Merge remote-tracking branch 'upstream/dev' into device_visualization

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -716,14 +716,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                     raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.")
                 # 首先应该对任务分组，然后每次1个/8个进行操作处理
                 if len(use_channels) == 1:
-                    tip = []
-                    for x in range(len(use_channels)):
-                        tip.extend(next(self.current_tip))
-                    await self.pick_up_tips(tip)
-
                     for _ in range(len(targets)):
+                        tip = []
+                        for x in range(len(use_channels)):
+                            tip.extend(next(self.current_tip))
+                        await self.pick_up_tips(tip)
+
                         await self.aspirate(
-                            resources=reagent_sources,
+                            resources=[reagent_sources[_]],
                             vols=[asp_vols[_]],
                             use_channels=use_channels,
                             flow_rates=[flow_rates[0]] if flow_rates else None,
@@ -759,17 +759,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                         if delays is not None:
                             await self.custom_delay(seconds=delays[1])
                         await self.touch_tip(targets[_])
-                    await self.discard_tips()
+                        await self.discard_tips()
 
                 elif len(use_channels) == 8:
                     # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理
                     if len(targets) % 8 != 0:
                         raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.")
-                    tip = []
-                    for _ in range(len(use_channels)):
-                        tip.extend(next(self.current_tip))
-                    await self.pick_up_tips(tip)
+
                     for i in range(0, len(targets), 8):
+                        tip = []
+                        for _ in range(len(use_channels)):
+                            tip.extend(next(self.current_tip))
+                        await self.pick_up_tips(tip)
                         current_targets = targets[i:i + 8]
                         current_reagent_sources = reagent_sources[i:i + 8]
                         current_asp_vols = asp_vols[i:i + 8]
@@ -819,7 +820,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                         if delays is not None:
                             await self.custom_delay(seconds=delays[1])
                         await self.touch_tip(current_targets)
-                    await self.discard_tips()
+                        await self.discard_tips()
 
 
         # except Exception as e:

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -400,6 +400,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
             )
         print(f"PRCXI9300Backend created solution with ID: {solution_id}")
         self.api_client.load_solution(solution_id)
+        print(json.dumps(self.steps_todo_list, indent=2))
         return self.api_client.start()
 
     @classmethod
@@ -976,9 +977,186 @@ if __name__ == "__main__":
     # 4.
 
     
-    deck = PRCXI9300Deck(name="PRCXI_Deck_9300", size_x=100, size_y=100, size_z=100)
+    # deck = PRCXI9300Deck(name="PRCXI_Deck_9300", size_x=100, size_y=100, size_z=100)
 
