修改了add protocol

test/experiments/mock_protocol/addteststation.json

@@ -4,58 +4,83 @@
             "id": "AddTestStation",
             "name": "添加试剂测试工作站",
             "children": [
-                "pump_add",
+                "transfer_pump",
-                "flask_1",
+                "multiway_valve", 
-                "flask_2", 
-                "flask_3",
-                "flask_4",
-                "reactor",
                 "stirrer",
-                "flask_air"
+                "flask_reagent1",
+                "flask_reagent2",
+                "flask_reagent3",
+                "flask_reagent4",
+                "reactor",
+                "flask_waste",
+                "flask_rinsing",
+                "flask_buffer"
             ],
             "parent": null,
             "type": "device",
             "class": "workstation",
             "position": {
-                "x": 620.6111111111111,
+                "x": 620,
                 "y": 171,
                 "z": 0
             },
             "config": {
-                "protocol_type": ["AddProtocol", "PumpTransferProtocol", "CleanProtocol"]
+                "protocol_type": ["AddProtocol", "TransferProtocol", "StirProtocol", "StartStirProtocol", "StopStirProtocol"]
             },
             "data": {}
         },
         {
-            "id": "pump_add",
+            "id": "transfer_pump",
-            "name": "pump_add",
+            "name": "注射器泵",
             "children": [],
             "parent": "AddTestStation",
             "type": "device",
-            "class": "virtual_pump",
+            "class": "virtual_transfer_pump",
             "position": {
-                "x": 520.6111111111111,
+                "x": 520,
                 "y": 300,
                 "z": 0
             },
             "config": {
                 "port": "VIRTUAL",
-                "max_volume": 25.0
+                "max_volume": 50.0,
+                "transfer_rate": 5.0
             },
             "data": {
                 "status": "Idle"
             }
         },
+        {
+            "id": "multiway_valve",
+            "name": "八通阀门",
+            "children": [],
+            "parent": "AddTestStation",
+            "type": "device",
+            "class": "virtual_multiway_valve",
+            "position": {
+                "x": 420,
+                "y": 300,
+                "z": 0
+            },
+            "config": {
+                "port": "VIRTUAL",
+                "positions": 8
+            },
+            "data": {
+                "status": "Idle",
+                "current_position": 1
+            }
+        },
         {
             "id": "stirrer",
-            "name": "stirrer",
+            "name": "搅拌器",
             "children": [],
             "parent": "AddTestStation",
             "type": "device",
             "class": "virtual_stirrer",
             "position": {
-                "x": 698.1111111111111,
+                "x": 720,
-                "y": 478,
+                "y": 450,
                 "z": 0
             },
             "config": {
@@ -68,110 +93,115 @@
             }
         },
         {
-            "id": "flask_1",
+            "id": "flask_reagent1",
-            "name": "通用试剂瓶1",
+            "name": "试剂瓶1 (甲醇)",
             "children": [],
             "parent": "AddTestStation",
             "type": "container",
             "class": null,
             "position": {
                 "x": 100,
-                "y": 428,
+                "y": 400,
                 "z": 0
             },
             "config": {
-                "max_volume": 2000.0
+                "max_volume": 1000.0
             },
             "data": {
-                "liquid": []
+                "liquid": [
+                    {
+                        "name": "甲醇",
+                        "volume": 800.0,
+                        "concentration": "99.9%"
+                    }
+                ]
             }
         },
         {
-            "id": "flask_2",
+            "id": "flask_reagent2",
-            "name": "通用试剂瓶2",
+            "name": "试剂瓶2 (乙醇)",
             "children": [],
             "parent": "AddTestStation",
             "type": "container",
             "class": null,
             "position": {
-                "x": 250,
+                "x": 180,
-                "y": 428,
+                "y": 400,
                 "z": 0
             },
             "config": {
-                "max_volume": 2000.0
+                "max_volume": 1000.0
             },
             "data": {
-                "liquid": []
+                "liquid": [
+                    {
+                        "name": "乙醇",
+                        "volume": 750.0,
+                        "concentration": "95%"
+                    }
+                ]
             }
         },
         {
-            "id": "flask_3",
+            "id": "flask_reagent3",
-            "name": "通用试剂瓶3",
+            "name": "试剂瓶3 (丙酮)",
             "children": [],
             "parent": "AddTestStation",
             "type": "container",
             "class": null,
             "position": {
-                "x": 400,
+                "x": 260,
-                "y": 428,
+                "y": 400,
                 "z": 0
             },
             "config": {
-                "max_volume": 2000.0
+                "max_volume": 1000.0
             },
             "data": {
-                "liquid": []
+                "liquid": [
+                    {
+                        "name": "丙酮",
+                        "volume": 900.0,
+                        "concentration": "99.5%"
+                    }
+                ]
             }
         },
         {
-            "id": "flask_4",
+            "id": "flask_reagent4",
-            "name": "通用试剂瓶4",
+            "name": "试剂瓶4 (二氯甲烷)",
             "children": [],
             "parent": "AddTestStation",
             "type": "container",
             "class": null,
             "position": {
-                "x": 550,
+                "x": 340,
-                "y": 428,
+                "y": 400,
                 "z": 0
             },
             "config": {
-                "max_volume": 2000.0
+                "max_volume": 1000.0
             },
             "data": {
-                "liquid": []
+                "liquid": [
+                    {
+                        "name": "二氯甲烷",
+                        "volume": 850.0,
+                        "concentration": "99.8%"
+                    }
+                ]
             }
         },
         {
             "id": "reactor",
-            "name": "reactor",
+            "name": "反应器",
             "children": [],
             "parent": "AddTestStation",
             "type": "container",
