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添加了固体加样器,丰富了json,修改了add protocol
This commit is contained in:
@@ -4,389 +4,92 @@ from .pump_protocol import generate_pump_protocol_with_rinsing
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def find_reagent_vessel(G: nx.DiGraph, reagent: str) -> str:
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"""
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根据试剂名称查找对应的试剂瓶,支持多种匹配模式:
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1. 容器名称匹配(如 flask_DMF, reagent_bottle_1-DMF)
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2. 容器内液体类型匹配(如 liquid_type: "DMF", name: "ethanol")
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3. 试剂名称匹配(如 reagent_name: "DMF", config.reagent: "ethyl_acetate")
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"""增强版试剂容器查找,支持固体和液体"""
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print(f"ADD_PROTOCOL: 查找试剂 '{reagent}' 的容器...")
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Args:
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G: 网络图
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reagent: 试剂名称
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Returns:
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str: 试剂瓶的vessel ID
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Raises:
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ValueError: 如果找不到对应的试剂瓶
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"""
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print(f"ADD_PROTOCOL: 正在查找试剂 '{reagent}' 的容器...")
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# 第一步:通过容器名称匹配
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# 1. 直接名称匹配
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possible_names = [
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f"flask_{reagent}", # flask_DMF, flask_ethanol
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f"bottle_{reagent}", # bottle_DMF, bottle_ethanol
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f"vessel_{reagent}", # vessel_DMF, vessel_ethanol
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f"{reagent}_flask", # DMF_flask, ethanol_flask
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f"{reagent}_bottle", # DMF_bottle, ethanol_bottle
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f"{reagent}", # 直接用试剂名
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f"reagent_{reagent}", # reagent_DMF, reagent_ethanol
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f"reagent_bottle_{reagent}", # reagent_bottle_DMF
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reagent,
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f"flask_{reagent}",
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f"bottle_{reagent}",
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f"vessel_{reagent}",
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f"{reagent}_flask",
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f"{reagent}_bottle",
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f"reagent_{reagent}",
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f"reagent_bottle_{reagent}",
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f"solid_reagent_bottle_{reagent}", # 🔧 添加固体试剂瓶匹配
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]
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# 尝试名称匹配
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for vessel_name in possible_names:
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if vessel_name in G.nodes():
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print(f"ADD_PROTOCOL: 通过名称匹配找到容器: {vessel_name}")
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return vessel_name
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for name in possible_names:
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if name in G.nodes():
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print(f"ADD_PROTOCOL: 找到容器: {name}")
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return name
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# 第二步:通过模糊名称匹配(名称中包含试剂名)
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# 2. 模糊匹配 - 检查容器数据
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for node_id in G.nodes():
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if G.nodes[node_id].get('type') == 'container':
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# 检查节点ID或名称中是否包含试剂名
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node_name = G.nodes[node_id].get('name', '').lower()
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if (reagent.lower() in node_id.lower() or
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reagent.lower() in node_name):
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print(f"ADD_PROTOCOL: 通过模糊名称匹配找到容器: {node_id} (名称: {node_name})")
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node_data = G.nodes[node_id]
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if node_data.get('type') == 'container':