-    from pylabrobot.resources.opentrons.tip_racks import opentrons_96_tiprack_300ul,opentrons_96_tiprack_10ul
+    # from pylabrobot.resources.opentrons.tip_racks import opentrons_96_tiprack_300ul,opentrons_96_tiprack_10ul
+    # from pylabrobot.resources.opentrons.plates import corning_96_wellplate_360ul_flat, nest_96_wellplate_2ml_deep
+
+    # def get_well_container(name: str) -> PRCXI9300Container:
+    #     well_containers = corning_96_wellplate_360ul_flat(name).serialize()
+    #     plate = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="plate",
+    #                        ordering=collections.OrderedDict())
+    #     plate_serialized = plate.serialize()
+    #     plate_serialized["parent_name"] = deck.name
+    #     well_containers.update({k: v for k, v in plate_serialized.items() if k not in ["children"]})
+    #     new_plate: PRCXI9300Container = PRCXI9300Container.deserialize(well_containers)
+    #     return new_plate
+
+    # def get_tip_rack(name: str) -> PRCXI9300Container:
+    #     tip_racks = opentrons_96_tiprack_300ul("name").serialize()
+    #     tip_rack = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="tip_rack",
+    #                        ordering=collections.OrderedDict())
+    #     tip_rack_serialized = tip_rack.serialize()
+    #     tip_rack_serialized["parent_name"] = deck.name
+    #     tip_racks.update({k: v for k, v in tip_rack_serialized.items() if k not in ["children"]})
+    #     new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks)
+    #     return new_tip_rack
+    
+    # plate1 = get_tip_rack("RackT1")
+    # plate1.load_state({
+    #     "Material": {
+    #         "uuid": "076250742950465b9d6ea29a225dfb00",
+    #         "Code": "ZX-001-300",
+    #         "Name": "300μL Tip头"
+    #     }
+    # })
+
+    # plate2 = get_well_container("PlateT2")
+    # plate2.load_state({
+    #     "Material": {
+    #         "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
+    #         "Code": "ZX-019-2.2",
+    #         "Name": "96深孔板"
+    #     }
+    # })
+
+
+    # plate3 = PRCXI9300Trash("trash", size_x=50, size_y=100, size_z=10, category="trash")
+    # plate3.load_state({
+    #     "Material": {
+    #         "uuid": "730067cf07ae43849ddf4034299030e9"
+    #     }
+    # })
+
+    # plate4 = get_well_container("PlateT4")
+    # plate4.load_state({
+    #     "Material": {
+    #         "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
+    #         "Code": "ZX-019-2.2",
+    #         "Name": "96深孔板"
+    #     }
+    # })
+
+    # plate5 = get_well_container("PlateT5")
+    # plate5.load_state({
+    #     "Material": {
+    #         "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
+    #         "Code": "ZX-019-2.2",
+    #         "Name": "96深孔板"
+    #     }
+    # })
+    # plate6 = get_well_container("PlateT6")
+
+    # plate6.load_state({
+    #     "Material": {
+    #         "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
+    #         "Code": "ZX-019-2.2",
+    #         "Name": "96深孔板"
+    #     }
+    # })
+
+    # deck.assign_child_resource(plate1, location=Coordinate(0, 0, 0))
+    # deck.assign_child_resource(plate2, location=Coordinate(0, 0, 0))
+    # deck.assign_child_resource(plate3, location=Coordinate(0, 0, 0))
+    # deck.assign_child_resource(plate4, location=Coordinate(0, 0, 0))
+    # deck.assign_child_resource(plate5, location=Coordinate(0, 0, 0))
+    # deck.assign_child_resource(plate6, location=Coordinate(0, 0, 0))
+
+    # # print(plate2)
+    # plate_2_liquids = [[('water', 500)]]*96
+    # plate2.set_well_liquids(plate_2_liquids)
+
+    # handler = PRCXI9300Handler(deck=deck, host="10.181.214.132", port=9999, 
+    #                            timeout=10.0, setup=False, debug=False, 
+    #                            matrix_id="71593",
+    #                            channel_num=8, axis="Left")  # Initialize the handler with the deck and host settings
