feat: RNA add guided siRNA manual load gate

- Expose siRNA order and material handles for manual-confirm load workflows.
- Gate scheduler start on explicit material-load confirmation before calling Bioyond RPC.
- Improve lazy API config diagnostics and Sirna warehouse/material resource handling.

unilabos/resources/bioyond/sirna_materials.py

@@ -4,8 +4,8 @@ Defines PyLabRobot resource classes for Bioyond Sirna station materials.
 Each class is decorated with @resource for AST-based registry discovery.
 """
 
-from typing import Optional
 from collections import OrderedDict
+
 from pylabrobot.resources import Plate, TipRack, Container
 
 from unilabos.registry.decorators import resource
@@ -19,20 +19,15 @@ from unilabos.registry.decorators import resource
 class BioyondSirna_G3_200ul_TipRack(TipRack):
     """G3-200ul tip rack for Sirna liquid handling."""
 
-    def __init__(
-        self,
-        name: str,
-        with_tips: bool = True,
-    ):
-        super().__init__(
-            name=name,
-            size_x=127.76,
-            size_y=85.48,
-            size_z=64.0,
-            model="bioyond_sirna_g3_200ul_tip_rack",
-            with_tips=with_tips,
-            ordering=OrderedDict(),  # Empty ordering to satisfy PyLabRobot requirement
-        )
+    def __init__(self, *args, **kwargs):
+        kwargs.setdefault("size_x", 127.76)
+        kwargs.setdefault("size_y", 85.48)
+        kwargs.setdefault("size_z", 64.0)
+        kwargs.setdefault("model", "bioyond_sirna_g3_200ul_tip_rack")
+        kwargs.setdefault("with_tips", True)
+        if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
+            kwargs["ordering"] = OrderedDict()
+        super().__init__(*args, **kwargs)
 
 
 @resource(
@@ -43,20 +38,15 @@ class BioyondSirna_G3_200ul_TipRack(TipRack):
 class BioyondSirna_G3_50ul_TipRack(TipRack):
     """G3-50ul tip rack for Sirna liquid handling."""
 
-    def __init__(
-        self,
-        name: str,
-        with_tips: bool = True,
-    ):
-        super().__init__(
-            name=name,
-            size_x=127.76,
-            size_y=85.48,
-            size_z=64.0,
-            model="bioyond_sirna_g3_50ul_tip_rack",
-            with_tips=with_tips,
-            ordering=OrderedDict(),  # Empty ordering to satisfy PyLabRobot requirement
-        )
+    def __init__(self, *args, **kwargs):
+        kwargs.setdefault("size_x", 127.76)
+        kwargs.setdefault("size_y", 85.48)
+        kwargs.setdefault("size_z", 64.0)
+        kwargs.setdefault("model", "bioyond_sirna_g3_50ul_tip_rack")
+        kwargs.setdefault("with_tips", True)
+        if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
+            kwargs["ordering"] = OrderedDict()
+        super().__init__(*args, **kwargs)
 
 
 @resource(
@@ -67,20 +57,15 @@ class BioyondSirna_G3_50ul_TipRack(TipRack):
 class BioyondSirna_384WellPlate(Plate):
     """384-well plate for Sirna reporter gene detection."""
 
-    def __init__(
-        self,
-        name: str,
-        lid: Optional[object] = None,
-    ):
-        super().__init__(
-            name=name,
-            size_x=127.76,
-            size_y=85.48,
-            size_z=14.35,
-            lid=lid,
-            model="bioyond_sirna_384_well_plate",
-            plate_type="skirted",
-        )
+    def __init__(self, *args, **kwargs):
+        kwargs.setdefault("size_x", 127.76)
+        kwargs.setdefault("size_y", 85.48)
+        kwargs.setdefault("size_z", 14.35)
+        kwargs.setdefault("model", "bioyond_sirna_384_well_plate")
+        kwargs.setdefault("plate_type", "skirted")
+        if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
+            kwargs["ordering"] = OrderedDict()
+        super().__init__(*args, **kwargs)
 
 
 @resource(
@@ -91,20 +76,15 @@ class BioyondSirna_384WellPlate(Plate):
 class BioyondSirna_CellCulturePlate(Plate):
     """Cell culture plate for Sirna experiments."""
 