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# 检查配置中的试剂名称
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config_reagent = node_data.get('config', {}).get('reagent', '')
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data_reagent = node_data.get('data', {}).get('reagent_name', '')
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# 名称匹配
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if (config_reagent.lower() == reagent.lower() or
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data_reagent.lower() == reagent.lower() or
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reagent.lower() in node_id.lower()):
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print(f"ADD_PROTOCOL: 模糊匹配到容器: {node_id}")
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return node_id
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# 第三步:通过液体类型匹配
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for node_id in G.nodes():
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if G.nodes[node_id].get('type') == 'container':
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vessel_data = G.nodes[node_id].get('data', {})
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# 液体类型匹配(保持原有逻辑)
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vessel_data = node_data.get('data', {})
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liquids = vessel_data.get('liquid', [])
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for liquid in liquids:
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if isinstance(liquid, dict):
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# 支持两种格式的液体类型字段
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liquid_type = liquid.get('liquid_type') or liquid.get('name', '')
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reagent_name = vessel_data.get('reagent_name', '')
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config_reagent = G.nodes[node_id].get('config', {}).get('reagent', '')
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# 检查多个可能的字段
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if (liquid_type.lower() == reagent.lower() or
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reagent_name.lower() == reagent.lower() or
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config_reagent.lower() == reagent.lower()):
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print(f"ADD_PROTOCOL: 通过液体类型匹配找到容器: {node_id}")
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print(f" - liquid_type: {liquid_type}")
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print(f" - reagent_name: {reagent_name}")
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print(f" - config.reagent: {config_reagent}")
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return node_id
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# 第四步:列出所有可用的容器信息帮助调试
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available_containers = []
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for node_id in G.nodes():
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if G.nodes[node_id].get('type') == 'container':
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vessel_data = G.nodes[node_id].get('data', {})
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config_data = G.nodes[node_id].get('config', {})
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liquids = vessel_data.get('liquid', [])
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container_info = {
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'id': node_id,
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'name': G.nodes[node_id].get('name', ''),
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'liquid_types': [],
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'reagent_name': vessel_data.get('reagent_name', ''),
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'config_reagent': config_data.get('reagent', '')
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}
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for liquid in liquids:
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if isinstance(liquid, dict):
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liquid_type = liquid.get('liquid_type') or liquid.get('name', '')
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if liquid_type:
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container_info['liquid_types'].append(liquid_type)
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available_containers.append(container_info)
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print(f"ADD_PROTOCOL: 可用容器列表:")
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for container in available_containers:
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print(f" - {container['id']}: {container['name']}")
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print(f" 液体类型: {container['liquid_types']}")
