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338 lines
11 KiB
Python
338 lines
11 KiB
Python
"""
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PRCXI transfer_liquid 集成测试。
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这些用例会启动 UniLiquidHandler RViz 仿真 backend，需要同时满足：
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1. 安装 pylabrobot 依赖；
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2. 设置环境变量 UNILAB_SIM_TEST=1；
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3. 具备 ROS 运行环境（rviz_backend 会创建 ROS 节点）。
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"""
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import asyncio
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import os
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from dataclasses import dataclass
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from typing import List, Sequence
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import pytest
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from unilabos.devices.liquid_handling.liquid_handler_abstract import LiquidHandlerAbstract
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from unilabos.devices.liquid_handling.prcxi.prcxi import PRCXI9300Deck, PRCXI9300Trash
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from unilabos.devices.liquid_handling.prcxi.prcxi_labware import (
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PRCXI_300ul_Tips,
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PRCXI_BioER_96_wellplate,
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)
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pytestmark = pytest.mark.slow
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try:
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from pylabrobot.resources import Coordinate, Deck, Plate, TipRack, Well
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except ImportError: # pragma: no cover - 测试环境缺少 pylabrobot 时直接跳过
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Coordinate = Deck = Plate = TipRack = Well = None # type: ignore[assignment]
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PYLABROBOT_AVAILABLE = False
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else:
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PYLABROBOT_AVAILABLE = True
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SIM_ENV_VAR = "UNILAB_SIM_TEST"
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@dataclass
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class SimulationContext:
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handler: LiquidHandlerAbstract
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deck: Deck
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tip_rack: TipRack
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source_plate: Plate
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target_plate: Plate
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waste_plate: Plate
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channel_num: int
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def run(coro):
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return asyncio.run(coro)
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def _ensure_unilabos_extra(well: Well) -> None:
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if not hasattr(well, "unilabos_extra") or well.unilabos_extra is None:
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well.unilabos_extra = {} # type: ignore[attr-defined]
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def _assign_sample_uuid(well: Well, value: str) -> None:
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_ensure_unilabos_extra(well)
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well.unilabos_extra["sample_uuid"] = value # type: ignore[attr-defined]
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def _zero_coordinate() -> Coordinate:
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if hasattr(Coordinate, "zero"):
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return Coordinate.zero()
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return Coordinate(0, 0, 0)
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def _zero_offsets(count: int) -> List[Coordinate]:
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return [_zero_coordinate() for _ in range(count)]
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def _build_simulation_deck() -> tuple[PRCXI9300Deck, TipRack, Plate, Plate, Plate, PRCXI9300Trash]:
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deck = PRCXI9300Deck(name="PRCXI_Deck", size_x=542, size_y=374, size_z=50)
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tip_rack = PRCXI_300ul_Tips("Tips")
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source_plate = PRCXI_BioER_96_wellplate("SourcePlate")
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target_plate = PRCXI_BioER_96_wellplate("TargetPlate")
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waste_plate = PRCXI_BioER_96_wellplate("WastePlate")
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trash = PRCXI9300Trash(name="trash", size_x=100, size_y=100, size_z=50)
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deck.assign_child_resource(tip_rack, location=Coordinate(0, 0, 0))
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deck.assign_child_resource(source_plate, location=Coordinate(150, 0, 0))
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deck.assign_child_resource(target_plate, location=Coordinate(300, 0, 0))
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deck.assign_child_resource(waste_plate, location=Coordinate(450, 0, 0))
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deck.assign_child_resource(trash, location=Coordinate(150, -120, 0))
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return deck, tip_rack, source_plate, target_plate, waste_plate, trash
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def _stop_backend(handler: LiquidHandlerAbstract) -> None:
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try:
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run(handler.backend.stop())
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except Exception: # pragma: no cover - 如果 backend 已经停止
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pass
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simulate_handler = getattr(handler, "_simulate_handler", None)
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if simulate_handler is not None and getattr(simulate_handler, "backend", None) is not None:
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try:
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run(simulate_handler.backend.stop())
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except Exception: # pragma: no cover
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pass
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@pytest.fixture(params=[1, 8])
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def prcxi_simulation(request) -> SimulationContext:
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if not PYLABROBOT_AVAILABLE:
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pytest.skip("pylabrobot is required for PRCXI simulation tests.")