+    
+
+    # handler.set_tiprack([plate1]) 
+
+    # asyncio.run(handler.setup())  # Initialize the handler and setup the connection
+    # from pylabrobot.resources import set_volume_tracking
+    # # from pylabrobot.resources import set_tip_tracking
+    # set_volume_tracking(enabled=True)
+    # from unilabos.resources.graphio import *
+    # A = tree_to_list([resource_plr_to_ulab(deck)])
+    # with open("deck_9300_new.json", "w", encoding="utf-8") as f:
+    #     json.dump(A, f, indent=4, ensure_ascii=False)
+    # asyncio.run(handler.create_protocol(protocol_name="Test Protocol"))  # Initialize the backend and setup the connection
+
+    # # asyncio.run(handler.pick_up_tips(plate1.children[:8],[0,1,2,3,4,5,6,7]))
+    # # print(plate1.children[:8])
+    # # asyncio.run(handler.aspirate(plate2.children[:8],[50]*8, [0,1,2,3,4,5,6,7]))
+    # # print(plate2.children[:8])
+    # # asyncio.run(handler.dispense(plate5.children[:8],[50]*8,[0,1,2,3,4,5,6,7]))
+    # # print(plate5.children[:8])
+
+    # # # # # asyncio.run(handler.drop_tips(tip_rack.children[8:16],[0,1,2,3,4,5,6,7]))
+    # # asyncio.run(handler.discard_tips())
+
+    # # asyncio.run(handler.mix(well_containers.children[:8
+    # # ], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100))
+    # # #print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2))  # Print matrix info
+    # # asyncio.run(handler.add_liquid(
+    # #     asp_vols=[100]*16,
+    # #     dis_vols=[100]*16,
+    # #     reagent_sources=plate2.children[:16],
+    # #     targets=plate5.children[:16],
+    # #     use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
+    # #     flow_rates=[None] * 32,
+    # #     offsets=[Coordinate(0, 0, 0)] * 32,
+    # #     liquid_height=[None] * 16,
+    # #     blow_out_air_volume=[None] * 16,
+    # #     delays=None,
+    # #     mix_time=3,
+    # #     mix_vol=50,
+    # #     spread="wide",
+    # # ))
+    # # asyncio.run(handler.run_protocol())  # Run the protocol
+    # # asyncio.run(handler.remove_liquid(
+    # #     vols=[100]*16,
+    # #     sources=plate2.children[-16:],
+    # #     waste_liquid=plate5.children[:16], # 这个有些奇怪，但是好像也只能这么写
+    # #     use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
+    # #     flow_rates=[None] * 32,
+    # #     offsets=[Coordinate(0, 0, 0)] * 32,
+    # #     liquid_height=[None] * 32,
+    # #     blow_out_air_volume=[None] * 32,
+    # #     spread="wide",
+    # # ))
+
+    # acid = [20]*8+[40]*8+[60]*8+[80]*8+[100]*8+[120]*8+[140]*8+[160]*8+[180]*8+[200]*8+[220]*8+[240]*8
+    # alkaline = acid[::-1]  # Reverse the acid list for alkaline
+    # asyncio.run(handler.transfer_liquid(
+    #     asp_vols=acid,
+    #     dis_vols=acid,
+    #     tip_racks=[plate1],
+    #     sources=plate2.children[:],
+    #     targets=plate5.children[:],
+    #     use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
+    #     offsets=[Coordinate(0, 0, 0)] * 32,
+    #     asp_flow_rates=[None] * 16,
+    #     dis_flow_rates=[None] * 16,
+    #     liquid_height=[None] * 32,
+    #     blow_out_air_volume=[None] * 32,
+    #     mix_times=3,
+    #     mix_vol=50,
+    #     spread="wide",
+    # ))
+    # asyncio.run(handler.run_protocol())  # Run the protocol
+    # # # input("Running protocol...")
+    # # # input("Press Enter to continue...")  # Wait for user input before proceeding
+    # # # print("PRCXI9300Handler initialized with deck and host settings.")
+
+    # # Example usage
+    # # 1. 用导出的json，给每个T1 T2板子设定相应的物料，如果是孔板和枪头盒，要对应区分
+    # # 2. 设计一个单点动作流程，可以跑
+    # # 3.
+
+
+    deck = PRCXI9300Deck(name="PRCXI_Deck", size_x=100, size_y=100, size_z=100)
+
+    from pylabrobot.resources.opentrons.tip_racks import tipone_96_tiprack_200ul,opentrons_96_tiprack_10ul
     from pylabrobot.resources.opentrons.plates import corning_96_wellplate_360ul_flat, nest_96_wellplate_2ml_deep
 