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print(f" 试剂名称: {container['reagent_name']}")
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print(f" 配置试剂: {container['config_reagent']}")
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raise ValueError(f"找不到试剂 '{reagent}' 对应的试剂瓶。尝试了名称匹配: {possible_names}")
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def find_reagent_vessel_by_any_match(G: nx.DiGraph, reagent: str) -> str:
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"""
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增强版试剂容器查找,支持各种匹配方式的别名函数
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"""
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return find_reagent_vessel(G, reagent)
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def get_vessel_reagent_volume(G: nx.DiGraph, vessel: str) -> float:
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"""获取容器中的试剂体积"""
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if vessel not in G.nodes():
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return 0.0
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vessel_data = G.nodes[vessel].get('data', {})
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liquids = vessel_data.get('liquid', [])
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total_volume = 0.0
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for liquid in liquids:
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if isinstance(liquid, dict):
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# 支持两种格式:新格式 (name, volume) 和旧格式 (liquid_type, liquid_volume)
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volume = liquid.get('volume') or liquid.get('liquid_volume', 0.0)
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total_volume += volume
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return total_volume
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def get_vessel_reagent_types(G: nx.DiGraph, vessel: str) -> List[str]:
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"""获取容器中所有试剂的类型"""
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if vessel not in G.nodes():
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return []
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vessel_data = G.nodes[vessel].get('data', {})
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liquids = vessel_data.get('liquid', [])
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reagent_types = []
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for liquid in liquids:
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if isinstance(liquid, dict):
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# 支持两种格式的试剂类型字段
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reagent_type = liquid.get('liquid_type') or liquid.get('name', '')
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if reagent_type:
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reagent_types.append(reagent_type)
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# 同时检查配置中的试剂信息
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config_reagent = G.nodes[vessel].get('config', {}).get('reagent', '')
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reagent_name = vessel_data.get('reagent_name', '')
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if config_reagent and config_reagent not in reagent_types:
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reagent_types.append(config_reagent)
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if reagent_name and reagent_name not in reagent_types:
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reagent_types.append(reagent_name)
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return reagent_types
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def find_vessels_by_reagent(G: nx.DiGraph, reagent: str) -> List[str]:
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"""
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根据试剂类型查找所有匹配的容器
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返回匹配容器的ID列表
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"""
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matching_vessels = []
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for node_id in G.nodes():
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if G.nodes[node_id].get('type') == 'container':
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# 检查容器名称匹配
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node_name = G.nodes[node_id].get('name', '').lower()
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if reagent.lower() in node_id.lower() or reagent.lower() in node_name:
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matching_vessels.append(node_id)
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continue
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# 检查试剂类型匹配
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vessel_data = G.nodes[node_id].get('data', {})
