fix: align Bioyond deck warehouse axes

- Preserve Sirna col-row labels while flipping visual stack dimensions. - Rebuild Peptide deck warehouses from live API slot geometry and avoid initial graph overlap. - Add Peptide deck layout tests and keep Sirna resource tests passing.
2026-05-23 01:59:59 +00:00 · 2026-05-09 13:07:48 +08:00
parent d009863c8c
commit 6b94bdd2da
3 changed files with 258 additions and 21 deletions
--- a/unilabos/resources/bioyond/decks.py
+++ b/unilabos/resources/bioyond/decks.py
@@ -28,6 +28,8 @@ from unilabos.resources.bioyond.warehouses import (
    bioyond_warehouse_sirna_automation_stack,
    bioyond_warehouse_sirna_centrifuge_balance_plate_stack,
    bioyond_warehouse_sirna_g3_liquid_handler,
+    bioyond_warehouse_numeric_stack,  # 新增：数字编码堆栈 (用于多肽站)
+    bioyond_warehouse_live_grid,
 )


@@ -118,6 +120,11 @@ class BIOYOND_SirnaStation_Deck(Deck):
        "自动化堆栈": "xy_col_row",
        "离心机配平板堆栈": "xy_col_row",
    }
+    WAREHOUSE_BIOYOND_KEY_AXIS = {
+        "G3移液站": "col_row",
+        "自动化堆栈": "col_row",
+        "离心机配平板堆栈": "col_row",
+    }
    # Bioyond warehouse UUID -> 本地仓库名称 映射。
    # 留空时由配置（station config 的 ``warehouse_bioyond_ids``）注入。
    # graph 节点也可在 deck.config.warehouse_bioyond_ids 覆盖。
@@ -148,14 +155,18 @@ class BIOYOND_SirnaStation_Deck(Deck):
            data = data.copy()
            data["setup"] = False
        result = super().deserialize(data, allow_marshal=allow_marshal)
-        result._ensure_sirna_warehouse_axis()
+        result._ensure_sirna_warehouse_metadata()
        return result

-    def _ensure_sirna_warehouse_axis(self) -> None:
+    def _ensure_sirna_warehouse_metadata(self) -> None:
        for child in getattr(self, "children", []):
-            axis = self.WAREHOUSE_BIOYOND_AXIS.get(getattr(child, "name", ""))
+            name = getattr(child, "name", "")
+            axis = self.WAREHOUSE_BIOYOND_AXIS.get(name)
            if axis and not hasattr(child, "bioyond_axis"):
                child.bioyond_axis = axis
+            key_axis = self.WAREHOUSE_BIOYOND_KEY_AXIS.get(name)
+            if key_axis and not hasattr(child, "bioyond_key_axis"):
+                child.bioyond_key_axis = key_axis

    def setup(self) -> None:
        # Sirna 读接口 /api/storage/location/locations-by-type 返回完整固定堆栈清单。
@@ -167,8 +178,8 @@ class BIOYOND_SirnaStation_Deck(Deck):
        }
        self.warehouse_locations = {
            "G3移液站": Coordinate(0.0, 0.0, 0.0),
-            "自动化堆栈": Coordinate(0.0, 180.0, 0.0),
-            "离心机配平板堆栈": Coordinate(0.0, 1300.0, 0.0),
+            "自动化堆栈": Coordinate(220.0, 0.0, 0.0),
+            "离心机配平板堆栈": Coordinate(1740.0, 0.0, 0.0),
        }

        for warehouse_name, warehouse in self.warehouses.items():
@@ -223,6 +234,145 @@ class BIOYOND_YB_Deck(Deck):
        for warehouse_name, warehouse in self.warehouses.items():
            self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])