     def get_well_container(name: str) -> PRCXI9300Container:
@@ -992,7 +1170,7 @@ if __name__ == "__main__":
         return new_plate
 
     def get_tip_rack(name: str) -> PRCXI9300Container:
-        tip_racks = opentrons_96_tiprack_300ul("name").serialize()
+        tip_racks = opentrons_96_tiprack_10ul("name").serialize()
         tip_rack = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="tip_rack",
                            ordering=collections.OrderedDict())
         tip_rack_serialized = tip_rack.serialize()
@@ -1001,333 +1179,157 @@ if __name__ == "__main__":
         new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks)
         return new_tip_rack
     
-    plate1 = get_tip_rack("RackT1")
+    plate1 = get_well_container("HPLCPlateT1")
     plate1.load_state({
         "Material": {
-            "uuid": "076250742950465b9d6ea29a225dfb00",
-            "Code": "ZX-001-300",
-            "Name": "300μL Tip头"
+            "uuid": "548bbc3df0d4447586f2c19d2c0c0c55",
+            "Code": "HPLC01",
+            "Name":  "HPLC料盘"
         }
     })
-
     plate2 = get_well_container("PlateT2")
     plate2.load_state({
         "Material": {
-            "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
-            "Code": "ZX-019-2.2",
-            "Name": "96深孔板"
+            "uuid": "04211a2dc93547fe9bf6121eac533650",
         }
     })
-
-
-    plate3 = PRCXI9300Trash("trash", size_x=50, size_y=100, size_z=10, category="trash")
+    plate3 = get_well_container("PlateT3")
     plate3.load_state({
+        "Material": {
+            "uuid": "04211a2dc93547fe9bf6121eac533650",
+        }
+    })
+    trash = PRCXI9300Trash(name="trash", size_x=50, size_y=50, size_z=10, category="trash")
+    trash.load_state({
         "Material": {
             "uuid": "730067cf07ae43849ddf4034299030e9"
         }
     })
-
-    plate4 = get_well_container("PlateT4")
-    plate4.load_state({
-        "Material": {
-            "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
-            "Code": "ZX-019-2.2",
-            "Name": "96深孔板"
-        }
-    })
-
     plate5 = get_well_container("PlateT5")
     plate5.load_state({
         "Material": {
-            "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
-            "Code": "ZX-019-2.2",
-            "Name": "96深孔板"
+            "uuid": "04211a2dc93547fe9bf6121eac533650",
         }
     })
     plate6 = get_well_container("PlateT6")
-
     plate6.load_state({
+        "Material": {
+            "uuid": "04211a2dc93547fe9bf6121eac533650"
+        }
+    })
+    plate7 = PRCXI9300Container(name="plateT7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict())
+    plate7.load_state({
+        "Material": {
+            "uuid": "04211a2dc93547fe9bf6121eac533650"
+        }
+    })
+    plate8 = get_tip_rack("RackT8")
+    plate8.load_state({
+        "Material": {
+            "uuid": "068b3815e36b4a72a59bae017011b29f",
+            "Code": "ZX-001-10+",
+            "Name": "10μL加长 Tip头"
+        }
+    })
+    plate9 = get_well_container("PlateT9")
+    plate9.load_state({
+        "Material": {
+            "uuid": "04211a2dc93547fe9bf6121eac533650"
+        }
+    })
+    plate10 = get_well_container("PlateT10")
+    plate10.load_state({
+        "Material": {
+            "uuid": "04211a2dc93547fe9bf6121eac533650"
+        }
+    })
+    plate11 = get_well_container("PlateT11")
+    plate11.load_state({
         "Material": {
             "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
-            "Code": "ZX-019-2.2",
-            "Name": "96深孔板"
+        }
+    })
+    plate12 = get_well_container("PlateT12")
+    plate12.load_state({
+        "Material": {
+            "uuid": "04211a2dc93547fe9bf6121eac533650"
+        }
+    })
+    plate13 = get_well_container("PlateT13")
+    plate13.load_state({
+        "Material": {
+            "uuid": "04211a2dc93547fe9bf6121eac533650"
         }
     })
 
+    # container_for_nothing = PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict())
+
     deck.assign_child_resource(plate1, location=Coordinate(0, 0, 0))
-    deck.assign_child_resource(plate2, location=Coordinate(0, 0, 0))
-    deck.assign_child_resource(plate3, location=Coordinate(0, 0, 0))
-    deck.assign_child_resource(plate4, location=Coordinate(0, 0, 0))
-    deck.assign_child_resource(plate5, location=Coordinate(0, 0, 0))
-    deck.assign_child_resource(plate6, location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing1", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing2", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(trash, location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing3", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing4", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(plate8, location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing5", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing6", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(plate11, location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
+    deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing8", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
 
-    # print(plate2)
-    plate_2_liquids = [[('water', 500)]]*96
-    plate2.set_well_liquids(plate_2_liquids)
-
-    handler = PRCXI9300Handler(deck=deck, host="10.181.214.132", port=9999, 
+    handler = PRCXI9300Handler(deck=deck, host="10.181.102.13", port=9999, 
                                timeout=10.0, setup=False, debug=False, 
-                               matrix_id="71593",
-                               channel_num=8, axis="Left")  # Initialize the handler with the deck and host settings
+                               matrix_id="fd383e6d-2d0e-40b5-9c01-1b2870b1f1b1",
+                               channel_num=1, axis="Right")  # Initialize the handler with the deck and host settings
     
-
-    handler.set_tiprack([plate1]) 
-
+    handler.set_tiprack([plate8])  # Set the tip rack for the handler
     asyncio.run(handler.setup())  # Initialize the handler and setup the connection
     from pylabrobot.resources import set_volume_tracking
     # from pylabrobot.resources import set_tip_tracking
     set_volume_tracking(enabled=True)
+
+    plate11.set_well_liquids([("Water", 100) if (i % 8 == 0 and i // 8 < 6) else (None, 100) for i in range(96)])  # Set liquids for every 8 wells in plate8
+
     from unilabos.resources.graphio import *
+
     A = tree_to_list([resource_plr_to_ulab(deck)])
-    with open("deck_9300_new.json", "w", encoding="utf-8") as f:
-        json.dump(A, f, indent=4, ensure_ascii=False)
+    # with open("deck.json", "w", encoding="utf-8") as f:
+    #     json.dump(A, f, indent=4, ensure_ascii=False)
+
+    print(plate11.get_well(0).tracker.get_used_volume())
     asyncio.run(handler.create_protocol(protocol_name="Test Protocol"))  # Initialize the backend and setup the connection
 
