Test

unilabos/devices/liquid_handling/biomek.py

@@ -1,7 +1,9 @@
-import requests
+# import requests
-from typing import List, Sequence, Optional, Union, Literal
+# from typing import List, Sequence, Optional, Union, Literal
+
+# from .liquid_handler_abstract import LiquidHandlerAbstract
+
 
-from .liquid_handler_abstract import LiquidHandlerAbstract
 
 
 class LiquidHandlerBiomek(LiquidHandlerAbstract):
@@ -16,6 +18,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         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 = {}
+        self.py32_path = "/opt/py32"  # Biomek的Python 3.2路径
 
     def create_protocol(self,
         protocol_name: str,
@@ -63,6 +66,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         Returns:
             dict: 执行结果
         """
+        #use popen or subprocess to create py32 process and communicate send the temp protocol to it
         if not self.temp_protocol:
             raise ValueError("No protocol created. Please create a protocol first.")
 

unilabos/devices/liquid_handling/convert_biomek.py

@@ -0,0 +1,158 @@
+
+import json
+from typing import Sequence, Optional, List, Union, Literal
+json_path = "/Users/guangxinzhang/Documents/Deep Potential/opentrons/convert/protocols/enriched_steps/sci-lucif-assay4.json"
+
+with open(json_path, "r") as f:
+    data = json.load(f)
+
+transfer_example = data[0]
+#print(transfer_example)
+
+
+temp_protocol = []
+
+sources = transfer_example["sources"]  # Assuming sources is a list of Container objects
+targets = transfer_example["targets"]  # Assuming targets is a list of Container objects
+tip_racks = transfer_example["tip_racks"]  # Assuming tip_racks is a list of TipRack objects
+asp_vols = transfer_example["asp_vols"]  # Assuming asp_vols is a list of volumes
+
+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[]] = 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() = 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] = []
+    ):
+        # -------- Build Biomek transfer step --------
+        # 1) Construct default parameter scaffold (values mirror Biomek “Transfer” block).
+        transfer_params = {
+            "Span8": False,
+            "Pod": "Pod1",
+            "items": {},                       # to be filled below
+            "Wash": False,
+            "Dynamic?": True,
+            "AutoSelectActiveWashTechnique": False,
+            "ActiveWashTechnique": "",
+            "ChangeTipsBetweenDests": True,
+            "ChangeTipsBetweenSources": False,
+            "DefaultCaption": "",              # filled after we know first pair/vol
+            "UseExpression": False,
+            "LeaveTipsOn": False,
+            "MandrelExpression": "",
+            "Repeats": "1",
+            "RepeatsByVolume": False,
+            "Replicates": "1",
+            "ShowTipHandlingDetails": False,
+            "ShowTransferDetails": True,
+            "Solvent": "Water",
+            "Span8Wash": False,
+            "Span8WashVolume": "2",
+            "Span8WasteVolume": "1",
+            "SplitVolume": False,
+            "SplitVolumeCleaning": False,
+            "Stop": "Destinations",
+            "TipLocation": "BC1025F",
+            "UseCurrentTips": False,
+            "UseDisposableTips": False,
+            "UseFixedTips": False,
+            "UseJIT": True,
+            "UseMandrelSelection": True,
+            "UseProbes": [True, True, True, True, True, True, True, True],
+            "WashCycles": "3",
+            "WashVolume": "110%",
+            "Wizard": False
+        }
+
+        # 2) Build the items mapping (source/dest/volume triplets).
+        #    Priority: user‑provided sources, targets, dis_vols.
+        items: dict = {}
+        for idx, (src, dst) in enumerate(zip(sources, targets)):
+            items[str(idx)] = {
+                "Source": str(src),
+                "Destination": str(dst),
+                "Volume": asp_vols[idx] 
+            }
+        transfer_params["items"] = items
+
+        return transfer_params
+
+        # # 3) Set a readable caption using the first source/target if available.
+        # if items:
+        #     first_item = next(iter(items.values()))
+        #     transfer_params["DefaultCaption"] = (
+        #         f"Transfer {first_item['Volume']} µL from "
+        #         f"{first_item['Source']} to {first_item['Destination']}"
+        #     )
+
+        # # 4) Append the fully‑formed step to the temp protocol.
+        # self.temp_protocol.setdefault("steps", []).append({"transfer": transfer_params})
+
+
+
+action = transfer_liquid(sources=sources,targets=targets,tip_racks=tip_racks)
+print(action)
+# print(action)
+
+
+
+
+"""
+      "transfer": {
+
+        "items": {},
+        "Wash": false,
+        "Dynamic?": true,
+        "AutoSelectActiveWashTechnique": false,
+        "ActiveWashTechnique": "",
+        "ChangeTipsBetweenDests": true,
+        "ChangeTipsBetweenSources": false,
+        "DefaultCaption": "Transfer 100 µL from P13 to P3",
+        "UseExpression": false,
+        "LeaveTipsOn": false,
+        "MandrelExpression": "",
+        "Repeats": "1",
+        "RepeatsByVolume": false,
+        "Replicates": "1",
+        "ShowTipHandlingDetails": false,
+        "ShowTransferDetails": true,
+        "Solvent": "Water",
+        "Span8Wash": false,
+        "Span8WashVolume": "2",
+        "Span8WasteVolume": "1",
+        "SplitVolume": false,
+        "SplitVolumeCleaning": false,
+        "Stop": "Destinations",
+        "TipLocation": "BC1025F",
+        "UseCurrentTips": false,
+        "UseDisposableTips": false,
+        "UseFixedTips": false,
+        "UseJIT": true,
+        "UseMandrelSelection": true,
+        "UseProbes": [true, true, true, true, true, true, true, true],
+        "WashCycles": "3",
+        "WashVolume": "110%",
+        "Wizard": false
+"""
+
+
+
+