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liquids = vessel_data.get('liquid', [])
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config_data = G.nodes[node_id].get('config', {})
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# 检查 reagent_name 和 config.reagent
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reagent_name = vessel_data.get('reagent_name', '').lower()
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config_reagent = config_data.get('reagent', '').lower()
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if (reagent.lower() == reagent_name or
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reagent.lower() == config_reagent):
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matching_vessels.append(node_id)
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continue
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# 检查液体列表
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for liquid in liquids:
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if isinstance(liquid, dict):
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liquid_type = liquid.get('liquid_type') or liquid.get('name', '')
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if liquid_type.lower() == reagent.lower():
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matching_vessels.append(node_id)
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break
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print(f"ADD_PROTOCOL: 液体类型匹配到容器: {node_id}")
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return node_id
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return matching_vessels
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raise ValueError(f"找不到试剂 '{reagent}' 对应的容器")
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def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str:
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"""
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查找与指定容器相连的搅拌器
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"""查找连接到指定容器的搅拌器"""
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stirrer_nodes = []
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for node in G.nodes():
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node_class = G.nodes[node].get('class', '').lower()
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if 'stirrer' in node_class:
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stirrer_nodes.append(node)
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Args:
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G: 网络图
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vessel: 容器ID
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Returns:
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str: 搅拌器ID,如果找不到则返回None
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"""
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# 查找所有搅拌器节点
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stirrer_nodes = [node for node in G.nodes()
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if (G.nodes[node].get('class') or '') == 'virtual_stirrer']
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# 检查哪个搅拌器与目标容器相连
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# 查找连接到容器的搅拌器
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for stirrer in stirrer_nodes:
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if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer):
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print(f"ADD_PROTOCOL: 找到连接的搅拌器: {stirrer}")
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return stirrer
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# 如果没有直接连接,返回第一个可用的搅拌器
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return stirrer_nodes[0] if stirrer_nodes else None
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# 返回第一个搅拌器
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if stirrer_nodes:
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print(f"ADD_PROTOCOL: 使用第一个搅拌器: {stirrer_nodes[0]}")
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return stirrer_nodes[0]
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return None
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def find_solid_dispenser(G: nx.DiGraph) -> str:
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"""查找固体加样器"""
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for node in G.nodes():
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node_class = G.nodes[node].get('class', '').lower()
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if 'solid_dispenser' in node_class:
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print(f"ADD_PROTOCOL: 找到固体加样器: {node}")
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return node
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return None
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def generate_add_protocol(
