mirror of
https://github.com/deepmodeling/Uni-Lab-OS
synced 2026-05-24 16:00:03 +00:00
26155b8343
- Add the Bioyond peptide station package with the station-facing Day2 submission flow inlined into BioyondPeptideStation. - Add LIMS sample Excel upload, Day2/Day3 order creation helpers, scheduler/reset controls, and manual-confirm start/reset actions. - Register peptide material PLR resource classes and default peptide material type mappings for runtime resource synchronization. - Add the Bioyond peptide deck definition and warehouse axis/key-axis metadata needed for peptide layout conversion. - Update shared Bioyond warehouse/resource conversion helpers so peptide deck coordinates round-trip correctly. - Include shared Bioyond raw-call debug logging support used by station actions, with a generic local debug output default. - Register the peptide deck in PLR additional resources for deserialization/import visibility. - Exclude private temp_benyao docs, HAR/API inputs, live diagnostics, and siRNA-only station/material files from this handoff commit.
531 lines
16 KiB
Python
531 lines
16 KiB
Python
from pylabrobot.resources import Coordinate
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from pylabrobot.resources.carrier import ResourceHolder, create_homogeneous_resources
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from unilabos.resources.warehouse import WareHouse, warehouse_factory
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class BioyondWareHouse(WareHouse):
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"""Bioyond 仓库，额外保存服务端 x/y 坐标和库位标签语义。"""
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def __init__(self, *args, bioyond_axis: str = "xy_row_col", bioyond_key_axis: str = "row_col", **kwargs):
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super().__init__(*args, **kwargs)
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self.bioyond_axis = bioyond_axis
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self.bioyond_key_axis = bioyond_key_axis
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def serialize(self) -> dict:
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data = super().serialize()
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data["bioyond_axis"] = self.bioyond_axis
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data["bioyond_key_axis"] = self.bioyond_key_axis
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return data
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def bioyond_warehouse_numeric_stack(
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name: str,
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rows: int = 10,
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columns: int = 17,
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bioyond_axis: str = "xy_row_col",
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bioyond_key_axis: str = "row_col",
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frontend_y_flip: bool = False,
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) -> WareHouse:
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"""创建 Bioyond 数字库位堆栈，库位名使用服务端返回的 行-列 格式。
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bioyond_axis: 仓库级别的 Bioyond 坐标轴约定，供 graphio 的坐标映射使用。
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- "xy_row_col" (default): Bioyond x→row, y→col (reaction/peptide 历史约定).
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- "xy_col_row": Bioyond x→col, y→row (Sirna live API 实测约定).
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bioyond_key_axis: 库位标签生成约定。
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- "row_col" (default): 视觉行列和标签行列一致，例如 10 行 x 17 列 → 1-1..10-17。
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- "col_row": 视觉行列转置，但标签仍保持 Bioyond row-col，例如
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17 行 x 10 列 → 1-1..10-17。
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未设置时 graphio 回退到默认 "xy_row_col"，其他调用方保持原行为。
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"""
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num_items_x = columns
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num_items_y = rows
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num_items_z = 1
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dx = 10.0
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dy = 10.0
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dz = 10.0
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item_dx = 147.0
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item_dy = 106.0
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item_dz = 130.0
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resource_size_x = 127.0
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resource_size_y = 86.0
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resource_size_z = 25.0
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size_y = dy + item_dy * num_items_y
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locations = []
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for row in range(num_items_y):
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display_y = dy + row * item_dy
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y = size_y - display_y - resource_size_y if frontend_y_flip else display_y
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for col in range(num_items_x):
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locations.append(Coordinate(dx + col * item_dx, y, dz))
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holders = create_homogeneous_resources(
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klass=ResourceHolder,
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locations=locations,
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resource_size_x=resource_size_x,
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resource_size_y=resource_size_y,
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resource_size_z=resource_size_z,
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name_prefix=name,
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)
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if bioyond_key_axis == "row_col":
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keys = [
