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Test
This commit is contained in:
Guangxin Zhang
@@ -1,7 +1,9 @@
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import requests
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from typing import List, Sequence, Optional, Union, Literal
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# import requests
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# from typing import List, Sequence, Optional, Union, Literal
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# from .liquid_handler_abstract import LiquidHandlerAbstract
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from .liquid_handler_abstract import LiquidHandlerAbstract
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class LiquidHandlerBiomek(LiquidHandlerAbstract):
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@@ -16,6 +18,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
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self._success = False # 初始成功状态为 False
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self._status_queue = kwargs.get("status_queue", None) # 状态队列
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self.temp_protocol = {}
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self.py32_path = "/opt/py32" # Biomek的Python 3.2路径
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def create_protocol(self,
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protocol_name: str,
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@@ -63,6 +66,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
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Returns:
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dict: 执行结果
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"""
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#use popen or subprocess to create py32 process and communicate send the temp protocol to it
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if not self.temp_protocol:
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raise ValueError("No protocol created. Please create a protocol first.")
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158
unilabos/devices/liquid_handling/convert_biomek.py
Normal file
158
unilabos/devices/liquid_handling/convert_biomek.py
Normal file
@@ -0,0 +1,158 @@
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import json
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from typing import Sequence, Optional, List, Union, Literal
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json_path = "/Users/guangxinzhang/Documents/Deep Potential/opentrons/convert/protocols/enriched_steps/sci-lucif-assay4.json"
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with open(json_path, "r") as f:
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data = json.load(f)
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transfer_example = data[0]
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#print(transfer_example)
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temp_protocol = []
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sources = transfer_example["sources"] # Assuming sources is a list of Container objects
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targets = transfer_example["targets"] # Assuming targets is a list of Container objects
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tip_racks = transfer_example["tip_racks"] # Assuming tip_racks is a list of TipRack objects
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asp_vols = transfer_example["asp_vols"] # Assuming asp_vols is a list of volumes
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def transfer_liquid(
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#self,
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sources,#: Sequence[Container],
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targets,#: Sequence[Container],
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tip_racks,#: Sequence[TipRack],
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# *,
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# use_channels: Optional[List[int]] = None,
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asp_vols: Union[List[float], float],
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# dis_vols: Union[List[float], float],
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# asp_flow_rates: Optional[List[Optional[float]]] = None,
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# dis_flow_rates: Optional[List[Optional[float]]] = None,
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# offsets,#: Optional[List[]] = None,
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# touch_tip: bool = False,
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# liquid_height: Optional[List[Optional[float]]] = None,
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# blow_out_air_volume: Optional[List[Optional[float]]] = None,
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# spread: Literal["wide", "tight", "custom"] = "wide",
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# is_96_well: bool = False,
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# mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
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# mix_times,#: Optional[list() = None,
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# mix_vol: Optional[int] = None,
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# mix_rate: Optional[int] = None,
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# mix_liquid_height: Optional[float] = None,
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# delays: Optional[List[int]] = None,
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# none_keys: List[str] = []
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):
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# -------- Build Biomek transfer step --------
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# 1) Construct default parameter scaffold (values mirror Biomek “Transfer” block).
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transfer_params = {
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"Span8": False,
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"Pod": "Pod1",
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"items": {}, # to be filled below
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"Wash": False,
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"Dynamic?": True,
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"AutoSelectActiveWashTechnique": False,
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"ActiveWashTechnique": "",
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"ChangeTipsBetweenDests": True,
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"ChangeTipsBetweenSources": False,
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"DefaultCaption": "", # filled after we know first pair/vol
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"UseExpression": False,
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"LeaveTipsOn": False,
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"MandrelExpression": "",
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"Repeats": "1",
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"RepeatsByVolume": False,
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"Replicates": "1",
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"ShowTipHandlingDetails": False,
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"ShowTransferDetails": True,
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"Solvent": "Water",
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"Span8Wash": False,
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"Span8WashVolume": "2",
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"Span8WasteVolume": "1",
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"SplitVolume": False,
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"SplitVolumeCleaning": False,
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"Stop": "Destinations",
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"TipLocation": "BC1025F",
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"UseCurrentTips": False,
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"UseDisposableTips": False,
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"UseFixedTips": False,
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"UseJIT": True,
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"UseMandrelSelection": True,
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"UseProbes": [True, True, True, True, True, True, True, True],
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"WashCycles": "3",
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"WashVolume": "110%",
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"Wizard": False
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}
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# 2) Build the items mapping (source/dest/volume triplets).
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# Priority: user‑provided sources, targets, dis_vols.
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items: dict = {}
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for idx, (src, dst) in enumerate(zip(sources, targets)):
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items[str(idx)] = {
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"Source": str(src),
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"Destination": str(dst),
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"Volume": asp_vols[idx]
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}
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transfer_params["items"] = items
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return transfer_params
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# # 3) Set a readable caption using the first source/target if available.
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# if items:
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# first_item = next(iter(items.values()))
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# transfer_params["DefaultCaption"] = (
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# f"Transfer {first_item['Volume']} µL from "
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# f"{first_item['Source']} to {first_item['Destination']}"
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# )
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# # 4) Append the fully‑formed step to the temp protocol.
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# self.temp_protocol.setdefault("steps", []).append({"transfer": transfer_params})
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action = transfer_liquid(sources=sources,targets=targets,tip_racks=tip_racks)
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print(action)
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# print(action)
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"""
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"transfer": {
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"items": {},
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"Wash": false,
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"Dynamic?": true,
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"AutoSelectActiveWashTechnique": false,
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"ActiveWashTechnique": "",
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"ChangeTipsBetweenDests": true,
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"ChangeTipsBetweenSources": false,
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"DefaultCaption": "Transfer 100 µL from P13 to P3",
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"UseExpression": false,
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"LeaveTipsOn": false,
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"MandrelExpression": "",
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"Repeats": "1",
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"RepeatsByVolume": false,
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"Replicates": "1",
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"ShowTipHandlingDetails": false,
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"ShowTransferDetails": true,
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"Solvent": "Water",
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"Span8Wash": false,
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"Span8WashVolume": "2",
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"Span8WasteVolume": "1",
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"SplitVolume": false,
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"SplitVolumeCleaning": false,
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"Stop": "Destinations",
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"TipLocation": "BC1025F",
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"UseCurrentTips": false,
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"UseDisposableTips": false,
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"UseFixedTips": false,
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"UseJIT": true,
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"UseMandrelSelection": true,
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"UseProbes": [true, true, true, true, true, true, true, true],
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"WashCycles": "3",
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"WashVolume": "110%",
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"Wizard": false
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"""
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