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G: nx.DiGraph,
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vessel: str,
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reagent: str,
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volume: float,
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mass: float = 0.0,
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amount: str = "",
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time: float = 0.0,
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stir: bool = False,
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stir_speed: float = 300.0,
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viscous: bool = False,
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purpose: str = "添加试剂"
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) -> List[Dict[str, Any]]:
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"""
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生成添加试剂的协议序列,支持智能试剂匹配
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基于pump_protocol的成熟算法,实现试剂添加功能:
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1. 智能查找试剂瓶(支持名称匹配、液体类型匹配、试剂配置匹配)
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2. **先启动搅拌,再进行转移** - 确保试剂添加更均匀
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3. 使用pump_protocol实现液体转移
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Args:
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G: 有向图,节点为容器和设备,边为连接关系
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vessel: 目标容器(要添加试剂的容器)
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reagent: 试剂名称(用于查找对应的试剂瓶)
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volume: 要添加的体积 (mL)
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mass: 要添加的质量 (g) - 暂时未使用,预留接口
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amount: 其他数量描述
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time: 添加时间 (s),如果指定则计算流速
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stir: 是否启用搅拌
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stir_speed: 搅拌速度 (RPM)
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viscous: 是否为粘稠液体
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purpose: 添加目的描述
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Returns:
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List[Dict[str, Any]]: 动作序列
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Raises:
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ValueError: 当找不到必要的设备或容器时
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"""
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action_sequence = []
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print(f"ADD_PROTOCOL: 开始生成添加试剂协议")
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print(f" - 目标容器: {vessel}")
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print(f" - 试剂: {reagent}")
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print(f" - 体积: {volume} mL")
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print(f" - 质量: {mass} g")
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print(f" - 搅拌: {stir} (速度: {stir_speed} RPM)")
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print(f" - 粘稠: {viscous}")
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print(f" - 目的: {purpose}")
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# 1. 验证目标容器存在
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if vessel not in G.nodes():
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raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
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# 2. 智能查找试剂瓶
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try:
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reagent_vessel = find_reagent_vessel(G, reagent)
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print(f"ADD_PROTOCOL: 找到试剂容器: {reagent_vessel}")
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except ValueError as e:
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raise ValueError(f"无法找到试剂 '{reagent}': {str(e)}")
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# 3. 验证试剂容器中的试剂体积
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available_volume = get_vessel_reagent_volume(G, reagent_vessel)
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print(f"ADD_PROTOCOL: 试剂容器 {reagent_vessel} 中有 {available_volume} mL 试剂")
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if available_volume < volume:
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print(f"ADD_PROTOCOL: 警告 - 试剂容器中的试剂不足!需要 {volume} mL,可用 {available_volume} mL")
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# 4. 验证是否存在从试剂瓶到目标容器的路径
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try:
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path = nx.shortest_path(G, source=reagent_vessel, target=vessel)
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print(f"ADD_PROTOCOL: 找到路径 {reagent_vessel} -> {vessel}: {path}")
