diff --git a/README.md b/README.md index 79b7bbe0..94010e9f 100644 --- a/README.md +++ b/README.md @@ -49,7 +49,7 @@ conda env update --file unilabos-[YOUR_OS].yml -n environment_name # Currently, you need to install the `unilabos_msgs` package # You can download the system-specific package from the Release page -conda install ros-humble-unilabos-msgs-0.9.5-xxxxx.tar.bz2 +conda install ros-humble-unilabos-msgs-0.9.7-xxxxx.tar.bz2 # Install PyLabRobot and other prerequisites git clone https://github.com/PyLabRobot/pylabrobot plr_repo diff --git a/README_zh.md b/README_zh.md index 382ea538..d4f77f4b 100644 --- a/README_zh.md +++ b/README_zh.md @@ -49,7 +49,7 @@ conda env update --file unilabos-[YOUR_OS].yml -n 环境名 # 现阶段，需要安装 `unilabos_msgs` 包 # 可以前往 Release 页面下载系统对应的包进行安装 -conda install ros-humble-unilabos-msgs-0.9.5-xxxxx.tar.bz2 +conda install ros-humble-unilabos-msgs-0.9.7-xxxxx.tar.bz2 # 安装PyLabRobot等前置 git clone https://github.com/PyLabRobot/pylabrobot plr_repo diff --git a/recipes/ros-humble-unilabos-msgs/recipe.yaml b/recipes/ros-humble-unilabos-msgs/recipe.yaml index 6a64f9ce..e476d1b8 100644 --- a/recipes/ros-humble-unilabos-msgs/recipe.yaml +++ b/recipes/ros-humble-unilabos-msgs/recipe.yaml @@ -1,6 +1,6 @@ package: name: ros-humble-unilabos-msgs - version: 0.9.5 + version: 0.9.7 source: path: ../../unilabos_msgs folder: ros-humble-unilabos-msgs/src/work @@ -50,12 +50,12 @@ requirements: - robostack-staging::ros-humble-rosidl-default-generators - robostack-staging::ros-humble-std-msgs - robostack-staging::ros-humble-geometry-msgs - - robostack-staging::ros2-distro-mutex=0.6.* + - robostack-staging::ros2-distro-mutex=0.5.* run: - robostack-staging::ros-humble-action-msgs - robostack-staging::ros-humble-ros-workspace - robostack-staging::ros-humble-rosidl-default-runtime - robostack-staging::ros-humble-std-msgs - robostack-staging::ros-humble-geometry-msgs - - robostack-staging::ros2-distro-mutex=0.6.* +# - robostack-staging::ros2-distro-mutex=0.6.* - sel(osx and x86_64): __osx >={{ MACOSX_DEPLOYMENT_TARGET|default('10.14') }} diff --git a/recipes/unilabos/recipe.yaml b/recipes/unilabos/recipe.yaml index 3e1cc66b..2a48b043 100644 --- a/recipes/unilabos/recipe.yaml +++ b/recipes/unilabos/recipe.yaml @@ -1,6 +1,6 @@ package: name: unilabos - version: "0.9.5" + version: "0.9.7" source: path: ../.. diff --git a/setup.py b/setup.py index c96103c5..8fd9bbc8 100644 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ setup( name=package_name, - version='0.9.5', + version='0.9.7', packages=find_packages(), include_package_data=True, install_requires=['setuptools'], @@ -17,6 +17,7 @@ entry_points={ 'console_scripts': [ "unilab = unilabos.app.main:main", + "unilab-register = unilabos.app.register:main" ], }, ) diff --git a/test/experiments/Protocol_Test_Station/add_protocol_test_station.json b/test/experiments/Protocol_Test_Station/add_protocol_test_station.json new file mode 100644 index 00000000..df7f8182 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/add_protocol_test_station.json @@ -0,0 +1,563 @@ +{ + "nodes": [ + { + "id": "AddProtocolTestStation", + "name": "添加协议测试站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "stirrer_1", + "stirrer_2", + "flask_DMF", + "flask_ethyl_acetate", + "flask_methanol", + "flask_acetone", + "flask_water", + "flask_air", + "main_reactor", + "secondary_reactor", + "waste_workup", + "collection_bottle_1", + "collection_bottle_2" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": ["PumpTransferProtocol", "AddProtocol"] + }, + "data": {} + }, + { + "id": "transfer_pump_1", + "name": "转移泵1", + "children": [], + "parent": "AddProtocolTestStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 250, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP1", + "max_volume": 25.0, + "transfer_rate": 5.0 + }, + "data": { + "position": 0.0, + "status": "Idle" + } + }, + { + "id": "transfer_pump_2", + "name": "转移泵2", + "children": [], + "parent": "AddProtocolTestStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 750, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP2", + "max_volume": 25.0, + "transfer_rate": 5.0 + }, + "data": { + "position": 0.0, + "status": "Idle" + } + }, + { + "id": "multiway_valve_1", + "name": "试剂分配阀", + "children": [], + "parent": "AddProtocolTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 250, + "y": 400, + "z": 0 + }, + "config": { + "port": "VIRTUAL_VALVE1", + "positions": 8 + }, + "data": { + "current_position": 1 + } + }, + { + "id": "multiway_valve_2", + "name": "反应器分配阀", + "children": [], + "parent": "AddProtocolTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 