-    def __init__(
-        self,
-        name: str,
-        lid: Optional[object] = None,
-    ):
-        super().__init__(
-            name=name,
-            size_x=127.76,
-            size_y=85.48,
-            size_z=14.35,
-            lid=lid,
-            model="bioyond_sirna_cell_culture_plate",
-            plate_type="skirted",
-        )
+    def __init__(self, *args, **kwargs):
+        kwargs.setdefault("size_x", 127.76)
+        kwargs.setdefault("size_y", 85.48)
+        kwargs.setdefault("size_z", 14.35)
+        kwargs.setdefault("model", "bioyond_sirna_cell_culture_plate")
+        kwargs.setdefault("plate_type", "skirted")
+        if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
+            kwargs["ordering"] = OrderedDict()
+        super().__init__(*args, **kwargs)
 
 
 @resource(
@@ -115,19 +95,13 @@ class BioyondSirna_CellCulturePlate(Plate):
 class BioyondSirna_ReagentTrough(Container):
     """Reagent trough for Sirna station reagents (RiboGreen, etc.)."""
 
-    def __init__(
-        self,
-        name: str,
-        max_volume: float = 300000.0,  # 300mL default
-    ):
-        super().__init__(
-            name=name,
-            size_x=127.76,
-            size_y=85.48,
-            size_z=44.0,
-            max_volume=max_volume,
-            model="bioyond_sirna_reagent_trough",
-        )
+    def __init__(self, *args, **kwargs):
+        kwargs.setdefault("size_x", 127.76)
+        kwargs.setdefault("size_y", 85.48)
+        kwargs.setdefault("size_z", 44.0)
+        kwargs.setdefault("max_volume", 300000.0)
+        kwargs.setdefault("model", "bioyond_sirna_reagent_trough")
+        super().__init__(*args, **kwargs)
 
 
 # Material type code mapping for dynamic instantiation

unilabos/resources/bioyond/warehouses.py

@@ -4,8 +4,19 @@ from pylabrobot.resources.carrier import ResourceHolder, create_homogeneous_reso
 from unilabos.resources.warehouse import WareHouse, warehouse_factory
 
 
-def bioyond_warehouse_numeric_stack(name: str, rows: int = 10, columns: int = 17) -> 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。"""
+def bioyond_warehouse_numeric_stack(
+    name: str,
+    rows: int = 10,
+    columns: int = 17,
+    bioyond_axis: str = "xy_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).
+    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
     num_items_y = rows
     num_items_z = 1
@@ -33,7 +44,7 @@ def bioyond_warehouse_numeric_stack(name: str, rows: int = 10, columns: int = 17
         for row in range(num_items_y)
         for col in range(num_items_x)
     ]
-    return WareHouse(
+    warehouse = WareHouse(
         name=name,
         size_x=dx + item_dx * num_items_x,
         size_y=dy + item_dy * num_items_y,
@@ -45,23 +56,25 @@ def bioyond_warehouse_numeric_stack(name: str, rows: int = 10, columns: int = 17
         sites={key: holder for key, holder in zip(keys, holders.values())},
         category="warehouse",
     )
+    warehouse.bioyond_axis = bioyond_axis
+    return warehouse
 
 
 # ================ 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)
+    return bioyond_warehouse_numeric_stack(name, rows=1, columns=14, bioyond_axis="xy_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)
+    return bioyond_warehouse_numeric_stack(name, rows=10, columns=17, bioyond_axis="xy_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)
+    return bioyond_warehouse_numeric_stack(name, rows=2, columns=1, bioyond_axis="xy_col_row")
 
 
 # ================ 反应站相关堆栈 ================

unilabos/resources/graphio.py

@@ -869,6 +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。
+                    bioyond_axis = getattr(warehouse, "bioyond_axis", "xy_row_col")
+                    if bioyond_axis == "xy_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)
                     if wh_name == "堆栈1右":
                         y = y - 4  # 将5-8映射到1-4