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f"{row + 1}-{col + 1}"
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for row in range(num_items_y)
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for col in range(num_items_x)
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]
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elif bioyond_key_axis == "col_row":
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keys = [
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f"{col + 1}-{row + 1}"
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for row in range(num_items_y)
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for col in range(num_items_x)
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]
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else:
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raise ValueError(f"未知 Bioyond 库位标签约定: {bioyond_key_axis!r}")
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warehouse = BioyondWareHouse(
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name=name,
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size_x=dx + item_dx * num_items_x,
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size_y=size_y,
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size_z=dz + item_dz * num_items_z,
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num_items_x=num_items_x,
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num_items_y=num_items_y,
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num_items_z=num_items_z,
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ordering_layout="row-major",
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sites={key: holder for key, holder in zip(keys, holders.values())},
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category="warehouse",
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bioyond_axis=bioyond_axis,
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bioyond_key_axis=bioyond_key_axis,
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)
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return warehouse
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def bioyond_warehouse_live_grid(
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name: str,
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rows: int,
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columns: int,
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slot_keys: list[str] | None = None,
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bioyond_axis: str = "xy_col_row",
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bioyond_key_axis: str = "row_col",
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frontend_y_flip: bool = False,
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) -> WareHouse:
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"""创建 Bioyond 实测库位网格，按服务端 code 保存位点标签。
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默认用于 Peptide live API 返回的坐标：x 是视觉列，y 是视觉行。
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当服务端 code 重复时，为保持 PLR ordering 唯一性，会给后续重复项追加 ``#N``。
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"""
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num_items_x = columns
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num_items_y = rows
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num_items_z = 1
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dx = 10.0
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dy = 10.0
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dz = 10.0
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item_dx = 147.0
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item_dy = 106.0
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item_dz = 130.0
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resource_size_x = 127.0
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resource_size_y = 86.0
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resource_size_z = 25.0
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size_y = dy + item_dy * num_items_y
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locations = []
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for row in range(num_items_y):
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display_y = dy + row * item_dy
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y = size_y - display_y - resource_size_y if frontend_y_flip else display_y
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for col in range(num_items_x):
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locations.append(Coordinate(dx + col * item_dx, y, dz))
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holders = create_homogeneous_resources(
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klass=ResourceHolder,
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locations=locations,
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resource_size_x=resource_size_x,
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resource_size_y=resource_size_y,
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resource_size_z=resource_size_z,
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name_prefix=name,
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)
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keys = slot_keys or [str(index + 1) for index in range(num_items_x * num_items_y)]
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if len(keys) != len(holders):
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raise ValueError(f"{name} 库位数量不匹配: keys={len(keys)}, holders={len(holders)}")
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seen: dict[str, int] = {}
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unique_keys: list[str] = []
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for key in keys:
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count = seen.get(key, 0) + 1
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seen[key] = count
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unique_keys.append(key if count == 1 else f"{key}#{count}")
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return BioyondWareHouse(
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name=name,
