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729a0fcf0c
* add biomek.py demo implementation * 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。 * Test * fix biomek success type * Convert LH action to biomek. * Update biomek.py * 注册表上报handle和schema (param input) * 修复biomek缺少的字段 * delete 's' * Remove warnings * Update biomek.py * Biomek test * Update biomek.py * 新增transfer_biomek的msg * New transfer_biomek * Updated transfer_biomek * 更新transfer_biomek的msg * 更新transfer_biomek的msg * 支持Biomek创建 * new action * fix key name typo * New parameter for biomek to run. * Refine * Update * new actions * new actions * 1 * registry * fix biomek startup add action handles * fix handles not as default entry * biomek_test.py biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json * Update biomek.py * biomek_test.py * fix liquid_handler.biomek handles * host node新增resource add时间统计 create_resource新增handle bump version to 0.9.2 * 修正物料上传时间 改用biomek_test 增加ResultInfoEncoder 支持返回结果上传 * 正确发送return_info结果 * 同步执行状态信息 * 取消raiseValueError提示 * Update biomek_test.py * 0608 DONE * 同步了Biomek.py 现在应可用 * biomek switch back to non-test * temp disable initialize resource * Refine biomek * Refine copy issue * Refine --------- Co-authored-by: Junhan Chang <changjh@pku.edu.cn> Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com> Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>
155 lines
5.4 KiB
Python
155 lines
5.4 KiB
Python
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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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TipLocation = "BC1025F" # Assuming this is a fixed tip location for the transfer
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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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solvent = "PBS"
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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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TipLocation,
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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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solvent: Optional[str] = None,
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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": False,
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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": True,
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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": "1",
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"WashVolume": "110%",
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"Wizard": False
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}
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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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transfer_params["Solvent"] = solvent if solvent else "Water"
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transfer_params["TipLocation"] = TipLocation
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if len(tip_racks) == 1:
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transfer_params['UseCurrentTips'] = True
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elif len(tip_racks) > 1:
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transfer_params["ChangeTipsBetweenDests"] = True
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return transfer_params
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action = transfer_liquid(sources=sources,targets=targets,tip_racks=tip_racks, asp_vols=asp_vols,solvent = solvent, TipLocation=TipLocation)
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print(json.dumps(action,indent=2))
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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": true,
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"ShowTransferDetails": true,
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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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