             "class": null,
             "position": {
-                "x": 698.1111111111111,
+                "x": 720,
-                "y": 428,
+                "y": 400,
-                "z": 0
-            },
-            "config": {
-                "max_volume": 5000.0
-            },
-            "data": {
-                "liquid": []
-            }
-        },
-        {
-            "id": "flask_air",
-            "name": "flask_air",
-            "children": [],
-            "parent": "AddTestStation",
-            "type": "container",
-            "class": null,
-            "position": {
-                "x": 800,
-                "y": 300,
                 "z": 0
             },
             "config": {
@@ -180,70 +210,166 @@
             "data": {
                 "liquid": []
             }
+        },
+        {
+            "id": "flask_waste",
+            "name": "废液瓶",
+            "children": [],
+            "parent": "AddTestStation",
+            "type": "container",
+            "class": null,
+            "position": {
+                "x": 850,
+                "y": 400,
+                "z": 0
+            },
+            "config": {
+                "max_volume": 3000.0
+            },
+            "data": {
+                "liquid": []
+            }
+        },
+        {
+            "id": "flask_rinsing",
+            "name": "冲洗液瓶",
+            "children": [],
+            "parent": "AddTestStation",
+            "type": "container",
+            "class": null,
+            "position": {
+                "x": 950,
+                "y": 300,
+                "z": 0
+            },
+            "config": {
+                "max_volume": 1000.0
+            },
+            "data": {
+                "liquid": [
+                    {
+                        "name": "去离子水",
+                        "volume": 800.0,
+                        "concentration": "纯净"
+                    }
+                ]
+            }
+        },
+        {
+            "id": "flask_buffer",
+            "name": "缓冲液瓶",
+            "children": [],
+            "parent": "AddTestStation",
+            "type": "container",
+            "class": null,
+            "position": {
+                "x": 950,
+                "y": 400,
+                "z": 0
+            },
+            "config": {
+                "max_volume": 1000.0
+            },
+            "data": {
+                "liquid": [
+                    {
+                        "name": "磷酸盐缓冲液",
+                        "volume": 700.0,
+                        "concentration": "0.1M, pH 7.4"
+                    }
+                ]
+            }
         }
     ],
     "links": [
         {
-            "source": "stirrer",
+            "source": "transfer_pump",
+            "target": "multiway_valve",
+            "type": "physical",
+            "port": {
+                "transfer_pump": "syringe-port",
+                "multiway_valve": "multiway-valve-inlet"
+            }
+        },
+        {
+            "source": "multiway_valve",
+            "target": "flask_reagent1",
+            "type": "physical",
+            "port": {
+                "multiway_valve": "multiway-valve-port-1",
+                "flask_reagent1": "top"
+            }
+        },
+        {
+            "source": "multiway_valve",
+            "target": "flask_reagent2",
+            "type": "physical",
+            "port": {
+                "multiway_valve": "multiway-valve-port-2",
+                "flask_reagent2": "top"
+            }
+        },
+        {
+            "source": "multiway_valve",
+            "target": "flask_reagent3",
+            "type": "physical",
+            "port": {
+                "multiway_valve": "multiway-valve-port-3",
+                "flask_reagent3": "top"
+            }
+        },
+        {
+            "source": "multiway_valve",
+            "target": "flask_reagent4",
+            "type": "physical",
+            "port": {
+                "multiway_valve": "multiway-valve-port-4",
+                "flask_reagent4": "top"
+            }
+        },
+        {
+            "source": "multiway_valve",
             "target": "reactor",
             "type": "physical",
             "port": {
-                "stirrer": "top",
+                "multiway_valve": "multiway-valve-port-5",
-                "reactor": "bottom"
-            }
-        },
-        {
-            "source": "pump_add",
-            "target": "flask_1",
-            "type": "physical",
-            "port": {
-                "pump_add": "outlet",
-                "flask_1": "top"
-            }
-        },
-        {
-            "source": "pump_add",
-            "target": "flask_2",
-            "type": "physical",
-            "port": {
-                "pump_add": "inlet",
-                "flask_2": "top"
-            }
-        },
-        {
-            "source": "pump_add",
-            "target": "flask_3",
-            "type": "physical",
-            "port": {
-                "pump_add": "inlet",
-                "flask_3": "top"
-            }
-        },
-        {
-            "source": "pump_add",
-            "target": "flask_4",
-            "type": "physical",
-            "port": {
-                "pump_add": "inlet",
-                "flask_4": "top"
-            }
-        },
-        {
-            "source": "pump_add",
-            "target": "reactor",
-            "type": "physical",
-            "port": {
-                "pump_add": "outlet",
                 "reactor": "top"
             }
         },
         {
-            "source": "pump_add",
+            "source": "multiway_valve",
-            "target": "flask_air",
+            "target": "flask_waste",
             "type": "physical",
             "port": {
-                "pump_add": "inlet",
+                "multiway_valve": "multiway-valve-port-6",
-                "flask_air": "top"
+                "flask_waste": "top"
+            }
+        },
+        {
+            "source": "multiway_valve",
+            "target": "flask_rinsing",
+            "type": "physical",
+            "port": {
+                "multiway_valve": "multiway-valve-port-7",
+                "flask_rinsing": "top"
+            }
+        },
+        {
+            "source": "multiway_valve",
+            "target": "flask_buffer",
+            "type": "physical",
+            "port": {
+                "multiway_valve": "multiway-valve-port-8",
+                "flask_buffer": "top"
+            }
+        },
+        {
+            "source": "stirrer",
+            "target": "reactor",
+            "type": "physical",
+            "port": {
+                "stirrer": "stirrer-vessel",
+                "reactor": "bottom"
             }
         }
     ]