-    # asyncio.run(handler.pick_up_tips(plate1.children[:8],[0,1,2,3,4,5,6,7]))
-    # print(plate1.children[:8])
-    # asyncio.run(handler.aspirate(plate2.children[:8],[50]*8, [0,1,2,3,4,5,6,7]))
-    # print(plate2.children[:8])
-    # asyncio.run(handler.dispense(plate5.children[:8],[50]*8,[0,1,2,3,4,5,6,7]))
-    # print(plate5.children[:8])
-
-    # # # # asyncio.run(handler.drop_tips(tip_rack.children[8:16],[0,1,2,3,4,5,6,7]))
+    # asyncio.run(handler.pick_up_tips([plate8.children[8]],[0]))
+    # print(plate8.children[8])
+    # # asyncio.run(handler.run_protocol())
+    # asyncio.run(handler.aspirate([plate11.children[0]],[10], [0]))
+    # print(plate11.children[0])
+    # # asyncio.run(handler.run_protocol())
+    # asyncio.run(handler.dispense([plate1.children[0]],[10],[0]))
+    # print(plate1.children[0])
+    # # asyncio.run(handler.run_protocol())
+    # asyncio.run(handler.mix([plate1.children[0]], mix_time=3, mix_vol=5, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100))
+    # print(plate1.children[0])
     # asyncio.run(handler.discard_tips())
 
-    # asyncio.run(handler.mix(well_containers.children[:8
-    # ], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100))
-    # #print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2))  # Print matrix info
-    # asyncio.run(handler.add_liquid(
-    #     asp_vols=[100]*16,
-    #     dis_vols=[100]*16,
-    #     reagent_sources=plate2.children[:16],
-    #     targets=plate5.children[:16],
-    #     use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
-    #     flow_rates=[None] * 32,
-    #     offsets=[Coordinate(0, 0, 0)] * 32,
-    #     liquid_height=[None] * 16,
-    #     blow_out_air_volume=[None] * 16,
-    #     delays=None,
-    #     mix_time=3,
-    #     mix_vol=50,
-    #     spread="wide",
-    # ))
-    # asyncio.run(handler.run_protocol())  # Run the protocol
-    # asyncio.run(handler.remove_liquid(
-    #     vols=[100]*16,
-    #     sources=plate2.children[-16:],
-    #     waste_liquid=plate5.children[:16], # 这个有些奇怪，但是好像也只能这么写
-    #     use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
-    #     flow_rates=[None] * 32,
-    #     offsets=[Coordinate(0, 0, 0)] * 32,
-    #     liquid_height=[None] * 32,
-    #     blow_out_air_volume=[None] * 32,
-    #     spread="wide",
-    # ))
+    asyncio.run(handler.add_liquid(
+    asp_vols=[10]*7,
+    dis_vols=[10]*7,
+    reagent_sources=plate11.children[:7],
+    targets=plate1.children[2:9],
+    use_channels=[0],
+    flow_rates=[None] * 7,
+    offsets=[Coordinate(0, 0, 0)] * 7,
+    liquid_height=[None] * 7,
+    blow_out_air_volume=[None] * 2,
+    delays=None,
+    mix_time=3,
+    mix_vol=5,
+    spread="custom",
+))
 
