.info(f"Bioyond更新工作流执行完成: {result['status']}")
+            return result
+            
+        except Exception as e:
+            logger.error(f"Bioyond更新工作流执行失败: {e}")
+            return {
+                "status": "error",
+                "message": str(e)
+            }
+    
+    def get_bioyond_status(self) -> Dict[str, Any]:
+        """获取Bioyond系统状态"""
+        try:
+            material_manager = self.material_management
+            
+            return {
+                "bioyond_connected": material_manager.bioyond_api_client is not None,
+                "sync_interval": material_manager.sync_interval,
+                "total_resources": len(material_manager.plr_resources),
+                "deck_size": {
+                    "x": material_manager.plr_deck.size_x,
+                    "y": material_manager.plr_deck.size_y,
+                    "z": material_manager.plr_deck.size_z
+                },
+                "bioyond_config": self.bioyond_config
+            }
+        except Exception as e:
+            logger.error(f"获取Bioyond状态失败: {e}")
+            return {
+                "error": str(e)
+            }
+    
+    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)
+            
+            # 获取物料管理模块
+            material_manager = self.material_management
+            
+            # 转换为UniLab格式
+            if isinstance(bioyond_data, dict) and "data" in bioyond_data:
+                unilab_resources = material_manager.resource_bioyond_container_to_ulab(bioyond_data)
+            else:
+                unilab_resources = material_manager.resource_bioyond_to_ulab(bioyond_data)
+            
+            # 分配到Deck
+            import asyncio
+            asyncio.create_task(material_manager._assign_resources_to_deck(unilab_resources))
+            
+            logger.info(f"从文件 {file_path} 加载了 {len(unilab_resources)} 个Bioyond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__":
+    # 创建示例工作站
+    #workstation = create_bioyond_workstation_example()
+    
+    # 从文件加载测试数据
+    #workstation.load_bioyond_data_from_file("bioyond_test_yibin.json")
+    
+    # 获取状态
+    #status = workstation.get_bioyond_status()
+    #print("Bioyond工作站状态:", status)
+
+    # 创建测试数据 - 使用resource_bioyond_container_to_ulab函数期望的格式
+  
+  # 读取 bioyond_resources_unilab_output3 copy.json 文件
+    from unilabos.resources.graphio import resource_ulab_to_plr, convert_resources_to_type
+    from Bioyond_wuliao import *
+    from typing import List
+    from pylabrobot.resources import Resource as PLRResource
+    import json
+    from pylabrobot.resources.deck import Deck
+    from pylabrobot.resources.coordinate import Coordinate
+    
+    with open("./bioyond_test_yibin3_unilab_result_corr.json", "r", encoding="utf-8") as f:
+        bioyond_resources_unilab = json.load(f)
+    print(f"成功读取 JSON 文件，包含 {len(bioyond_resources_unilab)} 个资源")
+    ulab_resources = convert_resources_to_type(bioyond_resources_unilab, List[PLRResource])
+    print(f"转换结果类型: {type(ulab_resources)}")
+    print(f"转换结果长度: {len(ulab_resources) if ulab_resources else 0}")
+    deck = Deck(size_x=2000,
+                size_y=653.5,
+                size_z=900)
+
+    Stack0 = Stack(name="Stack0", location=Coordinate(0, 100, 0))
+    Stack1 = Stack(name="Stack1", location=Coordinate(100, 100, 0))
+    Stack2 = Stack(name="Stack2", location=Coordinate(200, 100, 0))
+    Stack3 = Stack(name="Stack3", location=Coordinate(300, 100, 0))
+    Stack4 = Stack(name="Stack4", location=Coordinate(400, 100, 0))
+    Stack5 = Stack(name="Stack5", location=Coordinate(500, 100, 0))
+
+    deck.assign_child_resource(Stack1, Stack1.location)
+    deck.assign_child_resource(Stack2, Stack2.location)
+    deck.assign_child_resource(Stack3, Stack3.location)
+    deck.assign_child_resource(Stack4, Stack4.location)
+    deck.assign_child_resource(Stack5, Stack5.location)
+
+    Stack0.assign_child_resource(ulab_resources[0], Stack0.location)
+    Stack1.assign_child_resource(ulab_resources[1], Stack1.location)
+    Stack2.assign_child_resource(ulab_resources[2], Stack2.location)
+    Stack3.assign_child_resource(ulab_resources[3], Stack3.location)
+    Stack4.assign_child_resource(ulab_resources[4], Stack4.location)
+    Stack5.assign_child_resource(ulab_resources[5], Stack5.location)
+
+    from unilabos.resources.graphio import convert_resources_from_type
+    from unilabos.app.web.client import http_client
+
+    resources = convert_resources_from_type([deck], [PLRResource])
+
+    
+    print(resources)
+    http_client.remote_addr = "https://uni-lab.bohrium.com/api/v1"
+    #http_client.auth = "9F05593C"
+    http_client.auth = "ED634D1C"
+    http_client.resource_add(resources, database_process_later=False)