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if os.environ.get(SIM_ENV_VAR) != "1":
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pytest.skip(f"Set {SIM_ENV_VAR}=1 to run PRCXI simulation tests.")
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channel_num = request.param
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deck, tip_rack, source_plate, target_plate, waste_plate, _trash = _build_simulation_deck()
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backend_cfg = {
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"type": "unilabos.devices.liquid_handling.rviz_backend.UniLiquidHandlerRvizBackend",
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"channel_num": channel_num,
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"total_height": 310,
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"lh_device_id": f"pytest_prcxi_{channel_num}",
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}
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handler = LiquidHandlerAbstract(
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backend=backend_cfg,
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deck=deck,
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simulator=True,
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channel_num=channel_num,
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total_height=310,
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)
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run(handler.setup())
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handler.set_tiprack([tip_rack])
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handler.support_touch_tip = False
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context = SimulationContext(
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handler=handler,
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deck=deck,
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tip_rack=tip_rack,
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source_plate=source_plate,
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target_plate=target_plate,
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waste_plate=waste_plate,
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channel_num=channel_num,
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)
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yield context
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_stop_backend(handler)
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def _pick_wells(plate: Plate, start: int, count: int) -> List[Well]:
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wells = plate.children[start : start + count]
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for well in wells:
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_ensure_unilabos_extra(well)
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return wells
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def _assert_samples_match(sources: Sequence[Well], targets: Sequence[Well]) -> None:
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for src, tgt in zip(sources, targets):
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src_uuid = getattr(src, "unilabos_extra", {}).get("sample_uuid")
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tgt_uuid = getattr(tgt, "unilabos_extra", {}).get("sample_uuid")
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assert tgt_uuid == src_uuid
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def test_transfer_liquid_single_channel_one_to_one(prcxi_simulation: SimulationContext):
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if prcxi_simulation.channel_num != 1:
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pytest.skip("仅在单通道配置下运行")
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handler = prcxi_simulation.handler
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for well in prcxi_simulation.source_plate.children + prcxi_simulation.target_plate.children:
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_ensure_unilabos_extra(well)
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sources = prcxi_simulation.source_plate[0:3]
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targets = prcxi_simulation.target_plate["A4:A6"]
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for idx, src in enumerate(sources):
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_assign_sample_uuid(src, f"single_{idx}")
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offsets = _zero_offsets(max(len(sources), len(targets)))
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result = run(
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handler.transfer_liquid(
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sources=sources,
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targets=targets,
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tip_racks=[prcxi_simulation.tip_rack],
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use_channels=[0],
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asp_vols=[5.0, 6.0, 7.0],
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dis_vols=[10.0, 11.0, 12.0],
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offsets=offsets,
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mix_times=None,
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)
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)
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# assert result == """"""
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_assert_samples_match(sources, targets)
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def test_transfer_liquid_single_channel_one_to_many(prcxi_simulation: SimulationContext):
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if prcxi_simulation.channel_num != 1:
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pytest.skip("仅在单通道配置下运行")
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handler = prcxi_simulation.handler
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for well in prcxi_simulation.source_plate.children + prcxi_simulation.target_plate.children:
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_ensure_unilabos_extra(well)
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source = prcxi_simulation.source_plate.children[0]
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targets = prcxi_simulation.target_plate["A1:E1"]
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_assign_sample_uuid(source, "one_to_many_source")
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offsets = _zero_offsets(max(len(targets), 1))
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run(
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handler.transfer_liquid(
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sources=[source],
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targets=targets,
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tip_racks=[prcxi_simulation.tip_rack],
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use_channels=[0],
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asp_vols=10.0,
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dis_vols=[2.0, 2.0, 2.0, 2.0, 2.0],
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offsets=offsets,
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mix_times=0,
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)
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)
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for target in targets:
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assert getattr(target, "unilabos_extra", {}).get("sample_uuid") == "one_to_many_source"
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def test_transfer_liquid_single_channel_many_to_one(prcxi_simulation: SimulationContext):
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if prcxi_simulation.channel_num != 1:
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pytest.skip("仅在单通道配置下运行")
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handler = prcxi_simulation.handler
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for well in prcxi_simulation.source_plate.children + prcxi_simulation.target_plate.children:
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_ensure_unilabos_extra(well)