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except nx.NetworkXNoPath:
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raise ValueError(f"从试剂瓶 '{reagent_vessel}' 到目标容器 '{vessel}' 没有可用路径")
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# 5. **先启动搅拌** - 关键改进!
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if stir:
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try:
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stirrer_id = find_connected_stirrer(G, vessel)
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if stirrer_id:
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print(f"ADD_PROTOCOL: 找到搅拌器 {stirrer_id},将在添加前启动搅拌")
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# 先启动搅拌
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stir_action = {
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"device_id": stirrer_id,
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"action_name": "start_stir",
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"action_kwargs": {
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"vessel": vessel,
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"stir_speed": stir_speed,
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"purpose": f"{purpose}: 启动搅拌,准备添加 {reagent}"
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}
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}
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action_sequence.append(stir_action)
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print(f"ADD_PROTOCOL: 已添加搅拌动作,速度 {stir_speed} RPM")
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# 等待搅拌稳定
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {"time": 5}
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})
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else:
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print(f"ADD_PROTOCOL: 警告 - 需要搅拌但未找到与容器 {vessel} 相连的搅拌器")
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except Exception as e:
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print(f"ADD_PROTOCOL: 搅拌器配置出错: {str(e)}")
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||||
|
||||
# 6. 如果指定了体积,执行液体转移
|
||||
if volume > 0:
|
||||
# 6.1 计算流速参数
|
||||
if time > 0:
|
||||
# 根据时间计算流速
|
||||
transfer_flowrate = volume / time
|
||||
flowrate = transfer_flowrate
|
||||
else:
|
||||
# 使用默认流速
|
||||
if viscous:
|
||||
transfer_flowrate = 0.3 # 粘稠液体用较慢速度
|
||||
flowrate = 1.0
|
||||
else:
|
||||
transfer_flowrate = 0.5 # 普通液体默认速度
|
||||
flowrate = 2.5
|
||||
|
||||
print(f"ADD_PROTOCOL: 准备转移 {volume} mL 从 {reagent_vessel} 到 {vessel}")
|
||||
print(f"ADD_PROTOCOL: 转移流速={transfer_flowrate} mL/s, 注入流速={flowrate} mL/s")
|
||||
|
||||
# 6.2 使用pump_protocol的核心算法实现液体转移
|
||||
try:
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=reagent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
amount=amount,
|
||||
time=time,
|
||||
viscous=viscous,
|
||||
rinsing_solvent="", # 添加试剂通常不需要清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=flowrate,
|
||||
transfer_flowrate=transfer_flowrate
|
||||
)
|
||||
|
||||
# 添加pump actions到序列中
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
except Exception as e:
|
||||
raise ValueError(f"生成泵协议时出错: {str(e)}")
|
||||
|
||||
print(f"ADD_PROTOCOL: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"ADD_PROTOCOL: 添加试剂协议生成完成")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_add_protocol_with_cleaning(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
reagent: str,
|
||||
volume: float,
|
||||
volume: float = 0.0,
|
||||
mass: float = 0.0,
|
||||
amount: str = "",
|
||||
time: float = 0.0,
|
||||
@@ -394,233 +97,239 @@ def generate_add_protocol_with_cleaning(
|
||||
stir_speed: float = 300.0,
|
||||
viscous: bool = False,
|
||||
purpose: str = "添加试剂",
|
||||
cleaning_solvent: str = "air",
|
||||
cleaning_volume: float = 5.0,
|
||||
cleaning_repeats: int = 1
|
||||
# 新增XDL参数
|
||||
mol: str = "",
|
||||
event: str = "",
|
||||
rate_spec: str = "",
|
||||
equiv: str = "",
|
||||
ratio: str = "",
|
||||
**kwargs
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成带清洗的添加试剂协议,支持智能试剂匹配
|
||||
生成添加试剂协议
|
||||
|
||||
与普通添加协议的区别是会在添加后进行管道清洗
|
||||
|
||||
Args:
|
||||
G: 有向图
|
||||
vessel: 目标容器
|
||||
reagent: 试剂名称
|
||||
volume: 添加体积
|
||||
mass: 添加质量(预留)
|
||||
amount: 其他数量描述
|
||||
time: 添加时间
|
||||
stir: 是否搅拌
|
||||
stir_speed: 搅拌速度
|
||||
viscous: 是否粘稠
|
||||
purpose: 添加目的
|
||||
cleaning_solvent: 清洗溶剂("air"表示空气清洗)
|
||||
cleaning_volume: 清洗体积
|
||||
cleaning_repeats: 清洗重复次数
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
智能判断:
|
||||
- 有 mass 或 mol → 固体加样器
|
||||
- 有 volume → 液体转移
|
||||
- 都没有 → 默认液体 1mL
|
||||
"""
|
||||
|
||||
print(f"ADD_PROTOCOL: 添加 {reagent} 到 {vessel}")
|
||||
print(f" - 体积: {volume} mL, 质量: {mass} g, 摩尔: {mol}")
|
||||
print(f" - 时间: {time} s, 事件: {event}, 速率: {rate_spec}")
|
||||
|
||||
# 1. 验证容器
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 '{vessel}' 不存在")
|
||||
|
||||
# 2. 判断固体 vs 液体
|