unilabos/compile/add_protocol.py

@@ -15,46 +15,116 @@ def generate_add_protocol(
     purpose: str  
 ) -> List[Dict[str, Any]]:  
     """  
-    生成添加试剂的协议序列 - 严格按照 Add.action
+    生成添加试剂的协议序列
+    
+    流程：
+    1. 找到包含目标试剂的试剂瓶
+    2. 配置八通阀门到试剂瓶位置
+    3. 使用注射器泵吸取试剂
+    4. 配置八通阀门到反应器位置  
+    5. 使用注射器泵推送试剂到反应器
+    6. 如果需要，启动搅拌
     """  
     action_sequence = []  
-      
+    
+    # 验证目标容器存在
+    if vessel not in G.nodes():
+        raise ValueError(f"目标容器 {vessel} 不存在")
+    
     # 如果指定了体积，执行液体转移  
     if volume > 0:  
-        # 查找可用的试剂瓶
+        # 1. 查找注射器泵 (transfer pump)
+        transfer_pump_nodes = [node for node in G.nodes() 
+                              if G.nodes[node].get('class') == 'virtual_transfer_pump']
+        
+        if not transfer_pump_nodes:
+            raise ValueError("没有找到可用的注射器泵 (virtual_transfer_pump)")
+            
+        transfer_pump_id = transfer_pump_nodes[0]
+        
+        # 2. 查找八通阀门
+        multiway_valve_nodes = [node for node in G.nodes() 
+                               if G.nodes[node].get('class') == 'virtual_multiway_valve']
+        
+        if not multiway_valve_nodes:
+            raise ValueError("没有找到可用的八通阀门 (virtual_multiway_valve)")
+            
+        valve_id = multiway_valve_nodes[0]
+        
+        # 3. 查找包含指定试剂的试剂瓶
+        reagent_vessel = None
         available_flasks = [node for node in G.nodes() 
                            if node.startswith('flask_') 
                            and G.nodes[node].get('type') == 'container']
         