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size_x=dx + item_dx * num_items_x,
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size_y=size_y,
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size_z=dz + item_dz * num_items_z,
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num_items_x=num_items_x,
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num_items_y=num_items_y,
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num_items_z=num_items_z,
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ordering_layout="row-major",
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sites={key: holder for key, holder in zip(unique_keys, holders.values())},
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category="warehouse",
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bioyond_axis=bioyond_axis,
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bioyond_key_axis=bioyond_key_axis,
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)
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# ================ 小核酸工作站相关堆栈 ================
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def bioyond_warehouse_sirna_g3_liquid_handler(name: str = "G3移液站") -> WareHouse:
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"""创建小核酸 G3 移液站库位堆栈：显示为 14 行 x 1 列，标签保持 1-1..1-14。"""
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return bioyond_warehouse_numeric_stack(
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name, rows=14, columns=1, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
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)
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def bioyond_warehouse_sirna_automation_stack(name: str = "自动化堆栈") -> WareHouse:
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"""创建小核酸自动化堆栈：显示为 17 行 x 10 列，标签保持 1-1..10-17。"""
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return bioyond_warehouse_numeric_stack(
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name, rows=17, columns=10, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
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)
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def bioyond_warehouse_sirna_centrifuge_balance_plate_stack(name: str = "离心机配平板堆栈") -> WareHouse:
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"""创建小核酸离心机配平板堆栈：显示为 1 行 x 2 列，标签保持 1-1、2-1。"""
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return bioyond_warehouse_numeric_stack(
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name, rows=1, columns=2, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
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)
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# ================ 反应站相关堆栈 ================
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def bioyond_warehouse_1x4x4(name: str) -> WareHouse:
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"""创建BioYond 4x4x1仓库 (左侧堆栈: A01～D04)
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使用行优先排序，前端展示为:
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A01 | A02 | A03 | A04
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B01 | B02 | B03 | B04
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C01 | C02 | C03 | C04
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D01 | D02 | D03 | D04
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"""
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return warehouse_factory(
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name=name,
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num_items_x=4, # 4列
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num_items_y=4, # 4行
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num_items_z=1,
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=147.0,
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item_dy=106.0,
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item_dz=130.0,
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category="warehouse",
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col_offset=0, # 从01开始: A01, A02, A03, A04
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layout="row-major", # ⭐ 改为行优先排序
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)
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def bioyond_warehouse_1x4x4_right(name: str) -> WareHouse:
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"""创建BioYond 4x4x1仓库 (右侧堆栈: A05～D08)"""
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return warehouse_factory(
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name=name,
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num_items_x=4,
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num_items_y=4,
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num_items_z=1,
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=147.0,
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item_dy=106.0,
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item_dz=130.0,
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category="warehouse",
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col_offset=4, # 从05开始: A05, A06, A07, A08
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layout="row-major", # ⭐ 改为行优先排序
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)
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def bioyond_warehouse_density_vial(name: str) -> WareHouse:
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"""创建测量小瓶仓库(测密度) - 竖向排列2列3行
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布局（从下到上，从左到右）：
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| A03 | B03 | ← 顶部
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| A02 | B02 | ← 中部
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| A01 | B01 | ← 底部
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"""
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return warehouse_factory(
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name=name,
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num_items_x=2, # 2列（A, B）
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num_items_y=3, # 3行（01-03，从下到上）
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num_items_z=1, # 1层
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=40.0, # 列间距（A到B的横向距离）