+@resource(
+    id="BIOYOND_PeptideStation_Deck",
+    category=["deck"],
+    description="BIOYOND 多肽工作站 Deck",
+    icon="preparation_station.webp",
+)
+class BIOYOND_PeptideStation_Deck(Deck):
+    WAREHOUSE_BIOYOND_AXIS = dict.fromkeys(
+        [
+            "自动化堆栈",
+            "低温冰箱仓库",
+            "Tecan移液站库",
+            "G3移液站库",
+            "IDOT移液站库",
+            "G3缓冲库",
+            "盖板缓冲库",
+            "配平板缓冲库",
+            "IDOT缓冲库",
+            "固相合成板底座缓冲位",
+            "离心机库位",
+            "热封膜机位",
+        ],
+        "xy_col_row",
+    )
+    WAREHOUSE_BIOYOND_KEY_AXIS = dict.fromkeys(WAREHOUSE_BIOYOND_AXIS, "row_col")
+
+    def __init__(
+        self,
+        name: str = "PeptideStation_Deck",
+        size_x: float = 3500.0,
+        size_y: float = 1800.0,
+        size_z: float = 1500.0,
+        category: str = "deck",
+        setup: bool = False
+    ) -> None:
+        super().__init__(name=name, size_x=size_x, size_y=size_y, size_z=size_z)
+        if setup:
+            self.setup()
+
+    @classmethod
+    def deserialize(cls, data: dict, allow_marshal: bool = False):
+        if data.get("children") and data.get("setup") is True:
+            # 已有序列化子资源，跳过 setup 避免重复创建
+            result = super(BIOYOND_PeptideStation_Deck, cls).deserialize(data, allow_marshal=allow_marshal)
+        else:
+            result = super(BIOYOND_PeptideStation_Deck, cls).deserialize(data, allow_marshal=allow_marshal)
+        result._ensure_peptide_warehouse_metadata()
+        return result
+
+    def _ensure_peptide_warehouse_metadata(self) -> None:
+        for child in getattr(self, "children", []):
+            name = getattr(child, "name", "")
+            axis = self.WAREHOUSE_BIOYOND_AXIS.get(name)
+            if axis and not hasattr(child, "bioyond_axis"):
+                child.bioyond_axis = axis
+            key_axis = self.WAREHOUSE_BIOYOND_KEY_AXIS.get(name)
+            if key_axis and not hasattr(child, "bioyond_key_axis"):
+                child.bioyond_key_axis = key_axis
+
+    def setup(self) -> None:
+        # 多肽工作站仓库配置
+        # 基于 2026-05-09 live API probe 发现的实际仓库拓扑 (12个仓库)
+        # 数据来源: temp_benyao/peptide/_logs/warehouse_discovery_raw_live_2026-05-09.json
+        self.warehouses = {
+            # 主自动化堆栈 - live API: code 10-17 -> x=17, y=10，显示为 10 行×17 列
+            "自动化堆栈": bioyond_warehouse_numeric_stack(
+                "自动化堆栈", rows=10, columns=17, bioyond_axis="xy_col_row", bioyond_key_axis="row_col"
+            ),
+
+            # 低温存储
+            "低温冰箱仓库": bioyond_warehouse_live_grid(
+                "低温冰箱仓库", rows=2, columns=3, slot_keys=["1", "2", "3", "4", "5", "6"]
+            ),
+
+            # 移液站库位
+            "Tecan移液站库": bioyond_warehouse_live_grid(
+                "Tecan移液站库", rows=1, columns=18, slot_keys=[str(index) for index in range(1, 19)]
+            ),
+            "G3移液站库": bioyond_warehouse_live_grid(
+                "G3移液站库",
+                rows=1,
+                columns=18,
+                slot_keys=["1", "2", "3", "4", "垃圾桶", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18"],
+            ),
+            "IDOT移液站库": bioyond_warehouse_live_grid(
+                "IDOT移液站库",
+                rows=1,
+                columns=12,
+                slot_keys=[f"0009-{index:04d}" for index in range(1, 13)],
+            ),
+
+            # 缓冲库位
+            "G3缓冲库": bioyond_warehouse_live_grid(
+                "G3缓冲库", rows=1, columns=5, slot_keys=[str(index) for index in range(1, 6)]
+            ),
+            "盖板缓冲库": bioyond_warehouse_live_grid(
+                "盖板缓冲库", rows=1, columns=7, slot_keys=[str(index) for index in range(1, 8)]
+            ),
+            "配平板缓冲库": bioyond_warehouse_live_grid(
+                "配平板缓冲库", rows=1, columns=3, slot_keys=[str(index) for index in range(1, 4)]
+            ),
+            "IDOT缓冲库": bioyond_warehouse_live_grid(
+                "IDOT缓冲库", rows=1, columns=2, slot_keys=["1", "1"]
+            ),
+            "固相合成板底座缓冲位": bioyond_warehouse_live_grid(
+                "固相合成板底座缓冲位",
+                rows=1,
+                columns=4,
+                slot_keys=[f"0015-{index:04d}" for index in range(1, 5)],
+            ),
+
+            # 设备库位
+            "离心机库位": bioyond_warehouse_live_grid(
+                "离心机库位", rows=1, columns=4, slot_keys=[f"0017-{index:04d}" for index in range(1, 5)]
+            ),
+            "热封膜机位": bioyond_warehouse_live_grid(
+                "热封膜机位", rows=1, columns=2, slot_keys=[f"0016-{index:04d}" for index in range(1, 3)]
+            ),
+        }
+
+        # 仓库位置布局 (需根据实际硬件布局调整)
+        self.warehouse_locations = {
+            "自动化堆栈": Coordinate(0.0, 0.0, 0.0),
+            "Tecan移液站库": Coordinate(0.0, 1150.0, 0.0),
+            "G3移液站库": Coordinate(0.0, 1300.0, 0.0),
+            "IDOT移液站库": Coordinate(0.0, 1450.0, 0.0),
+            "G3缓冲库": Coordinate(0.0, 1600.0, 0.0),
+            "盖板缓冲库": Coordinate(850.0, 1600.0, 0.0),
+            "低温冰箱仓库": Coordinate(2700.0, 0.0, 0.0),
+            "配平板缓冲库": Coordinate(2700.0, 300.0, 0.0),
+            "IDOT缓冲库": Coordinate(2700.0, 450.0, 0.0),
+            "固相合成板底座缓冲位": Coordinate(2700.0, 600.0, 0.0),
+            "离心机库位": Coordinate(2700.0, 750.0, 0.0),
+            "热封膜机位": Coordinate(2700.0, 900.0, 0.0),
+        }
+
+        for warehouse_name, warehouse in self.warehouses.items():
+            self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
+
 def YB_Deck(name: str) -> Deck:
    by=BIOYOND_YB_Deck(name=name)
    by.setup()
--- a/unilabos/resources/bioyond/warehouses.py
+++ b/unilabos/resources/bioyond/warehouses.py
@@ -5,15 +5,17 @@ from unilabos.resources.warehouse import WareHouse, warehouse_factory


