Convert LH action to biomek.

unilabos/devices/liquid_handling/biomek.py

@@ -1,7 +1,7 @@
-# import requests
-# from typing import List, Sequence, Optional, Union, Literal
+import requests
+from typing import List, Sequence, Optional, Union, Literal
 
-# from .liquid_handler_abstract import LiquidHandlerAbstract
+from .liquid_handler_abstract import LiquidHandlerAbstract
 
 
 
@@ -125,6 +125,8 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         sources: Sequence[Container],
         targets: Sequence[Container],
         tip_racks: Sequence[TipRack],
+        solvent: Optional[str] = None,
+        TipLocation: Optional[str] = None,
         *,
         use_channels: Optional[List[int]] = None,
         asp_vols: Union[List[float], float],
@@ -145,27 +147,62 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         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,
-        })
+
+        transfer_params = {
+            "Span8": False,
+            "Pod": "Pod1",
+            "items": {},                      
+            "Wash": False,
+            "Dynamic?": True,
+            "AutoSelectActiveWashTechnique": False,
+            "ActiveWashTechnique": "",
+            "ChangeTipsBetweenDests": False,
+            "ChangeTipsBetweenSources": False,
+            "DefaultCaption": "",             
+            "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": True,
+            "UseFixedTips": False,
+            "UseJIT": True,
+            "UseMandrelSelection": True,
+            "UseProbes": [True, True, True, True, True, True, True, True],
+            "WashCycles": "1",
+            "WashVolume": "110%",
+            "Wizard": False
+        }
+
+        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
+        transfer_params["Solvent"] =  solvent if solvent else "Water"
+        transfer_params["TipLocation"] = TipLocation
+
+        if len(tip_racks) == 1:
+             transfer_params['UseCurrentTips'] = True
+        elif len(tip_racks) > 1:
+            transfer_params["ChangeTipsBetweenDests"] = True
+
+        self.temp_protocol["steps"].append(transfer_params)
+        
+        return 
+    

unilabos/devices/liquid_handling/test liquid handler/convert_biomek.py

@@ -11,20 +11,23 @@ transfer_example = data[0]
 
 
 temp_protocol = []
-
+TipLocation = "BC1025F"  # Assuming this is a fixed tip location for the transfer
 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
+solvent = "PBS"
 
 def transfer_liquid(
         #self,
         sources,#: Sequence[Container],
         targets,#: Sequence[Container],
         tip_racks,#: Sequence[TipRack],
+        TipLocation,
         # *,
         # use_channels: Optional[List[int]] = None,
         asp_vols: Union[List[float], float],
+        solvent: Optional[str] = None,
         # dis_vols: Union[List[float], float],
         # asp_flow_rates: Optional[List[Optional[float]]] = None,
         # dis_flow_rates: Optional[List[Optional[float]]] = None,
@@ -44,6 +47,7 @@ def transfer_liquid(
     ):
         # -------- Build Biomek transfer step --------
         # 1) Construct default parameter scaffold (values mirror Biomek “Transfer” block).
+
         transfer_params = {
             "Span8": False,
             "Pod": "Pod1",
@@ -52,7 +56,7 @@ def transfer_liquid(
             "Dynamic?": True,
             "AutoSelectActiveWashTechnique": False,
             "ActiveWashTechnique": "",
-            "ChangeTipsBetweenDests": True,
+            "ChangeTipsBetweenDests": False,
             "ChangeTipsBetweenSources": False,
             "DefaultCaption": "",              # filled after we know first pair/vol
             "UseExpression": False,
@@ -72,18 +76,16 @@ def transfer_liquid(
             "Stop": "Destinations",
             "TipLocation": "BC1025F",
             "UseCurrentTips": False,
-            "UseDisposableTips": False,
+            "UseDisposableTips": True,
             "UseFixedTips": False,
             "UseJIT": True,
             "UseMandrelSelection": True,
             "UseProbes": [True, True, True, True, True, True, True, True],
-            "WashCycles": "3",
+            "WashCycles": "1",
             "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)] = {
@@ -92,24 +94,18 @@ def transfer_liquid(
                 "Volume": asp_vols[idx] 
             }
         transfer_params["items"] = items
+        transfer_params["Solvent"] =  solvent if solvent else "Water"
+        transfer_params["TipLocation"] = TipLocation
+
+        if len(tip_racks) == 1:
+             transfer_params['UseCurrentTips'] = True
+        elif len(tip_racks) > 1:
+            transfer_params["ChangeTipsBetweenDests"] = True
 
         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)
+action = transfer_liquid(sources=sources,targets=targets,tip_racks=tip_racks, asp_vols=asp_vols,solvent = solvent, TipLocation=TipLocation)
+print(json.dumps(action,indent=2))  
 # print(action)
 
 
@@ -132,9 +128,9 @@ print(action)
         "Repeats": "1",
         "RepeatsByVolume": false,
         "Replicates": "1",
-        "ShowTipHandlingDetails": false,
+        "ShowTipHandlingDetails": true,
         "ShowTransferDetails": true,
-        "Solvent": "Water",
+        
         "Span8Wash": false,
         "Span8WashVolume": "2",
         "Span8WasteVolume": "1",