add layout serializer & converter

Corrects resource assignment in ItemizedCarrier by using the correct spot key from _ordering. Updates graphio to use 'typeName' instead of 'name' for type mapping in resource_bioyond_to_plr. Renames DummyWorkstation to BioyondWorkstation in workstation_http_service for clarity.

test/resources/test_resourcetreeset.py

@@ -0,0 +1,68 @@
+import pytest
+import json
+import os
+
+from pylabrobot.resources import Resource as ResourcePLR
+from unilabos.resources.graphio import resource_bioyond_to_plr
+from unilabos.ros.nodes.resource_tracker import ResourceTreeSet
+from unilabos.registry.registry import lab_registry
+
+from unilabos.resources.bioyond.decks import BIOYOND_PolymerReactionStation_Deck
+
+lab_registry.setup()
+
+
+type_mapping = {
+    "烧杯": ("BIOYOND_PolymerStation_1FlaskCarrier", "3a14196b-24f2-ca49-9081-0cab8021bf1a"),
+    "试剂瓶": ("BIOYOND_PolymerStation_1BottleCarrier", ""),
+    "样品板": ("BIOYOND_PolymerStation_6StockCarrier", "3a14196e-b7a0-a5da-1931-35f3000281e9"),
+    "分装板": ("BIOYOND_PolymerStation_6VialCarrier", "3a14196e-5dfe-6e21-0c79-fe2036d052c4"),
+    "样品瓶": ("BIOYOND_PolymerStation_Solid_Stock", "3a14196a-cf7d-8aea-48d8-b9662c7dba94"),
+    "90%分装小瓶": ("BIOYOND_PolymerStation_Solid_Vial", "3a14196c-cdcf-088d-dc7d-5cf38f0ad9ea"),
+    "10%分装小瓶": ("BIOYOND_PolymerStation_Liquid_Vial", "3a14196c-76be-2279-4e22-7310d69aed68"),
+}
+
+
+@pytest.fixture
+def bioyond_materials_reaction() -> list[dict]:
+    print("加载 BioYond 物料数据...")
+    print(os.getcwd())
+    with open("bioyond_materials_reaction.json", "r", encoding="utf-8") as f:
+        data = json.load(f)
+    print(f"加载了 {len(data)} 条物料数据")
+    return data
+
+
+@pytest.fixture
+def bioyond_materials_liquidhandling_1() -> list[dict]:
+    print("加载 BioYond 物料数据...")
+    print(os.getcwd())
+    with open("bioyond_materials_liquidhandling_1.json", "r", encoding="utf-8") as f:
+        data = json.load(f)
+    print(f"加载了 {len(data)} 条物料数据")
+    return data
+
+
+@pytest.fixture
+def bioyond_materials_liquidhandling_2() -> list[dict]:
+    print("加载 BioYond 物料数据...")
+    print(os.getcwd())
+    with open("bioyond_materials_liquidhandling_2.json", "r", encoding="utf-8") as f:
+        data = json.load(f)
+    print(f"加载了 {len(data)} 条物料数据")
+    return data
+
+
+@pytest.mark.parametrize("materials_fixture", [
+    "bioyond_materials_reaction",
+    "bioyond_materials_liquidhandling_1",
+])
+def test_resourcetreeset_from_plr(materials_fixture, request) -> list[dict]:
+    materials = request.getfixturevalue(materials_fixture)
+    deck = BIOYOND_PolymerReactionStation_Deck("test_deck")
+    output = resource_bioyond_to_plr(materials, type_mapping=type_mapping, deck=deck)
+    print(deck.summary())
+
+    r = ResourceTreeSet.from_plr_resources([deck])
+    print(r.dump())
+    # json.dump(deck.serialize(), open("test.json", "w", encoding="utf-8"), indent=4)

unilabos/devices/workstation/bioyond_studio/reaction_station.py

@@ -545,7 +545,7 @@ class BioyondReactionStation(BioyondWorkstation):
 
         # 清空工作流序列和参数，防止下次执行时累积重复
         self.pending_task_params = []
-        self.clear_workflows()  
+        self.clear_workflows()  # 清空工作流序列，避免重复累积
 
