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fix: Protocol node resource run (#65)

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* stir和adjustph的中的bug修不好

* fix sub-resource query in protocol node compiling

* add resource placeholder to vessels

* add the rest yaml

* Update work_station.yaml

---------

Co-authored-by: KCFeng425 <2100011801@stu.pku.edu.cn>
This commit is contained in:
Junhan Chang
2025-07-19 04:19:57 +08:00
committed by GitHub
parent 4cd40865b4
commit c2dfe689aa
11 changed files with 252 additions and 148 deletions
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17
unilabos/compile/adjustph_protocol.py
View File

@@ -1,6 +1,6 @@
import networkx as nx
import logging
from typing import List, Dict, Any
from typing import List, Dict, Any, Union
from .pump_protocol import generate_pump_protocol_with_rinsing
logger = logging.getLogger(__name__)
@@ -216,7 +216,7 @@ def calculate_reagent_volume(target_ph_value: float, reagent: str, vessel_volume
def generate_adjust_ph_protocol(
G: nx.DiGraph,
vessel: dict, # 🔧 修改：从字符串改为字典类型
vessel:Union[dict,str], # 🔧 修改：从字符串改为字典类型
ph_value: float,
reagent: str,
**kwargs
@@ -235,8 +235,17 @@ def generate_adjust_ph_protocol(
List[Dict[str, Any]]: 动作序列
"""
# 🔧 核心修改：从字典中提取容器ID
vessel_id = vessel["id"]
# 统一处理vessel参数
if isinstance(vessel, dict):
vessel_id = list(vessel.values())[0].get("id", "")
vessel_data = vessel.get("data", {})
else:
vessel_id = str(vessel)
vessel_data = G.nodes[vessel_id].get("data", {}) if vessel_id in G.nodes() else {}
if not vessel_id:
debug_print(f"❌ vessel 参数无效，必须包含id字段或直接提供容器ID. vessel: {vessel}")
raise ValueError("vessel 参数无效，必须包含id字段或直接提供容器ID")
debug_print("=" * 60)
debug_print("🧪 开始生成pH调节协议")

18
unilabos/compile/evaporate_protocol.py
View File

@@ -22,7 +22,7 @@ def parse_time_input(time_input: Union[str, float]) -> float:
"""
if isinstance(time_input, (int, float)):
debug_print(f"⏱️ 时间输入为数字: {time_input}s ✨")
return float(time_input)
return float(time_input) # 🔧 确保返回float
if not time_input or not str(time_input).strip():
debug_print(f"⚠️ 时间输入为空，使用默认值: 180s (3分钟) 🕐")
@@ -48,7 +48,7 @@ def parse_time_input(time_input: Union[str, float]) -> float:
try:
value = float(time_str)
debug_print(f"✅ 时间解析成功: {time_str} → {value}s（无单位，默认秒）⏰")
return value
return float(value) # 🔧 确保返回float
except ValueError:
debug_print(f"❌ 无法解析时间: '{time_str}'，使用默认值180s (3分钟) 😅")
return 180.0
@@ -70,7 +70,7 @@ def parse_time_input(time_input: Union[str, float]) -> float:
time_sec = value # 已经是s
debug_print(f"🕐 时间转换: {value}s → {time_sec}s (已是秒) ⏰")
return time_sec
return float(time_sec) # 🔧 确保返回float
def find_rotavap_device(G: nx.DiGraph, vessel: str = None) -> Optional[str]:
"""
@@ -389,12 +389,12 @@ def generate_evaporate_protocol(
"device_id": rotavap_device,
"action_name": "evaporate",
"action_kwargs": {
"vessel": target_vessel, # 使用 target_vessel
"pressure": pressure,
"temp": temp,
"time": final_time,
"stir_speed": stir_speed,
"solvent": solvent
"vessel": target_vessel,
"pressure": float(pressure),
"temp": float(temp),
"time": float(final_time), # 🔧 强制转换为float类型
"stir_speed": float(stir_speed),
"solvent": str(solvent)
}
}
action_sequence.append(evaporate_action)