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item_dy=40.0, # 行间距（01到02到03的竖向距离）
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item_dz=50.0,
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# ⭐ 竖向warehouse：槽位尺寸也是竖向的（小瓶已经是正方形，无需调整）
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resource_size_x=30.0,
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resource_size_y=30.0,
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resource_size_z=12.0,
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category="warehouse",
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col_offset=0,
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layout="vertical-col-major", # ⭐ 竖向warehouse专用布局
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)
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def bioyond_warehouse_reagent_storage(name: str) -> WareHouse:
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"""创建BioYond站内试剂存放堆栈 - 竖向排列1列2行
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布局（竖向，从下到上）：
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| A02 | ← 顶部
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| A01 | ← 底部
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"""
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return warehouse_factory(
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name=name,
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num_items_x=1, # 1列
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num_items_y=2, # 2行（01-02，从下到上）
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num_items_z=1, # 1层
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=96.0, # 列间距（这里只有1列，不重要）
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item_dy=137.0, # 行间距（A01到A02的竖向距离）
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item_dz=120.0,
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# ⭐ 竖向warehouse：交换槽位尺寸，使槽位框也是竖向的
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resource_size_x=86.0, # 原来的 resource_size_y
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resource_size_y=127.0, # 原来的 resource_size_x
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resource_size_z=25.0,
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category="warehouse",
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layout="vertical-col-major", # ⭐ 竖向warehouse专用布局
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)
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def bioyond_warehouse_tipbox_storage_left(name: str) -> WareHouse:
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"""创建BioYond站内Tip盒堆栈左侧部分（A02～B03），2列2行"""
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return warehouse_factory(
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name=name,
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num_items_x=2, # 2列
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num_items_y=2, # 2行（A-B）
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num_items_z=1, # 1层
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=137.0,
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item_dy=96.0,
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item_dz=120.0,
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category="warehouse",
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col_offset=1, # 从02开始: A02, A03
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layout="row-major",
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)
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def bioyond_warehouse_tipbox_storage_right(name: str) -> WareHouse:
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"""创建BioYond站内Tip盒堆栈右侧部分（A01～B01），1列2行"""
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return warehouse_factory(
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name=name,
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num_items_x=1, # 1列
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num_items_y=2, # 2行（A-B）
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num_items_z=1, # 1层
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=137.0,
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item_dy=96.0,
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item_dz=120.0,
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category="warehouse",
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col_offset=0, # 从01开始: A01
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layout="row-major",
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)
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def bioyond_warehouse_liquid_preparation(name: str) -> WareHouse:
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"""已弃用,创建BioYond移液站内10%分装液体准备仓库（A01～B04）"""
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return warehouse_factory(
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name=name,
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num_items_x=4, # 4列（01-04）
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num_items_y=2, # 2行（A-B）
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num_items_z=1, # 1层
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=137.0,
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item_dy=96.0,
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item_dz=120.0,
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category="warehouse",
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col_offset=0,
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layout="row-major",
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)
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# ================ 配液站相关堆栈 ================
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def bioyond_warehouse_reagent_stack(name: str) -> WareHouse:
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"""创建BioYond 试剂堆栈 2x4x1 (2行×4列: A01-A04, B01-B04)
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使用行优先排序，前端展示为:
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A01 | A02 | A03 | A04
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B01 | B02 | B03 | B04
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"""
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return warehouse_factory(