         # print(f"\n✅ 任务创建成功: {result}")
         # print(f"\n✅ 任务创建成功")

unilabos/devices/workstation/workstation_http_service.py

@@ -668,7 +668,7 @@ __all__ = [
 
 if __name__ == "__main__":
     # 简单测试HTTP服务
-    class DummyWorkstation:
+    class BioyondWorkstation:
         device_id = "WS-001"
         
         def process_step_finish_report(self, report_request):

unilabos/resources/graphio.py

@@ -643,15 +643,15 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
             for detail in material["detail"]:
                 number = (
                     (detail.get("z", 0) - 1) * plr_material.num_items_x * plr_material.num_items_y
-                    + (detail.get("x", 0) - 1) * plr_material.num_items_x
-                    + (detail.get("y", 0) - 1)
+                    + (detail.get("y", 0) - 1) * plr_material.num_items_y
+                    + (detail.get("x", 0) - 1)
                 )
                 bottle = plr_material[number]
-                if detail["name"] in type_mapping:
+                if detail["typeName"] in type_mapping:
                     # plr_material.unassign_child_resource(bottle)
                     plr_material.sites[number] = None
                     plr_material[number] = initialize_resource(
-                        {"name": f'{detail["name"]}_{number}', "class": type_mapping[detail["name"]][0]}, resource_type=ResourcePLR
+                        {"name": f'{detail["name"]}_{number}', "class": type_mapping[detail["typeName"]][0]}, resource_type=ResourcePLR
                     )
                 else:
                     bottle.tracker.liquids = [

unilabos/resources/itemized_carrier.py

@@ -74,6 +74,7 @@ class ItemizedCarrier(ResourcePLR):
     num_items_x: int = 0,
     num_items_y: int = 0,
     num_items_z: int = 0,
+    layout: str = "x-y",
     sites: Optional[Dict[Union[int, str], Optional[ResourcePLR]]] = None,
     category: Optional[str] = "carrier",
     model: Optional[str] = None,
@@ -88,6 +89,8 @@ class ItemizedCarrier(ResourcePLR):
     )
     self.num_items = len(sites)
     self.num_items_x, self.num_items_y, self.num_items_z = num_items_x, num_items_y, num_items_z
+    self.layout = "z-y" if self.num_items_z > 1 and self.num_items_x == 1 else "x-z" if self.num_items_z > 1 and self.num_items_y == 1 else "x-y"
+
     if isinstance(sites, dict):
       sites = sites or {}
       self.sites: List[Optional[ResourcePLR]] = list(sites.values())
@@ -150,7 +153,7 @@ class ItemizedCarrier(ResourcePLR):
   def assign_resource_to_site(self, resource: ResourcePLR, spot: int):
     if self.sites[spot] is not None and not isinstance(self.sites[spot], ResourceHolder):
       raise ValueError(f"spot {spot} already has a resource, {resource}")
-    self.assign_child_resource(resource, location=self.child_locations.get(str(spot)), spot=spot)
+    self.assign_child_resource(resource, location=self.child_locations.get(list(self._ordering.keys())[spot]), spot=spot)
 
   def unassign_child_resource(self, resource: ResourcePLR):
     found = False
@@ -403,6 +406,7 @@ class ItemizedCarrier(ResourcePLR):
       "num_items_x": self.num_items_x,
       "num_items_y": self.num_items_y,
       "num_items_z": self.num_items_z,
+      "layout": self.layout,
       "sites": [{
         "label": str(identifier),
         "visible": True if self[identifier] is not None else False,

unilabos/resources/warehouse.py

@@ -5,10 +5,13 @@ from pylabrobot.resources.carrier import ResourceHolder, create_homogeneous_reso
 from unilabos.resources.itemized_carrier import ItemizedCarrier, ResourcePLR
 