77
unilabos/compile/recrystallize_protocol.py
View File

@@ -170,33 +170,94 @@ def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
debug_print(f" 🎉 通过名称匹配找到容器: {vessel_name} ✨")
return vessel_name
# 第二步：通过模糊匹配
# 第二步：通过模糊匹配（节点ID和名称）
debug_print(" 🔍 步骤2: 模糊名称匹配...")
for node_id in G.nodes():
if G.nodes[node_id].get('type') == 'container':
node_name = G.nodes[node_id].get('name', '').lower()
if solvent.lower() in node_id.lower() or solvent.lower() in node_name:
debug_print(f" 🎉 通过模糊匹配找到容器: {node_id} ✨")
debug_print(f" 🎉 通过模糊匹配找到容器: {node_id} (名称: {node_name}) ✨")
return node_id
# 第三步：通过液体类型匹配
debug_print(" 🧪 步骤3: 液体类型匹配...")
# 第三步：通过配置中的试剂信息匹配
debug_print(" 🧪 步骤3: 配置试剂信息匹配...")
for node_id in G.nodes():
if G.nodes[node_id].get('type') == 'container':
# 检查 config 中的 reagent 字段
node_config = G.nodes[node_id].get('config', {})
config_reagent = node_config.get('reagent', '').lower()
if config_reagent and solvent.lower() == config_reagent:
debug_print(f" 🎉 通过config.reagent匹配找到容器: {node_id} (试剂: {config_reagent}) ✨")
return node_id
# 第四步：通过数据中的试剂信息匹配
debug_print(" 🧪 步骤4: 数据试剂信息匹配...")
for node_id in G.nodes():
if G.nodes[node_id].get('type') == 'container':
vessel_data = G.nodes[node_id].get('data', {})
liquids = vessel_data.get('liquid', [])
# 检查 data 中的 reagent_name 字段
reagent_name = vessel_data.get('reagent_name', '').lower()
if reagent_name and solvent.lower() == reagent_name:
debug_print(f" 🎉 通过data.reagent_name匹配找到容器: {node_id} (试剂: {reagent_name}) ✨")
return node_id
# 检查 data 中的液体信息
liquids = vessel_data.get('liquid', [])
for liquid in liquids:
if isinstance(liquid, dict):
liquid_type = (liquid.get('liquid_type') or liquid.get('name', '')).lower()
reagent_name = vessel_data.get('reagent_name', '').lower()
if solvent.lower() in liquid_type or solvent.lower() in reagent_name:
debug_print(f" 🎉 通过液体类型匹配找到容器: {node_id} ✨")
if solvent.lower() in liquid_type:
debug_print(f" 🎉 通过液体类型匹配找到容器: {node_id} (液体类型: {liquid_type}) ✨")
return node_id
# 第五步：部分匹配（如果前面都没找到）
debug_print(" 🔍 步骤5: 部分匹配...")
for node_id in G.nodes():
if G.nodes[node_id].get('type') == 'container':
node_config = G.nodes[node_id].get('config', {})
node_data = G.nodes[node_id].get('data', {})
node_name = G.nodes[node_id].get('name', '').lower()
config_reagent = node_config.get('reagent', '').lower()
data_reagent = node_data.get('reagent_name', '').lower()
# 检查是否包含溶剂名称
if (solvent.lower() in config_reagent or
solvent.lower() in data_reagent or
solvent.lower() in node_name or
solvent.lower() in node_id.lower()):
debug_print(f" 🎉 通过部分匹配找到容器: {node_id} ✨")
debug_print(f" - 节点名称: {node_name}")
debug_print(f" - 配置试剂: {config_reagent}")
debug_print(f" - 数据试剂: {data_reagent}")
return node_id
# 调试信息：列出所有容器
debug_print(" 🔎 调试信息：列出所有容器...")
container_list = []
for node_id in G.nodes():
if G.nodes[node_id].get('type') == 'container':
node_config = G.nodes[node_id].get('config', {})
node_data = G.nodes[node_id].get('data', {})
node_name = G.nodes[node_id].get('name', '')
container_info = {
'id': node_id,
'name': node_name,
'config_reagent': node_config.get('reagent', ''),
'data_reagent': node_data.get('reagent_name', '')
}
container_list.append(container_info)
debug_print(f" - 容器: {node_id}, 名称: {node_name}, config试剂: {node_config.get('reagent', '')}, data试剂: {node_data.get('reagent_name', '')}")
debug_print(f"❌ 找不到溶剂 '{solvent}' 对应的容器 😭")
debug_print(f"🔍 查找的溶剂: '{solvent}' (小写: '{solvent.lower()}')")
debug_print(f"📊 总共发现 {len(container_list)} 个容器")
raise ValueError(f"找不到溶剂 '{solvent}' 对应的容器")

2
unilabos/compile/stir_protocol.py
View File

@@ -149,7 +149,7 @@ def extract_vessel_id(vessel: Union[str, dict]) -> str:
str: vessel_id
"""
if isinstance(vessel, dict):
vessel_id = vessel.get("id", "")
vessel_id = list(vessel.values())[0].get("id", "")
debug_print(f"🔧 从vessel字典提取ID: {vessel_id}")
return vessel_id
elif isinstance(vessel, str):

2
unilabos/compile/wash_solid_protocol.py
View File

@@ -165,7 +165,7 @@ def extract_vessel_id(vessel: Union[str, dict]) -> str:
str: vessel_id
"""
if isinstance(vessel, dict):
vessel_id = vessel.get("id", "")
vessel_id = list(vessel.values())[0].get("id", "")
debug_print(f"🔧 从vessel字典提取ID: {vessel_id}")
return vessel_id
elif isinstance(vessel, str):