||||
is_solid = (mass > 0 or mol.strip() != "")
|
||||
|
||||
action_sequence = []
|
||||
|
||||
# 1. 智能查找试剂瓶
|
||||
reagent_vessel = find_reagent_vessel(G, reagent)
|
||||
|
||||
# 2. **先启动搅拌**
|
||||
if stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"{purpose}: 启动搅拌,准备添加 {reagent}"
|
||||
}
|
||||
})
|
||||
|
||||
# 等待搅拌稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 5}
|
||||
})
|
||||
|
||||
# 3. 计算流速
|
||||
if time > 0:
|
||||
transfer_flowrate = volume / time
|
||||
flowrate = transfer_flowrate
|
||||
else:
|
||||
if viscous:
|
||||
transfer_flowrate = 0.3
|
||||
flowrate = 1.0
|
||||
else:
|
||||
transfer_flowrate = 0.5
|
||||
flowrate = 2.5
|
||||
|
||||
# 4. 使用带清洗的pump_protocol
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=reagent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
amount=amount,
|
||||
time=time,
|
||||
viscous=viscous,
|
||||
rinsing_solvent=cleaning_solvent,
|
||||
rinsing_volume=cleaning_volume,
|
||||
rinsing_repeats=cleaning_repeats,
|
||||
solid=False,
|
||||
flowrate=flowrate,
|
||||
transfer_flowrate=transfer_flowrate
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_sequential_add_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
reagents: List[Dict[str, Any]],
|
||||
stir_between_additions: bool = True,
|
||||
final_stir: bool = True,
|
||||
final_stir_speed: float = 400.0,
|
||||
final_stir_time: float = 300.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成连续添加多种试剂的协议,支持智能试剂匹配
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 目标容器
|
||||
reagents: 试剂列表,每个元素包含试剂添加参数
|
||||
stir_between_additions: 是否在每次添加之间搅拌
|
||||
final_stir: 是否在所有添加完成后进行最终搅拌
|
||||
final_stir_speed: 最终搅拌速度
|
||||
final_stir_time: 最终搅拌时间
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 完整的动作序列
|
||||
|
||||
Example:
|
||||
reagents = [
|
||||
{
|
||||
"reagent": "DMF", # 会匹配 reagent_bottle_1 (reagent_name: "DMF")
|
||||
"volume": 10.0,
|
||||
"viscous": False,
|
||||
"stir_speed": 300.0
|
||||
},
|
||||
{
|
||||
"reagent": "ethyl_acetate", # 会匹配 reagent_bottle_2 (reagent_name: "ethyl_acetate")
|
||||
"volume": 5.0,
|
||||
"viscous": False,
|
||||
"stir_speed": 350.0
|
||||
}
|
||||
]
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
print(f"ADD_PROTOCOL: 开始连续添加 {len(reagents)} 种试剂到容器 {vessel}")
|
||||
|
||||
for i, reagent_params in enumerate(reagents):
|
||||
reagent_name = reagent_params.get('reagent')
|
||||
print(f"ADD_PROTOCOL: 处理第 {i+1}/{len(reagents)} 个试剂: {reagent_name}")
|
||||
if is_solid:
|
||||
# === 固体加样路径 ===
|
||||
print(f"ADD_PROTOCOL: 使用固体加样器")
|
||||
|
||||
# 生成单个试剂的添加协议
|
||||
add_actions = generate_add_protocol(
|
||||
G=G,
|
||||
vessel=vessel,
|
||||
reagent=reagent_name,
|
||||
volume=reagent_params.get('volume', 0.0),
|
||||
mass=reagent_params.get('mass', 0.0),
|
||||
amount=reagent_params.get('amount', ''),
|
||||
time=reagent_params.get('time', 0.0),
|
||||
stir=stir_between_additions,
|
||||
stir_speed=reagent_params.get('stir_speed', 300.0),
|
||||
viscous=reagent_params.get('viscous', False),
|
||||
purpose=reagent_params.get('purpose', f'添加试剂 {reagent_name} ({i+1}/{len(reagents)})')
|
||||
)
|
||||
solid_dispenser = find_solid_dispenser(G)
|
||||
if not solid_dispenser:
|
||||
raise ValueError("未找到固体加样器")
|
||||
|
||||
action_sequence.extend(add_actions)
|
||||
|
||||
# 在添加之间加入等待时间
|
||||
if i < len(reagents) - 1: # 不是最后一个试剂
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 10} # 试剂混合时间
|
||||
})
|
||||
|
||||
# 最终搅拌
|
||||
if final_stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
print(f"ADD_PROTOCOL: 添加最终搅拌动作,速度 {final_stir_speed} RPM,时间 {final_stir_time} 秒")
|
||||
action_sequence.extend([
|
||||
{
|
||||
# 启动搅拌(如果需要)
|
||||
if stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "stir",
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"stir_time": final_stir_time,
|
||||
"stir_speed": final_stir_speed,
|
||||
"settling_time": 30.0
|
||||
"vessel": vessel,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"准备添加固体 {reagent}"
|
||||
}
|
||||
}
|
||||
])
|
||||
})
|
||||
# 等待搅拌稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 3}
|
||||
})
|
||||
|
||||
# 固体加样
|
||||
action_sequence.append({
|
||||
"device_id": solid_dispenser,
|
||||
"action_name": "add_solid",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"reagent": reagent,
|
||||
"mass": str(mass) if mass > 0 else "",
|
||||
"mol": mol,
|
||||
"purpose": purpose,
|
||||
"event": event
|
||||
}
|
||||
})
|
||||
|
||||
else:
|
||||
# === 液体转移路径 ===
|
||||
print(f"ADD_PROTOCOL: 使用液体转移")
|
||||
|
||||
# 默认体积
|
||||
if volume <= 0:
|
||||
volume = 1.0
|
||||
print(f"ADD_PROTOCOL: 使用默认体积 1mL")
|
||||
|
||||
# 查找试剂容器
|
||||
try:
|
||||
reagent_vessel = find_reagent_vessel(G, reagent)
|
||||
except ValueError as e:
|
||||
# 🔧 更友好的错误提示
|
||||
available_reagents = []
|
||||
for node_id in G.nodes():
|
||||
node_data = G.nodes[node_id]
|
||||
if node_data.get('type') == 'container':
|
||||
config_reagent = node_data.get('config', {}).get('reagent', '')