-    acid = [20]*8+[40]*8+[60]*8+[80]*8+[100]*8+[120]*8+[140]*8+[160]*8+[180]*8+[200]*8+[220]*8+[240]*8
-    alkaline = acid[::-1]  # Reverse the acid list for alkaline
-    asyncio.run(handler.transfer_liquid(
-        asp_vols=acid,
-        dis_vols=acid,
-        tip_racks=[plate1],
-        sources=plate2.children[:],
-        targets=plate5.children[:],
-        use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
-        offsets=[Coordinate(0, 0, 0)] * 32,
-        asp_flow_rates=[None] * 16,
-        dis_flow_rates=[None] * 16,
-        liquid_height=[None] * 32,
-        blow_out_air_volume=[None] * 32,
-        mix_times=3,
-        mix_vol=50,
-        spread="wide",
-    ))
     asyncio.run(handler.run_protocol())  # Run the protocol
-    # # input("Running protocol...")
-    # # input("Press Enter to continue...")  # Wait for user input before proceeding
-    # # print("PRCXI9300Handler initialized with deck and host settings.")
-
-    # Example usage
-    # 1. 用导出的json，给每个T1 T2板子设定相应的物料，如果是孔板和枪头盒，要对应区分
-    # 2. 设计一个单点动作流程，可以跑
-    # 3.
-
-
-#     deck = PRCXI9300Deck(name="PRCXI_Deck", size_x=100, size_y=100, size_z=100)
-
-#     from pylabrobot.resources.opentrons.tip_racks import tipone_96_tiprack_200ul,opentrons_96_tiprack_10ul
-#     from pylabrobot.resources.opentrons.plates import corning_96_wellplate_360ul_flat, nest_96_wellplate_2ml_deep
-
-#     def get_well_container(name: str) -> PRCXI9300Container:
-#         well_containers = corning_96_wellplate_360ul_flat(name).serialize()
-#         plate = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="plate",
-#                            ordering=collections.OrderedDict())
-#         plate_serialized = plate.serialize()
-#         plate_serialized["parent_name"] = deck.name
-#         well_containers.update({k: v for k, v in plate_serialized.items() if k not in ["children"]})
-#         new_plate: PRCXI9300Container = PRCXI9300Container.deserialize(well_containers)
-#         return new_plate
-
-#     def get_tip_rack(name: str) -> PRCXI9300Container:
-#         tip_racks = opentrons_96_tiprack_10ul("name").serialize()
-#         tip_rack = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="tip_rack",
-#                            ordering=collections.OrderedDict())
-#         tip_rack_serialized = tip_rack.serialize()
-#         tip_rack_serialized["parent_name"] = deck.name
-#         tip_racks.update({k: v for k, v in tip_rack_serialized.items() if k not in ["children"]})
-#         new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks)
-#         return new_tip_rack
-    
-#     plate1 = get_well_container("HPLCPlateT1")
-#     plate1.load_state({
-#         "Material": {
-#             "uuid": "548bbc3df0d4447586f2c19d2c0c0c55",
-#             "Code": "HPLC01",
-#             "Name":  "HPLC料盘"
-#         }
-#     })
-#     plate2 = get_well_container("PlateT2")
-#     plate2.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650",
-#         }
-#     })
-#     plate3 = get_well_container("PlateT3")
-#     plate3.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650",
-#         }
-#     })
-#     trash = PRCXI9300Trash(name="trash", size_x=50, size_y=50, size_z=10, category="trash")
-#     trash.load_state({
-#         "Material": {
-#             "uuid": "730067cf07ae43849ddf4034299030e9"
-#         }
-#     })
-#     plate5 = get_well_container("PlateT5")
-#     plate5.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650",
-#         }
-#     })
-#     plate6 = get_well_container("PlateT6")
-#     plate6.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650"
-#         }
-#     })
-#     plate7 = PRCXI9300Container(name="plateT7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict())
-#     plate7.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650"
-#         }
-#     })
-#     plate8 = get_tip_rack("RackT8")
-#     plate8.load_state({
-#         "Material": {
-#             "uuid": "068b3815e36b4a72a59bae017011b29f",
-#             "Code": "ZX-001-10+",
-#             "Name": "10μL加长 Tip头"
-#         }
-#     })
-#     plate9 = get_well_container("PlateT9")
-#     plate9.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650"
-#         }
-#     })
-#     plate10 = get_well_container("PlateT10")
-#     plate10.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650"
-#         }
-#     })
-#     plate11 = get_well_container("PlateT11")
-#     plate11.load_state({
-#         "Material": {
-#             "uuid": "57b1e4711e9e4a32b529f3132fc5931f",
-#         }
-#     })
-#     plate12 = get_well_container("PlateT12")
-#     plate12.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650"
-#         }
-#     })
-#     plate13 = get_well_container("PlateT13")
-#     plate13.load_state({
-#         "Material": {
-#             "uuid": "04211a2dc93547fe9bf6121eac533650"
-#         }
-#     })
-
-#     # container_for_nothing = PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict())
-
-#     deck.assign_child_resource(plate1, location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing1", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing2", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(trash, location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing3", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing4", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(plate8, location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing5", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing6", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(plate11, location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-#     deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing8", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0))
-
-#     handler = PRCXI9300Handler(deck=deck, host="10.181.102.13", port=9999, 
-#                                timeout=10.0, setup=False, debug=False, 
-#                                matrix_id="fd383e6d-2d0e-40b5-9c01-1b2870b1f1b1",
-#                                channel_num=1, axis="Right")  # Initialize the handler with the deck and host settings
-    
-#     handler.set_tiprack([plate8])  # Set the tip rack for the handler
-#     asyncio.run(handler.setup())  # Initialize the handler and setup the connection
-#     from pylabrobot.resources import set_volume_tracking
-#     # from pylabrobot.resources import set_tip_tracking
-#     set_volume_tracking(enabled=True)
-
-#     plate11.set_well_liquids([("Water", 100) if (i % 8 == 0 and i // 8 < 6) else (None, 100) for i in range(96)])  # Set liquids for every 8 wells in plate8
-
-#     from unilabos.resources.graphio import *
-
-#     A = tree_to_list([resource_plr_to_ulab(deck)])
-#     # with open("deck.json", "w", encoding="utf-8") as f:
-#     #     json.dump(A, f, indent=4, ensure_ascii=False)
-
-#     print(plate11.get_well(0).tracker.get_used_volume())
-#     asyncio.run(handler.create_protocol(protocol_name="Test Protocol"))  # Initialize the backend and setup the connection
-
-#     # asyncio.run(handler.pick_up_tips([plate8.children[8]],[0]))
-#     # print(plate8.children[8])
-#     # # asyncio.run(handler.run_protocol())
-#     # asyncio.run(handler.aspirate([plate11.children[0]],[10], [0]))
-#     # print(plate11.children[0])
-#     # # asyncio.run(handler.run_protocol())
-#     # asyncio.run(handler.dispense([plate1.children[0]],[10],[0]))
-#     # print(plate1.children[0])
-#     # # asyncio.run(handler.run_protocol())
-#     # asyncio.run(handler.mix([plate1.children[0]], mix_time=3, mix_vol=5, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100))
-#     # print(plate1.children[0])
-#     # asyncio.run(handler.discard_tips())
-
-#     asyncio.run(handler.add_liquid(
-#     asp_vols=[10]*7,
-#     dis_vols=[10]*7,
-#     reagent_sources=[plate11.children[0]],
-#     targets=plate1.children[2:9],
-#     use_channels=[0],
-#     flow_rates=[None] * 4,
-#     offsets=[Coordinate(0, 0, 0)] * 4,
-#     liquid_height=[None] * 2,
-#     blow_out_air_volume=[None] * 2,
-#     delays=None,
-#     mix_time=3,
-#     mix_vol=5,
-#     spread="wide",
-# ))
-
 # #     asyncio.run(handler.transfer_liquid(
 # #     asp_vols=[10]*2,
 # #     dis_vols=[10]*2,
@@ -1390,7 +1392,7 @@ if __name__ == "__main__":
 #     #     mix_vol=50,
 #     #     spread="wide",
 #     # ))
-#     print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2))  # Print matrix info
+    print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2))  # Print matrix info
 #     # input("pick_up_tips add step")
 #     #asyncio.run(handler.run_protocol())  # Run the protocol
 #     # input("Running protocol...")