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sources = prcxi_simulation.source_plate[0:3]
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target = prcxi_simulation.target_plate.children[4]
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for idx, src in enumerate(sources):
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_assign_sample_uuid(src, f"many_to_one_{idx}")
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offsets = _zero_offsets(max(len(sources), len([target])))
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run(
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handler.transfer_liquid(
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sources=sources,
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targets=[target],
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tip_racks=[prcxi_simulation.tip_rack],
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use_channels=[0],
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asp_vols=[8.0, 9.0, 10.0],
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dis_vols=1,
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offsets=offsets,
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mix_stage="after",
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mix_times=1,
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mix_vol=5,
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)
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)
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assert getattr(target, "unilabos_extra", {}).get("sample_uuid") == "many_to_one_2"
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def test_transfer_liquid_eight_channel_batches(prcxi_simulation: SimulationContext):
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if prcxi_simulation.channel_num != 8:
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pytest.skip("仅在八通道配置下运行")
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handler = prcxi_simulation.handler
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for well in prcxi_simulation.source_plate.children + prcxi_simulation.target_plate.children:
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_ensure_unilabos_extra(well)
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sources = prcxi_simulation.source_plate[0:8]
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targets = prcxi_simulation.target_plate[16:24]
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for idx, src in enumerate(sources):
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_assign_sample_uuid(src, f"batch_{idx}")
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offsets = _zero_offsets(len(targets))
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use_channels = list(range(8))
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asp_vols = [float(i + 1) * 2 for i in range(8)]
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dis_vols = [float(i + 10) for i in range(8)]
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run(
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handler.transfer_liquid(
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sources=sources,
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targets=targets,
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tip_racks=[prcxi_simulation.tip_rack],
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use_channels=use_channels,
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asp_vols=asp_vols,
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dis_vols=dis_vols,
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offsets=offsets,
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mix_times=0,
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)
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)
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_assert_samples_match(sources, targets)
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@pytest.mark.parametrize("mix_stage", ["before", "after", "both"])
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def test_transfer_liquid_mix_stages(prcxi_simulation: SimulationContext, mix_stage: str):
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if prcxi_simulation.channel_num != 1:
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pytest.skip("仅在单通道配置下运行")
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handler = prcxi_simulation.handler
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for well in prcxi_simulation.source_plate.children + prcxi_simulation.target_plate.children:
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_ensure_unilabos_extra(well)
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target = prcxi_simulation.target_plate[70]
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sources = prcxi_simulation.source_plate[80:82]
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for idx, src in enumerate(sources):
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_assign_sample_uuid(src, f"mix_stage_{mix_stage}_{idx}")
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run(
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handler.transfer_liquid(
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sources=sources,
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targets=[target],
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tip_racks=[prcxi_simulation.tip_rack],
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use_channels=[0],
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asp_vols=[4.0, 5.0],
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dis_vols=1,
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offsets=_zero_offsets(len(sources)),
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mix_stage=mix_stage,
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mix_times=2,
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mix_vol=3,
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)
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)
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# mix_stage 前后都应该保留最新源的 sample_uuid
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assert getattr(target, "unilabos_extra", {}).get("sample_uuid") == f"mix_stage_{mix_stage}_1"
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if prcxi_simulation.channel_num != 8:
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pytest.skip("仅在八通道配置下运行")
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handler = prcxi_simulation.handler
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sources = prcxi_simulation.source_plate[0:8]
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targets = prcxi_simulation.target_plate[16:24]
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for idx, src in enumerate(sources):
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_assign_sample_uuid(src, f"batch_{idx}")
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offsets = _zero_offsets(len(targets))
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use_channels = list(range(8))
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asp_vols = [float(i + 1) * 2 for i in range(8)]
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dis_vols = [float(i + 10) for i in range(8)]
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run(
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handler.transfer_liquid(
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sources=sources,
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targets=targets,
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tip_racks=[prcxi_simulation.tip_rack],
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use_channels=use_channels,
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asp_vols=asp_vols,
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dis_vols=dis_vols,
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offsets=offsets,
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mix_stage="after",
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mix_times=2,
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mix_vol=3,
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)
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)
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_assert_samples_match(sources, targets)
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