750, + "y": 400, + "z": 0 + }, + "config": { + "port": "VIRTUAL_VALVE2", + "positions": 8 + }, + "data": { + "current_position": 1 + } + }, + { + "id": "stirrer_1", + "name": "主反应器搅拌器", + "children": [], + "parent": "AddProtocolTestStation", + "type": "device", + "class": "virtual_stirrer", + "position": { + "x": 600, + "y": 450, + "z": 0 + }, + "config": { + "port": "VIRTUAL_STIRRER1", + "max_speed": 1500.0, + "default_speed": 300.0 + }, + "data": { + "speed": 0.0, + "status": "Stopped" + } + }, + { + "id": "stirrer_2", + "name": "副反应器搅拌器", + "children": [], + "parent": "AddProtocolTestStation", + "type": "device", + "class": "virtual_stirrer", + "position": { + "x": 900, + "y": 450, + "z": 0 + }, + "config": { + "port": "VIRTUAL_STIRRER2", + "max_speed": 1500.0, + "default_speed": 300.0 + }, + "data": { + "speed": 0.0, + "status": "Stopped" + } + }, + { + "id": "flask_DMF", + "name": "DMF试剂瓶", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 50, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "DMF", + "liquid_volume": 800.0 + } + ] + } + }, + { + "id": "flask_ethyl_acetate", + "name": "乙酸乙酯试剂瓶", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 150, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "ethyl_acetate", + "liquid_volume": 800.0 + } + ] + } + }, + { + "id": "flask_methanol", + "name": "甲醇试剂瓶", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 250, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "methanol", + "liquid_volume": 800.0 + } + ] + } + }, + { + "id": "flask_acetone", + "name": "丙酮试剂瓶", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 350, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "acetone", + "liquid_volume": 800.0 + } + ] + } + }, + { + "id": "flask_water", + "name": "蒸馏水瓶", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 450, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "water", + "liquid_volume": 800.0 + } + ] + } + }, + { + "id": "flask_air", + "name": "空气瓶", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 550, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "main_reactor", + "name": "主反应器", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 600, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 2000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "secondary_reactor", + "name": "副反应器", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 900, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "waste_workup", + "name": "废液处理瓶", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 700, + "y": 600, + "z": 0 + }, + "config": { + "max_volume": 2000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "collection_bottle_1", + "name": "收集瓶1", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 800, + "y": 600, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "collection_bottle_2", + "name": "收集瓶2", + "children": [], + "parent": "AddProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 900, + "y": 600, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + } + ], + "links": [ + { + "id": "link_pump1_valve1", + "source": "transfer_pump_1", + "target": "multiway_valve_1", + "type": "fluid", + "port": { + "transfer_pump_1": "transferpump", + "multiway_valve_1": "transferpump" + } + }, + { + "id": "link_pump2_valve2", + "source": "transfer_pump_2", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "transfer_pump_2": "transferpump", + "multiway_valve_2": "transferpump" + } + }, + { + "id": "link_valve1_valve2", + "source": "multiway_valve_1", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "multiway_valve_1": "8", + "multiway_valve_2": "1" + } + }, + { + "id": "link_valve1_DMF", + "source": "multiway_valve_1", + "target": "flask_DMF", + "type": "fluid", + "port": { + "multiway_valve_1": "1", + "flask_DMF": "outlet" + } + }, + { + "id": "link_valve1_ethyl_acetate", + "source": "multiway_valve_1", + "target": "flask_ethyl_acetate", + "type": "fluid", + "port": { + "multiway_valve_1": "2", + "flask_ethyl_acetate": "outlet" + } + }, + { + "id": "link_valve1_methanol", + "source": "multiway_valve_1", + "target": "flask_methanol", + "type": "fluid", + "port": { + "multiway_valve_1": "3", + "flask_methanol": "outlet" + } + }, + { + "id": "link_valve1_acetone", + "source": "multiway_valve_1", + "target": "flask_acetone", + "type": "fluid", + "port": { + "multiway_valve_1": "4", + "flask_acetone": "outlet" + } + }, + { + "id": "link_valve1_water", + "source": "multiway_valve_1", + "target": "flask_water", + "type": "fluid", + "port": { + "multiway_valve_1": "5", + "flask_water": "outlet" + } + }, + { + "id": "link_valve1_air", + "