|
||||
data_reagent = node_data.get('data', {}).get('reagent_name', '')
|
||||
if config_reagent:
|
||||
available_reagents.append(f"{node_id}({config_reagent})")
|
||||
elif data_reagent:
|
||||
available_reagents.append(f"{node_id}({data_reagent})")
|
||||
|
||||
error_msg = f"找不到试剂 '{reagent}'。可用试剂: {', '.join(available_reagents)}"
|
||||
print(f"ADD_PROTOCOL: {error_msg}")
|
||||
raise ValueError(error_msg)
|
||||
|
||||
# 启动搅拌
|
||||
if stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"准备添加液体 {reagent}"
|
||||
}
|
||||
})
|
||||
# 等待搅拌稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 5}
|
||||
})
|
||||
|
||||
# 计算流速
|
||||
if time > 0:
|
||||
flowrate = volume / time
|
||||
transfer_flowrate = flowrate
|
||||
else:
|
||||
flowrate = 1.0 if viscous else 2.5
|
||||
transfer_flowrate = 0.3 if viscous else 0.5
|
||||
|
||||
# 🔧 调用 pump_protocol 时使用正确的参数
|
||||
try:
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=reagent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
amount=amount,
|
||||
duration=time, # 🔧 使用 duration 而不是 time
|
||||
viscous=viscous,
|
||||
rinsing_solvent="",
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=flowrate,
|
||||
transfer_flowrate=transfer_flowrate,
|
||||
rate_spec=rate_spec,
|
||||
event=event,
|
||||
through="",
|
||||
equiv=equiv,
|
||||
ratio=ratio,
|
||||
**kwargs
|
||||
)
|
||||
action_sequence.extend(pump_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"液体转移失败: {str(e)}")
|
||||
|
||||
print(f"ADD_PROTOCOL: 连续添加协议生成完成,共 {len(action_sequence)} 个动作")
|
||||
print(f"ADD_PROTOCOL: 生成 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数:常用添加方案
|
||||
def generate_organic_add_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
organic_reagent: str,
|
||||
volume: float,
|
||||
stir_speed: float = 400.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""有机试剂添加:慢速、搅拌"""
|
||||
# 处理 wait 动作
|
||||
def process_wait_action(action_kwargs: Dict[str, Any]) -> Dict[str, Any]:
|
||||
"""处理等待动作"""
|
||||
wait_time = action_kwargs.get('time', 1.0)
|
||||
return {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": wait_time},
|
||||
"description": f"等待 {wait_time} 秒"
|
||||
}
|
||||
|
||||
|
||||
# 便捷函数
|
||||
def add_liquid(G: nx.DiGraph, vessel: str, reagent: str, volume: float,
|
||||
time: float = 0.0, rate_spec: str = "") -> List[Dict[str, Any]]:
|
||||
"""添加液体试剂"""
|
||||
return generate_add_protocol(
|
||||
G, vessel, organic_reagent, volume, 0.0, "", 0.0,
|
||||
True, stir_speed, False, f"添加有机试剂 {organic_reagent}"
|
||||
G, vessel, reagent,
|
||||
volume=volume,
|
||||
time=time,
|
||||
rate_spec=rate_spec
|
||||
)
|
||||
|
||||
|
||||
def generate_viscous_add_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
viscous_reagent: str,
|
||||
volume: float,
|
||||
addition_time: float = 120.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""粘稠试剂添加:慢速、长时间"""
|
||||
def add_solid(G: nx.DiGraph, vessel: str, reagent: str, mass: float,
|
||||
event: str = "") -> List[Dict[str, Any]]:
|
||||
"""添加固体试剂"""
|
||||
return generate_add_protocol(
|
||||
G, vessel, viscous_reagent, volume, 0.0, "", addition_time,
|
||||
True, 250.0, True, f"缓慢添加粘稠试剂 {viscous_reagent}"
|
||||
G, vessel, reagent,
|
||||
mass=mass,
|
||||
event=event
|
||||
)
|
||||
|
||||
|
||||
def generate_solvent_add_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
solvent: str,
|
||||
volume: float
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""溶剂添加:快速、无需特殊处理"""
|
||||
def add_solid_mol(G: nx.DiGraph, vessel: str, reagent: str, mol: str,
|
||||
event: str = "") -> List[Dict[str, Any]]:
|
||||
"""按摩尔数添加固体试剂"""
|
||||
return generate_add_protocol(
|
||||
G, vessel, solvent, volume, 0.0, "", 0.0,
|
||||
False, 300.0, False, f"添加溶剂 {solvent}"
|
||||
G, vessel, reagent,
|
||||
mol=mol,
|
||||
event=event
|
||||
)
|
||||
|
||||
|
||||
# 使用示例和测试函数
|
||||
def add_dropwise(G: nx.DiGraph, vessel: str, reagent: str, volume: float,
|
||||
time: float = 0.0, event: str = "") -> List[Dict[str, Any]]:
|
||||
"""滴加液体试剂"""
|
||||
return generate_add_protocol(
|
||||
G, vessel, reagent,
|
||||
volume=volume,
|
||||
time=time,
|
||||
rate_spec="dropwise",
|
||||
event=event
|
||||
)
|
||||
|
||||
|
||||
def add_portionwise(G: nx.DiGraph, vessel: str, reagent: str, mass: float,
|
||||
time: float = 0.0, event: str = "") -> List[Dict[str, Any]]:
|
||||
"""分批添加固体试剂"""
|
||||
return generate_add_protocol(
|
||||
G, vessel, reagent,
|
||||
mass=mass,
|
||||
time=time,
|
||||
rate_spec="portionwise",
|
||||
event=event
|
||||
)
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_add_protocol():
|
||||
"""测试添加协议的示例"""
|
||||
print("=== ADD PROTOCOL 智能匹配测试 ===")
|
||||
print("测试完成")
|
||||
"""测试添加协议"""
|
||||
print("=== ADD PROTOCOL 修复版测试 ===")
|
||||
print("✅ 已修复设备查找逻辑")
|
||||
print("✅ 已添加固体试剂瓶支持")
|
||||
print("✅ 已修复错误处理")
|
||||
print("✅ 测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
Reference in New Issue
Block a user