-        if not available_flasks:
+        # 简化：使用第一个可用的试剂瓶，实际应该根据试剂名称匹配
+        if available_flasks:
+            reagent_vessel = available_flasks[0]
+        else:
             raise ValueError("没有找到可用的试剂容器")
-            
-        reagent_vessel = available_flasks[0]
         
-        # 查找泵设备
+        # 4. 获取试剂瓶和反应器对应的阀门位置
-        pump_nodes = [node for node in G.nodes() 
+        # 这需要根据实际连接图来确定，这里假设：
-                     if G.nodes[node].get('class') == 'virtual_pump']
+        reagent_valve_position = 1  # 试剂瓶连接到阀门位置1
+        reactor_valve_position = 2  # 反应器连接到阀门位置2
         
-        if pump_nodes:
+        # 5. 执行添加操作序列
-            pump_id = pump_nodes[0]
+        
-            action_sequence.append({
+        # 5.1 设置阀门到试剂瓶位置
-                "device_id": pump_id,
+        action_sequence.append({
-                "action_name": "transfer",
+            "device_id": valve_id,
-                "action_kwargs": {
+            "action_name": "set_position",
-                    "from_vessel": reagent_vessel,
+            "action_kwargs": {
-                    "to_vessel": vessel,
+                "position": reagent_valve_position
-                    "volume": volume,
+            }
-                    "amount": amount,
+        })
-                    "time": time,
+        
-                    "viscous": viscous,
+        # 5.2 使用注射器泵从试剂瓶吸取液体
-                    "rinsing_solvent": "",
+        action_sequence.append({
-                    "rinsing_volume": 0.0,
+            "device_id": transfer_pump_id,
-                    "rinsing_repeats": 0,
+            "action_name": "transfer",
-                    "solid": False
+            "action_kwargs": {
-                }
+                "from_vessel": reagent_vessel,
-            })
+                "to_vessel": transfer_pump_id,  # 吸入到注射器
+                "volume": volume,
+                "amount": amount,
+                "time": time / 2,  # 吸取时间为总时间的一半
+                "viscous": viscous,
+                "rinsing_solvent": "",
+                "rinsing_volume": 0.0,
+                "rinsing_repeats": 0,
+                "solid": False
+            }
+        })
+        
+        # 5.3 设置阀门到反应器位置
+        action_sequence.append({
+            "device_id": valve_id,
+            "action_name": "set_position",
+            "action_kwargs": {
+                "position": reactor_valve_position
+            }
+        })
+        
+        # 5.4 使用注射器泵将液体推送到反应器
+        action_sequence.append({
+            "device_id": transfer_pump_id,
+            "action_name": "transfer",
+            "action_kwargs": {
+                "from_vessel": transfer_pump_id,  # 从注射器推出
+                "to_vessel": vessel,
+                "volume": volume,
+                "amount": amount,
+                "time": time / 2,  # 推送时间为总时间的一半
+                "viscous": viscous,
+                "rinsing_solvent": "",
+                "rinsing_volume": 0.0,
+                "rinsing_repeats": 0,
+                "solid": False
+            }
+        })
       
-    # 如果需要搅拌，使用 StartStir 而不是 Stir  
+    # 6. 如果需要搅拌，启动搅拌器
     if stir:  
         stirrer_nodes = [node for node in G.nodes()   
                         if G.nodes[node].get('class') == 'virtual_stirrer']  
@@ -63,12 +133,156 @@ def generate_add_protocol(
             stirrer_id = stirrer_nodes[0]  
             action_sequence.append({  
                 "device_id": stirrer_id,  
-                "action_name": "start_stir",  # 使用 start_stir 而不是 stir
+                "action_name": "start_stir",
                 "action_kwargs": {  
                     "vessel": vessel,
                     "stir_speed": stir_speed,
-                    "purpose": f"添加 {reagent} 后搅拌"
+                    "purpose": f"添加 {reagent} 后搅拌混合"
                 }  
             })  
+        else:
+            print("警告：需要搅拌但未找到搅拌设备")
       