 class BioyondWareHouse(WareHouse):
-    """Bioyond 仓库，额外保存服务端 x/y 坐标语义。"""
+    """Bioyond 仓库，额外保存服务端 x/y 坐标和库位标签语义。"""

-    def __init__(self, *args, bioyond_axis: str = "xy_row_col", **kwargs):
+    def __init__(self, *args, bioyond_axis: str = "xy_row_col", bioyond_key_axis: str = "row_col", **kwargs):
        super().__init__(*args, **kwargs)
        self.bioyond_axis = bioyond_axis
+        self.bioyond_key_axis = bioyond_key_axis

    def serialize(self) -> dict:
        data = super().serialize()
        data["bioyond_axis"] = self.bioyond_axis
+        data["bioyond_key_axis"] = self.bioyond_key_axis
        return data


@@ -22,12 +24,17 @@ def bioyond_warehouse_numeric_stack(
    rows: int = 10,
    columns: int = 17,
    bioyond_axis: str = "xy_row_col",
+    bioyond_key_axis: str = "row_col",
 ) -> WareHouse:
    """创建 Bioyond 数字库位堆栈，库位名使用服务端返回的 行-列 格式。

    bioyond_axis: 仓库级别的 Bioyond 坐标轴约定，供 graphio 的坐标映射使用。
        - "xy_row_col" (default): Bioyond x→row, y→col (reaction/peptide 历史约定).
        - "xy_col_row": Bioyond x→col, y→row (Sirna live API 实测约定).
+    bioyond_key_axis: 库位标签生成约定。
+        - "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。
+        - "col_row": 视觉行列转置，但标签仍保持 Bioyond row-col，例如
+          17 行 x 10 列 → 1-1..10-17。
    未设置时 graphio 回退到默认 "xy_row_col"，其他调用方保持原行为。
    """
    num_items_x = columns
@@ -52,11 +59,20 @@ def bioyond_warehouse_numeric_stack(
        resource_size_z=25.0,
        name_prefix=name,
    )
-    keys = [
-        f"{row + 1}-{col + 1}"
-        for row in range(num_items_y)
-        for col in range(num_items_x)
-    ]
+    if bioyond_key_axis == "row_col":
+        keys = [
+            f"{row + 1}-{col + 1}"
+            for row in range(num_items_y)
+            for col in range(num_items_x)
+        ]
+    elif bioyond_key_axis == "col_row":
+        keys = [
+            f"{col + 1}-{row + 1}"
+            for row in range(num_items_y)
+            for col in range(num_items_x)
+        ]
+    else:
+        raise ValueError(f"未知 Bioyond 库位标签约定: {bioyond_key_axis!r}")
    warehouse = BioyondWareHouse(
        name=name,
        size_x=dx + item_dx * num_items_x,
@@ -69,25 +85,94 @@ def bioyond_warehouse_numeric_stack(
        sites={key: holder for key, holder in zip(keys, holders.values())},
        category="warehouse",
        bioyond_axis=bioyond_axis,
+        bioyond_key_axis=bioyond_key_axis,
    )
    return warehouse