unilabos/registry/devices/liquid_handler.yaml

@@ -4388,11 +4388,11 @@ liquid_handler:
         deck:
           type: string
         simulator:
+          default: false
           type: boolean
       required:
       - backend
       - deck
-      - simulator
       type: object
     data:
       properties: {}

unilabos/registry/devices/virtual_device.yaml

@@ -2187,65 +2187,65 @@ virtual_multiway_valve:
     data_source: executor
     data_type: fluid
     description: 八通阀门端口1
-    handler_key: 1
+    handler_key: "1"
     io_type: source
-    label: 1
+    label: "1"
     side: NORTH
   - data_key: fluid_port_2
     data_source: executor
     data_type: fluid
     description: 八通阀门端口2
-    handler_key: 2
+    handler_key: "2"
     io_type: source
-    label: 2
+    label: "2"
     side: EAST
   - data_key: fluid_port_3
     data_source: executor
     data_type: fluid
     description: 八通阀门端口3
-    handler_key: 3
+    handler_key: "3"
     io_type: source
-    label: 3
+    label: "3"
     side: EAST
   - data_key: fluid_port_4
     data_source: executor
     data_type: fluid
     description: 八通阀门端口4
-    handler_key: 4
+    handler_key: "4"
     io_type: source
-    label: 4
+    label: "4"
     side: SOUTH
   - data_key: fluid_port_5
     data_source: executor
     data_type: fluid
     description: 八通阀门端口5
-    handler_key: 5
+    handler_key: "5"
     io_type: source
-    label: 5
+    label: "5"
     side: SOUTH
   - data_key: fluid_port_6
     data_source: executor
     data_type: fluid
     description: 八通阀门端口6
-    handler_key: 6
+    handler_key: "6"
     io_type: source
-    label: 6
+    label: "6"
     side: WEST
   - data_key: fluid_port_7
     data_source: executor
     data_type: fluid
     description: 八通阀门端口7
-    handler_key: 7
+    handler_key: "7"
     io_type: source
-    label: 7
+    label: "7"
     side: WEST
   - data_key: fluid_port_8
     data_source: executor
     data_type: fluid
     description: 八通阀门端口8
-    handler_key: 8
+    handler_key: "8"
     io_type: source
-    label: 8
+    label: "8"
     side: NORTH
   icon: EightPipeline.webp
   init_param_schema:

unilabos/registry/registry.py

@@ -110,7 +110,7 @@ class Registry:
                                 "placeholder_keys": {
                                     "res_id": "unilabos_resources",  # 将当前实验室的全部物料id作为下拉框可选择
                                     "device_id": "unilabos_devices",  # 将当前实验室的全部设备id作为下拉框可选择
-                                    "parent": "unilabos_resources",  # 将当前实验室的全部物料id作为下拉框可选择
+                                    "parent": "unilabos_nodes",  # 将当前实验室的设备/物料作为下拉框可选择
                                 },
                             },
                             "test_latency": {
@@ -131,7 +131,7 @@ class Registry:
                     "config_info": [],
                     "icon": "icon_device.webp",
                     "registry_type": "device",
-                    "handles": [],
+                    "handles": [],  # virtue采用了不同的handle
                     "init_param_schema": {},
                     "file_path": "/",
                 }
@@ -499,7 +499,7 @@ class Registry:
                         )
                         for action_name, action_config in device_config["class"]["action_value_mappings"].items():
                             if "handles" not in action_config:
-                                action_config["handles"] = []
+                                action_config["handles"] = {}
                             if "type" in action_config:
                                 action_type_str: str = action_config["type"]
                                 # 通过Json发放指令，而不是通过特殊的ros action进行处理
@@ -544,7 +544,7 @@ class Registry:
                                         )
                                     )
                                 ),
-                                "handles": [],
+                                "handles": {},
                             }
                     if "registry_type" not in device_config:
                         device_config["registry_type"] = "device"

unilabos/resources/graphio.py

@@ -84,7 +84,7 @@ def canonicalize_links_ports(data: dict) -> dict:
     # 第一遍处理：将字符串类型的port转换为字典格式
     for link in data.get("links", []):
         port = link.get("port")
-        if link["type"] == "physical":
+        if link.get("type", "physical") == "physical":
             link["type"] = "fluid"
         if isinstance(port, int):
             port = str(port)

unilabos/ros/nodes/presets/host_node.py

@@ -364,7 +364,16 @@ class HostNode(BaseROS2DeviceNode):
             resources, device_ids, bind_parent_ids, bind_locations, other_calling_params
         ):
             # 这里要求device_id传入必须是edge_device_id
-            namespace = "/devices/" + device_id
+            if device_id not in self.devices_names:
+                self.lab_logger().error(f"[Host Node] Device {device_id} not found in devices_names. Create resource failed.")
+                raise ValueError(f"[Host Node] Device {device_id} not found in devices_names. Create resource failed.")
+
+            device_key = f"{self.devices_names[device_id]}/{device_id}"
+            if device_key not in self._online_devices:
+                self.lab_logger().error(f"[Host Node] Device {device_key} is offline. Create resource failed.")
+                raise ValueError(f"[Host Node] Device {device_key} is offline. Create resource failed.")
+
+            namespace = self.devices_names[device_id]
             srv_address = f"/srv{namespace}/append_resource"
             sclient = self.create_client(SerialCommand, srv_address)
             sclient.wait_for_service()

unilabos/ros/nodes/presets/protocol_node.py

@@ -84,7 +84,11 @@ class ROS2ProtocolNode(BaseROS2DeviceNode):
                 self.communication_node_id_to_instance[device_id] = d
                 continue
 
+        for device_id, device_config in self.children.items():
+            if device_config.get("type", "device") != "device":
+                continue
             # 设置硬件接口代理
+            d = self.sub_devices[device_id]
             if d:
                 hardware_interface = d.ros_node_instance._hardware_interface
                 if (
@@ -108,6 +112,8 @@ class ROS2ProtocolNode(BaseROS2DeviceNode):
                             f"添加了{write}方法(来源：{name} {communicate_hardware_info['read']})"
                         )
 
+        self.lab_logger().info(f"ROS2ProtocolNode {device_id} initialized with protocols: {self.protocol_names}")
+
     def _setup_protocol_names(self, protocol_type):
         # 处理协议类型
         if isinstance(protocol_type, str):