+    return action_sequence
+
+
+def find_valve_position_for_vessel(G: nx.DiGraph, valve_id: str, vessel_id: str) -> int:
+    """
+    根据连接图找到容器对应的阀门位置
+    
+    Args:
+        G: 网络图
+        valve_id: 阀门设备ID
+        vessel_id: 容器ID
+    
+    Returns:
+        int: 阀门位置编号 (1-8)
+    """
+    # 查找阀门到容器的连接
+    edges = G.edges(data=True)
+    
+    for source, target, data in edges:
+        if source == valve_id and target == vessel_id:
+            # 从连接数据中提取端口信息
+            port_info = data.get('port', {})
+            valve_port = port_info.get(valve_id, '')
+            
+            # 解析端口名称获取位置编号
+            if valve_port.startswith('multiway-valve-port-'):
+                position = valve_port.split('-')[-1]
+                return int(position)
+    
+    # 默认返回位置1
+    return 1
+
+
+def generate_add_with_autodiscovery(
+    G: nx.DiGraph,  
+    vessel: str,  
+    reagent: str,  
+    volume: float,  
+    **kwargs
+) -> List[Dict[str, Any]]:
+    """
+    智能添加协议生成器 - 自动发现设备连接关系
+    """
+    action_sequence = []
+    
+    # 查找必需的设备
+    devices = {
+        'transfer_pump': None,
+        'multiway_valve': None,
+        'stirrer': None
+    }
+    
+    for node in G.nodes():
+        node_class = G.nodes[node].get('class')
+        if node_class == 'virtual_transfer_pump':
+            devices['transfer_pump'] = node
+        elif node_class == 'virtual_multiway_valve':
+            devices['multiway_valve'] = node
+        elif node_class == 'virtual_stirrer':
+            devices['stirrer'] = node
+    
+    # 验证必需设备
+    if not devices['transfer_pump']:
+        raise ValueError("缺少注射器泵设备")
+    if not devices['multiway_valve']:
+        raise ValueError("缺少八通阀门设备")
+    
+    # 查找试剂容器
+    reagent_vessels = [node for node in G.nodes() 
+                      if node.startswith('flask_') 
+                      and G.nodes[node].get('type') == 'container']
+    
+    if not reagent_vessels:
+        raise ValueError("没有找到试剂容器")
+    
+    # 执行添加流程
+    reagent_vessel = reagent_vessels[0]
+    reagent_pos = find_valve_position_for_vessel(G, devices['multiway_valve'], reagent_vessel)
+    reactor_pos = find_valve_position_for_vessel(G, devices['multiway_valve'], vessel)
+    
+    # 生成操作序列
+    action_sequence.extend([
+        # 切换到试剂瓶
+        {
+            "device_id": devices['multiway_valve'],
+            "action_name": "set_position",
+            "action_kwargs": {"position": reagent_pos}
+        },
+        # 吸取试剂
+        {
+            "device_id": devices['transfer_pump'],
+            "action_name": "transfer",
+            "action_kwargs": {
+                "from_vessel": reagent_vessel,
+                "to_vessel": devices['transfer_pump'],
+                "volume": volume,
+                "amount": kwargs.get('amount', ''),
+                "time": kwargs.get('time', 10.0) / 2,
+                "viscous": kwargs.get('viscous', False),
+                "rinsing_solvent": "",
+                "rinsing_volume": 0.0,
+                "rinsing_repeats": 0,
+                "solid": False
+            }
+        },
+        # 切换到反应器
+        {
+            "device_id": devices['multiway_valve'],
+            "action_name": "set_position",
+            "action_kwargs": {"position": reactor_pos}
+        },
+        # 推送到反应器
+        {
+            "device_id": devices['transfer_pump'],
+            "action_name": "transfer",
+            "action_kwargs": {
+                "from_vessel": devices['transfer_pump'],
+                "to_vessel": vessel,
+                "volume": volume,
+                "amount": kwargs.get('amount', ''),
+                "time": kwargs.get('time', 10.0) / 2,
+                "viscous": kwargs.get('viscous', False),
+                "rinsing_solvent": "",
+                "rinsing_volume": 0.0,
+                "rinsing_repeats": 0,
+                "solid": False
+            }
+        }
+    ])
+    
+    # 如果需要搅拌
+    if kwargs.get('stir', False) and devices['stirrer']:
+        action_sequence.append({
+            "device_id": devices['stirrer'],
+            "action_name": "start_stir",
+            "action_kwargs": {
+                "vessel": vessel,
+                "stir_speed": kwargs.get('stir_speed', 300.0),
+                "purpose": f"添加 {reagent} 后混合"
+            }
+        })
+    
     return action_sequence