add biomek.py demo implementation

unilabos/devices/liquid_handling/biomek.py

@@ -0,0 +1,167 @@
+import requests
+from typing import List, Sequence, Optional, Union, Literal
+
+from .liquid_handler_abstract import LiquidHandlerAbstract
+
+
+class LiquidHandlerBiomek(LiquidHandlerAbstract):
+    """
+    Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
+    该类用于处理Biomek液体处理器的特定操作。
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._status = "Idle"  # 初始状态为 Idle
+        self._success = False  # 初始成功状态为 False
+        self._status_queue = kwargs.get("status_queue", None)  # 状态队列
+        self.temp_protocol = {}
+
+    def create_protocol(self,
+        protocol_name: str,
+        protocol_description: str,
+        protocol_version: str,
+        protocol_author: str,
+        protocol_date: str,
+    ):
+        """
+        创建一个新的协议。
+
+        Args:
+            protocol_name (str): 协议名称
+            protocol_description (str): 协议描述
+            protocol_version (str): 协议版本
+            protocol_author (str): 协议作者
+            protocol_date (str): 协议日期
+            protocol_type (str): 协议类型
+            none_keys (List[str]): 需要设置为None的键列表
+
+        Returns:
+            dict: 创建的协议字典
+        """
+        self.temp_protocol = {
+            "meta": {
+                "name": protocol_name,
+                "description": protocol_description,
+                "version": protocol_version,
+                "author": protocol_author,
+                "date": protocol_date,
+            },
+            "labwares": [],
+            "steps": [],
+        }
+        return self.temp_protocol
+
+    def run_protocol(self):
+        """
+        执行创建的实验流程。
+        工作站的完整执行流程是，
+        从 create_protocol 开始，创建新的 method，
+        随后执行 transfer_liquid 等操作向实验流程添加步骤，
+        最后 run_protocol 执行整个方法。
+
+        Returns:
+            dict: 执行结果
+        """
+        if not self.temp_protocol:
+            raise ValueError("No protocol created. Please create a protocol first.")
+
+        # 模拟执行协议
+        self._status = "Running"
+        self._success = True
+        # 在这里可以添加实际执行协议的逻辑
+
+        response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
+
+    def create_resource(
+        self,
+        device_id: str,
+        res_id: str,
+        class_name: str,
+        parent: str,
+        bind_locations: Point,
+        liquid_input_slot: list[int],
+        liquid_type: list[str],
+        liquid_volume: list[int],
+        slot_on_deck: int,
+    ):
+        """
+        创建一个新的资源。
+
+        Args:
+            device_id (str): 设备ID
+            res_id (str): 资源ID
+            class_name (str): 资源类名
+            parent (str): 父级ID
+            bind_locations (Point): 绑定位置
+            liquid_input_slot (list[int]): 液体输入槽列表
+            liquid_type (list[str]): 液体类型列表
+            liquid_volume (list[int]): 液体体积列表
+            slot_on_deck (int): 甲板上的槽位
+
+        Returns:
+            dict: 创建的资源字典
+        """
+        # TODO：需要对好接口，下面这个是临时的
+        resource = {
+            "id": res_id,
+            "class": class_name,
+            "parent": parent,
+            "bind_locations": bind_locations.to_dict(),
+            "liquid_input_slot": liquid_input_slot,
+            "liquid_type": liquid_type,
+            "liquid_volume": liquid_volume,
+            "slot_on_deck": slot_on_deck,
+        }
+        self.temp_protocol["labwares"].append(resource)
+        return resource
+
+    def transfer_liquid(
+        self,
+        sources: Sequence[Container],
+        targets: Sequence[Container],
+        tip_racks: Sequence[TipRack],
+        *,
+        use_channels: Optional[List[int]] = None,
+        asp_vols: Union[List[float], float],
+        dis_vols: Union[List[float], float],
+        asp_flow_rates: Optional[List[Optional[float]]] = None,
+        dis_flow_rates: Optional[List[Optional[float]]] = None,
+        offsets: Optional[List[Coordinate]] = None,
+        touch_tip: bool = False,
+        liquid_height: Optional[List[Optional[float]]] = None,
+        blow_out_air_volume: Optional[List[Optional[float]]] = None,
+        spread: Literal["wide", "tight", "custom"] = "wide",
+        is_96_well: bool = False,
+        mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
+        mix_times: Optional[List(int)] = None,
+        mix_vol: Optional[int] = None,
+        mix_rate: Optional[int] = None,
+        mix_liquid_height: Optional[float] = None,
+        delays: Optional[List[int]] = None,
+        none_keys: List[str] = []
+    ):
+        # TODO：需要对好接口，下面这个是临时的
+        self.temp_protocol["steps"].append({
+            "type": "transfer",
+            "sources": [source.to_dict() for source in sources],
+            "targets": [target.to_dict() for target in targets],
+            "tip_racks": [tip_rack.to_dict() for tip_rack in tip_racks],
+            "use_channels": use_channels,
+            "asp_vols": asp_vols,
+            "dis_vols": dis_vols,
+            "asp_flow_rates": asp_flow_rates,
+            "dis_flow_rates": dis_flow_rates,
+            "offsets": offsets,
+            "touch_tip": touch_tip,
+            "liquid_height": liquid_height,
+            "blow_out_air_volume": blow_out_air_volume,
+            "spread": spread,
+            "is_96_well": is_96_well,
+            "mix_stage": mix_stage,
+            "mix_times": mix_times,
+            "mix_vol": mix_vol,
+            "mix_rate": mix_rate,
+            "mix_liquid_height": mix_liquid_height,
+            "delays": delays,
+        })

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -21,6 +21,18 @@ class LiquidHandlerAbstract(LiquidHandler):
     # REMOVE LIQUID --------------------------------------------------
     # ---------------------------------------------------------------
 
+    async def create_protocol(self,
+        protocol_name: str,
+        protocol_description: str,
+        protocol_version: str,
+        protocol_author: str,
+        protocol_date: str,
+        protocol_type: str,
+        none_keys: List[str] = []
+    ):
+        """Create a new protocol with the given metadata."""
+        pass
+
     async def remove_liquid(
         self,
         vols: List[float],
@@ -158,13 +170,13 @@ class LiquidHandlerAbstract(LiquidHandler):
     # ---------------------------------------------------------------
     async def transfer_liquid(
         self,
-        asp_vols: Union[List[float], float],
-        dis_vols: Union[List[float], float],
         sources: Sequence[Container],
         targets: Sequence[Container],
         tip_racks: Sequence[TipRack],
         *,
         use_channels: Optional[List[int]] = None,
+        asp_vols: Union[List[float], float],
+        dis_vols: Union[List[float], float],
         asp_flow_rates: Optional[List[Optional[float]]] = None,
         dis_flow_rates: Optional[List[Optional[float]]] = None,
         offsets: Optional[List[Coordinate]] = None,
@@ -266,9 +278,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                 print(f"Done: {msg}")
                 print(f"Current time: {time.strftime('%H:%M:%S')}")
 
-    async def touch_tip(self,
+    async def touch_tip(self, targets: Sequence[Container]):
-                        targets: Sequence[Container],
-                        ):
         """Touch the tip to the side of the well."""
         await self.aspirate(
             resources=[targets],