 
+LETTERS = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+
+
 def warehouse_factory(
     name: str,
-    num_items_x: int = 4,
-    num_items_y: int = 1,
+    num_items_x: int = 1,
+    num_items_y: int = 4,
     num_items_z: int = 4,
     dx: float = 137.0,
     dy: float = 96.0,
@@ -33,13 +36,16 @@ def warehouse_factory(
                 locations.append(Coordinate(x, y, z))
     if removed_positions:
         locations = [loc for i, loc in enumerate(locations) if i not in removed_positions]
-    sites = create_homogeneous_resources(
+    _sites = create_homogeneous_resources(
         klass=ResourceHolder,
         locations=locations,
         resource_size_x=127.0,
         resource_size_y=86.0,
         name_prefix=name,
     )
+    len_x, len_y = (num_items_x, num_items_y) if num_items_z == 1 else (num_items_y, num_items_z) if num_items_x == 1 else (num_items_x, num_items_z)
+    keys = [f"{LETTERS[j]}{i + 1}" for i in range(len_x) for j in range(len_y)]
+    sites = {i: site for i, site in zip(keys, _sites.values())}
     
     return WareHouse(
         name=name,

unilabos/ros/nodes/resource_tracker.py

@@ -32,7 +32,7 @@ class ResourceDictPositionObject(BaseModel):
 class ResourceDictPosition(BaseModel):
     size: ResourceDictPositionSize = Field(description="Resource size", default_factory=ResourceDictPositionSize)
     scale: ResourceDictPositionScale = Field(description="Resource scale", default_factory=ResourceDictPositionScale)
-    layout: Literal["2d"] = Field(description="Resource layout", default="2d")
+    layout: Literal["2d", "x-y", "z-y", "x-z"] = Field(description="Resource layout", default="x-y")
     position: ResourceDictPositionObject = Field(
         description="Resource position", default_factory=ResourceDictPositionObject
     )
@@ -42,6 +42,7 @@ class ResourceDictPosition(BaseModel):
     rotation: ResourceDictPositionObject = Field(
         description="Resource rotation", default_factory=ResourceDictPositionObject
     )
+    cross_section_type: Literal["rectangle", "circle", "rounded_rectangle"] = Field(description="Cross section type", default="rectangle")
 
 
 # 统一的资源字典模型，parent 自动序列化为 parent_uuid，children 不序列化
@@ -58,6 +59,7 @@ class ResourceDict(BaseModel):
     type: Literal["device"] | str = Field(description="Resource type")
     klass: str = Field(alias="class", description="Resource class name")
     position: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
+    pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
     config: Dict[str, Any] = Field(description="Resource configuration")
     data: Dict[str, Any] = Field(description="Resource data")
 
@@ -136,6 +138,8 @@ class ResourceDictInstance(object):
             content["config"] = {}
         if not content.get("data"):
             content["data"] = {}
+        if "pose" not in content:
+            content["pose"] = content.get("position", {})
         return ResourceDictInstance(ResourceDict.model_validate(content))
 
     def get_nested_dict(self) -> Dict[str, Any]:
@@ -330,6 +334,21 @@ class ResourceTreeSet(object):
         ) -> ResourceDictInstance:
             current_uuid = uuids.pop(0)
 
+            raw_pos = (
+                {"x": d["location"]["x"], "y": d["location"]["y"], "z": d["location"]["z"]}
+                if d["location"]
+                else {"x": 0, "y": 0, "z": 0}
+            )
+            pos = {
+                "size": {"width": d["size_x"], "height": d["size_y"], "depth": d["size_z"]},
+                "scale": {"x": 1.0, "y": 1.0, "z": 1.0},
+                "layout": d.get("layout", "x-y"),
+                "position": raw_pos,
+                "position3d": raw_pos,
+                "rotation": d["rotation"],
+                "cross_section_type": d.get("cross_section_type", "rectangle"),
+            }
+
             # 先构建当前节点的字典（不包含children）
             r_dict = {
                 "id": d["name"],
@@ -338,12 +357,10 @@ class ResourceTreeSet(object):
                 "parent": parent_resource,  # 直接传入 ResourceDict 对象
                 "type": replace_plr_type(d.get("category", "")),
                 "class": d.get("class", ""),
-                "position": (
-                    {"x": d["location"]["x"], "y": d["location"]["y"], "z": d["location"]["z"]}
-                    if d["location"]
-                    else {"x": 0, "y": 0, "z": 0}
-                ),
-                "config": {k: v for k, v in d.items() if k not in ["name", "children", "parent_name", "location"]},
+                "position": pos,
+                "pose": pos,
+                "config": {k: v for k, v in d.items() if k not in
+                           ["name", "children", "parent_name", "location", "rotation", "size_x", "size_y", "size_z", "cross_section_type", "bottom_type"]},
                 "data": states[d["name"]],
             }