Add Mock Device for Organic Synthesis\添加有机合成的虚拟仪器和Protocol (#43)

* Add Device MockChiller

Add device MockChiller

* Add Device MockFilter

* Add Device MockPump

* Add Device MockRotavap

* Add Device MockSeparator

* Add Device MockStirrer

* Add Device MockHeater

* Add Device MockVacuum

* Add Device MockSolenoidValve

* Add Device Mock \_init_.py

* 规范模拟设备代码与注册表信息

* 更改Mock大写文件夹名

* 删除大写目录

* Edited Mock device json

* Match mock device with action

* Edit mock device yaml

* Add new action

* Add Virtual Device, Action, YAML, Protocol for Organic Syn

* 单独分类测试的protocol文件夹

* 更名Action

---------

Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com>

unilabos/compile/run_column_protocol.py

@@ -0,0 +1,102 @@
+from typing import List, Dict, Any
+import networkx as nx
+
+def generate_run_column_protocol(
+    G: nx.DiGraph,
+    from_vessel: str,
+    to_vessel: str,
+    column: str
+) -> List[Dict[str, Any]]:
+    """
+    生成柱层析分离的协议序列
+    
+    Args:
+        G: 有向图，节点为设备和容器
+        from_vessel: 源容器的名称，即样品起始所在的容器
+        to_vessel: 目标容器的名称，分离后的样品要到达的容器
+        column: 所使用的柱子的名称
+    
+    Returns:
+        List[Dict[str, Any]]: 柱层析分离操作的动作序列
+    
+    Raises:
+        ValueError: 当找不到必要的设备时抛出异常
+    
+    Examples:
+        run_column_protocol = generate_run_column_protocol(G, "reactor", "collection_flask", "silica_column")
+    """
+    action_sequence = []
+    
+    # 验证容器是否存在
+    if from_vessel not in G.nodes():
+        raise ValueError(f"源容器 {from_vessel} 不存在于图中")
+    
+    if to_vessel not in G.nodes():
+        raise ValueError(f"目标容器 {to_vessel} 不存在于图中")
+    
+    # 查找转移泵设备（用于样品转移）
+    pump_nodes = [node for node in G.nodes() 
+                  if G.nodes[node].get('class') == 'virtual_transfer_pump']
+    
+    if not pump_nodes:
+        raise ValueError("没有找到可用的转移泵设备")
+    
+    pump_id = pump_nodes[0]
+    
+    # 查找柱层析设备
+    column_nodes = [node for node in G.nodes() 
+                   if G.nodes[node].get('class') == 'virtual_column']
+    
+    if not column_nodes:
+        raise ValueError("没有找到可用的柱层析设备")
+    
+    column_id = column_nodes[0]
+    
+    # 步骤1：将样品从源容器转移到柱子上
+    action_sequence.append({
+        "device_id": pump_id,
+        "action_name": "transfer",
+        "action_kwargs": {
+            "from_vessel": from_vessel,
+            "to_vessel": column_id,  # 将样品转移到柱子设备
+            "volume": 0.0,  # 转移所有液体，体积由系统确定
+            "amount": f"样品上柱 - 使用 {column}",
+            "time": 0.0,
+            "viscous": False,
+            "rinsing_solvent": "",
+            "rinsing_volume": 0.0,
+            "rinsing_repeats": 0,
+            "solid": False
+        }
+    })
+    
+    # 步骤2：运行柱层析分离
+    action_sequence.append({
+        "device_id": column_id,
+        "action_name": "run_column",
+        "action_kwargs": {
+            "from_vessel": from_vessel,
+            "to_vessel": to_vessel,
+            "column": column
+        }
+    })
+    
+    # 步骤3：将分离后的产物从柱子转移到目标容器
+    action_sequence.append({
+        "device_id": pump_id,
+        "action_name": "transfer",
+        "action_kwargs": {
+            "from_vessel": column_id,  # 从柱子设备转移
+            "to_vessel": to_vessel,
+            "volume": 0.0,  # 转移所有液体，体积由系统确定
+            "amount": f"收集分离产物 - 来自 {column}",
+            "time": 0.0,
+            "viscous": False,
+            "rinsing_solvent": "",
+            "rinsing_volume": 0.0,
+            "rinsing_repeats": 0,
+            "solid": False
+        }
+    })
+    
+    return action_sequence