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name=name,
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num_items_x=4, # 4列 (01-04)
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num_items_y=2, # 2行 (A-B)
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num_items_z=1, # 1层
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=147.0,
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item_dy=106.0,
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item_dz=130.0,
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category="warehouse",
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col_offset=0, # 从01开始
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layout="row-major", # ⭐ 使用行优先排序: A01,A02,A03,A04, B01,B02,B03,B04
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)
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# 定义bioyond的堆栈
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# =================== Other ===================
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def bioyond_warehouse_1x4x2(name: str) -> WareHouse:
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"""创建BioYond 4x2x1仓库"""
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return warehouse_factory(
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name=name,
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num_items_x=1,
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num_items_y=4,
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num_items_z=2,
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=137.0,
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item_dy=96.0,
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item_dz=120.0,
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category="warehouse",
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removed_positions=None
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)
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def bioyond_warehouse_1x2x2(name: str) -> WareHouse:
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"""创建BioYond 1x2x2仓库"""
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return warehouse_factory(
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name=name,
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num_items_x=1,
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num_items_y=2,
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num_items_z=2,
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=137.0,
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item_dy=96.0,
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item_dz=120.0,
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category="warehouse",
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)
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def bioyond_warehouse_10x1x1(name: str) -> WareHouse:
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"""创建BioYond 10x1x1仓库"""
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return warehouse_factory(
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name=name,
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num_items_x=10,
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num_items_y=1,
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num_items_z=1,
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dx=10.0,
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dy=10.0,
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dz=10.0,
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item_dx=137.0,
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item_dy=96.0,
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item_dz=120.0,
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category="warehouse",
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)
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|
||
def bioyond_warehouse_1x3x3(name: str) -> WareHouse:
|
||
"""创建BioYond 1x3x3仓库"""
|
||
return warehouse_factory(
|
||
name=name,
|
||
num_items_x=1,
|
||
num_items_y=3,
|
||
num_items_z=3,
|
||
dx=10.0,
|
||
dy=10.0,
|
||
dz=10.0,
|
||
item_dx=137.0,
|
||
item_dy=96.0,
|
||
item_dz=120.0,
|
||
category="warehouse",
|
||
)
|
||
|
||
def bioyond_warehouse_2x1x3(name: str) -> WareHouse:
|
||
"""创建BioYond 2x1x3仓库"""
|
||
return warehouse_factory(
|
||
name=name,
|
||
num_items_x=2,
|
||
num_items_y=1,
|
||
num_items_z=3,
|
||
dx=10.0,
|
||
dy=10.0,
|
||
dz=10.0,
|
||
item_dx=137.0,
|
||
item_dy=96.0,
|
||
item_dz=120.0,
|
||
category="warehouse",
|
||
)
|
||
|
||
def bioyond_warehouse_3x3x1(name: str) -> WareHouse:
|
||
"""创建BioYond 3x3x1仓库"""
|
||
return warehouse_factory(
|
||
name=name,
|
||
num_items_x=3,
|
||
num_items_y=3,
|
||
num_items_z=1,
|
||
dx=10.0,
|
||
dy=10.0,
|
||
dz=10.0,
|
||
item_dx=137.0,
|
||
item_dy=96.0,
|
||
item_dz=120.0,
|
||
category="warehouse",
|
||
)
|
||
|
||
def bioyond_warehouse_5x1x1(name: str) -> WareHouse:
|
||
"""已弃用：创建BioYond 5x1x1仓库"""
|
||
return warehouse_factory(
|
||
name=name,
|
||
num_items_x=5,
|
||
num_items_y=1,
|
||
num_items_z=1,
|
||
dx=10.0,
|
||
dy=10.0,
|
||
dz=10.0,
|
||
item_dx=137.0,
|
||
item_dy=96.0,
|
||
item_dz=120.0,
|
||
category="warehouse",
|
||
)
|
||
|
||
def bioyond_warehouse_3x3x1_2(name: str) -> WareHouse:
|
||
"""已弃用：创建BioYond 3x3x1仓库"""
|
||
return warehouse_factory(
|
||
name=name,
|
||
num_items_x=3,
|
||
num_items_y=3,
|
||
num_items_z=1,
|
||
dx=12.0,
|
||
dy=12.0,
|
||
dz=12.0,
|
||
item_dx=137.0,
|
||
item_dy=96.0,
|
||
item_dz=120.0,
|
||
category="warehouse",
|
||
)
|
||
|
||
def bioyond_warehouse_liquid_and_lid_handling(name: str) -> WareHouse:
|
||
"""创建BioYond开关盖加液模块台面"""
|
||
return warehouse_factory(
|
||
name=name,
|
||
num_items_x=2,
|
||
num_items_y=5,
|
||
num_items_z=1,
|
||
dx=10.0,
|
||
dy=10.0,
|
||
dz=10.0,
|
||
item_dx=137.0,
|
||
item_dy=96.0,
|
||
item_dz=120.0,
|
||
category="warehouse",
|
||
removed_positions=None
|
||
)
|
||
|
||
def bioyond_warehouse_1x8x4(name: str) -> WareHouse:
|
||
"""创建BioYond 8x4x1反应站堆栈（A01～D08）"""
|
||
return warehouse_factory(
|
||
name=name,
|
||
num_items_x=8, # 8列（01-08）
|
||
num_items_y=4, # 4行（A-D）
|
||
num_items_z=1, # 1层
|
||
dx=10.0,
|
||
dy=10.0,
|
||
dz=10.0,
|
||
item_dx=147.0,
|
||
item_dy=106.0,
|
||
item_dz=130.0,
|
||
category="warehouse",
|
||
)
|