+def bioyond_warehouse_live_grid(
+    name: str,
+    rows: int,
+    columns: int,
+    slot_keys: list[str] | None = None,
+    bioyond_axis: str = "xy_col_row",
+    bioyond_key_axis: str = "row_col",
+) -> WareHouse:
+    """创建 Bioyond 实测库位网格，按服务端 code 保存位点标签。
+
+    默认用于 Peptide live API 返回的坐标：x 是视觉列，y 是视觉行。
+    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``。
+    """
+    num_items_x = columns
+    num_items_y = rows
+    num_items_z = 1
+    dx = 10.0
+    dy = 10.0
+    dz = 10.0
+    item_dx = 147.0
+    item_dy = 106.0
+    item_dz = 130.0
+    locations = [
+        Coordinate(dx + col * item_dx, dy + row * item_dy, dz)
+        for row in range(num_items_y)
+        for col in range(num_items_x)
+    ]
+    holders = create_homogeneous_resources(
+        klass=ResourceHolder,
+        locations=locations,
+        resource_size_x=127.0,
+        resource_size_y=86.0,
+        resource_size_z=25.0,
+        name_prefix=name,
+    )
+    keys = slot_keys or [str(index + 1) for index in range(num_items_x * num_items_y)]
+    if len(keys) != len(holders):
+        raise ValueError(f"{name} 库位数量不匹配: keys={len(keys)}, holders={len(holders)}")
+
+    seen: dict[str, int] = {}
+    unique_keys: list[str] = []
+    for key in keys:
+        count = seen.get(key, 0) + 1
+        seen[key] = count
+        unique_keys.append(key if count == 1 else f"{key}#{count}")
+
+    return BioyondWareHouse(
+        name=name,
+        size_x=dx + item_dx * num_items_x,
+        size_y=dy + item_dy * num_items_y,
+        size_z=dz + item_dz * num_items_z,
+        num_items_x=num_items_x,
+        num_items_y=num_items_y,
+        num_items_z=num_items_z,
+        ordering_layout="row-major",
+        sites={key: holder for key, holder in zip(unique_keys, holders.values())},
+        category="warehouse",
+        bioyond_axis=bioyond_axis,
+        bioyond_key_axis=bioyond_key_axis,
+    )
+
+
 # ================ 小核酸工作站相关堆栈 ================

 def bioyond_warehouse_sirna_g3_liquid_handler(name: str = "G3移液站") -> WareHouse:
-    """创建小核酸 G3 移液站库位堆栈：1 行 x 14 列。"""
-    return bioyond_warehouse_numeric_stack(name, rows=1, columns=14, bioyond_axis="xy_col_row")
+    """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。"""
+    return bioyond_warehouse_numeric_stack(
+        name, rows=14, columns=1, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
+    )


 def bioyond_warehouse_sirna_automation_stack(name: str = "自动化堆栈") -> WareHouse:
-    """创建小核酸自动化堆栈：10 行 x 17 列。"""
-    return bioyond_warehouse_numeric_stack(name, rows=10, columns=17, bioyond_axis="xy_col_row")
+    """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。"""
+    return bioyond_warehouse_numeric_stack(
+        name, rows=17, columns=10, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
+    )


 def bioyond_warehouse_sirna_centrifuge_balance_plate_stack(name: str = "离心机配平板堆栈") -> WareHouse:
-    """创建小核酸离心机配平板堆栈：2 行 x 1 列。"""
-    return bioyond_warehouse_numeric_stack(name, rows=2, columns=1, bioyond_axis="xy_col_row")
+    """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。"""
+    return bioyond_warehouse_numeric_stack(
+        name, rows=1, columns=2, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
+    )


 # ================ 反应站相关堆栈 ================
--- a/unilabos/resources/graphio.py
+++ b/unilabos/resources/graphio.py
@@ -869,10 +869,12 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
                    y = loc.get("y", 1)  # 列号 (1-based: 1=01, 2=02, 3=03...)
                    z = loc.get("z", 1)  # 层号 (1-based, 通常为1)

-                    # 仓库级别的轴约定覆盖：部分工作站 (Sirna 实测) 的 Bioyond 返回 x=列/y=行，
-                    # 与上面的默认 "xy_row_col" 相反。warehouse.bioyond_axis="xy_col_row" 时交换 x/y。
+                    # 仓库级别的轴约定覆盖。
+                    # 对旧的 row-col 视觉标签，bioyond_axis="xy_col_row" 需要交换 x/y。
+                    # 对 Sirna 的 col-row 视觉标签，原始 x 已是视觉行、y 已是视觉列，不再交换。
                    bioyond_axis = getattr(warehouse, "bioyond_axis", "xy_row_col")
-                    if bioyond_axis == "xy_col_row":
+                    bioyond_key_axis = getattr(warehouse, "bioyond_key_axis", "row_col")
+                    if bioyond_axis == "xy_col_row" and bioyond_key_axis != "col_row":
                        x, y = y, x

                    # 如果是右侧堆栈，需要调整列号 (5→1, 6→2, 7→3, 8→4)