source": "multiway_valve_1", + "target": "flask_air", + "type": "fluid", + "port": { + "multiway_valve_1": "6", + "flask_air": "top" + } + }, + { + "id": "link_valve2_main_reactor", + "source": "multiway_valve_2", + "target": "main_reactor", + "type": "fluid", + "port": { + "multiway_valve_2": "2", + "main_reactor": "inlet" + } + }, + { + "id": "link_valve2_secondary_reactor", + "source": "multiway_valve_2", + "target": "secondary_reactor", + "type": "fluid", + "port": { + "multiway_valve_2": "3", + "secondary_reactor": "inlet" + } + }, + { + "id": "link_valve2_waste", + "source": "multiway_valve_2", + "target": "waste_workup", + "type": "fluid", + "port": { + "multiway_valve_2": "6", + "waste_workup": "inlet" + } + }, + { + "id": "link_valve2_collection1", + "source": "multiway_valve_2", + "target": "collection_bottle_1", + "type": "fluid", + "port": { + "multiway_valve_2": "7", + "collection_bottle_1": "inlet" + } + }, + { + "id": "link_valve2_collection2", + "source": "multiway_valve_2", + "target": "collection_bottle_2", + "type": "fluid", + "port": { + "multiway_valve_2": "8", + "collection_bottle_2": "inlet" + } + }, + { + "id": "link_stirrer1_main_reactor", + "source": "stirrer_1", + "target": "main_reactor", + "type": "mechanical", + "port": { + "stirrer_1": "stirrer_head", + "main_reactor": "stirrer_port" + } + }, + { + "id": "link_stirrer2_secondary_reactor", + "source": "stirrer_2", + "target": "secondary_reactor", + "type": "mechanical", + "port": { + "stirrer_2": "stirrer_head", + "secondary_reactor": "stirrer_port" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/Protocol_Test_Station/centrifuge_protocol_test_station.json b/test/experiments/Protocol_Test_Station/centrifuge_protocol_test_station.json new file mode 100644 index 00000000..affb6e8b --- /dev/null +++ b/test/experiments/Protocol_Test_Station/centrifuge_protocol_test_station.json @@ -0,0 +1,438 @@ +{ + "nodes": [ + { + "id": "CentrifugeProtocolTestStation", + "name": "离心协议测试站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "centrifuge_1", + "reaction_mixture", + "centrifuge_tube", + "collection_bottle_1", + "flask_water", + "flask_ethanol", + "flask_acetone", + "flask_air", + "waste_workup" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": [ + "CentrifugeProtocol", + "PumpTransferProtocol" + ] + }, + "data": {} + }, + { + "id": "transfer_pump_1", + "name": "主转移泵", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 200, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP1", + "max_volume": 25.0, + "transfer_rate": 2.0 + }, + "data": { + "position": 0.0, + "status": "Idle" + } + }, + { + "id": "transfer_pump_2", + "name": "副转移泵", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 400, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP2", + "max_volume": 25.0, + "transfer_rate": 2.0 + }, + "data": { + "position": 0.0, + "status": "Idle" + } + }, + { + "id": "multiway_valve_1", + "name": "溶剂分配阀", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 200, + "y": 400, + "z": 0 + }, + "config": { + "port": "VIRTUAL_VALVE1", + "positions": 8 + }, + "data": { + "current_position": 1 + } + }, + { + "id": "multiway_valve_2", + "name": "样品分配阀", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 400, + "y": 400, + "z": 0 + }, + "config": { + "port": "VIRTUAL_VALVE2", + "positions": 8 + }, + "data": { + "current_position": 1 + } + }, + { + "id": "centrifuge_1", + "name": "离心机", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "device", + "class": "virtual_centrifuge", + "position": { + "x": 600, + "y": 350, + "z": 0 + }, + "config": { + "port": "VIRTUAL_CENTRIFUGE1", + "max_speed": 15000.0, + "max_temp": 40.0, + "min_temp": 4.0 + }, + "data": { + "status": "Idle" + } + }, + { + "id": "reaction_mixture", + "name": "反应混合物", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 100, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 500.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "cell_suspension", + "liquid_volume": 200.0 + } + ] + } + }, + { + "id": "centrifuge_tube", + "name": "离心管", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 600, + "y": 450, + "z": 0 + }, + "config": { + "max_volume": 15.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "collection_bottle_1", + "name": "上清液收集瓶", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 700, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 500.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "flask_water", + "name": "蒸馏水瓶", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 200, + "y": 600, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "water", + "liquid_volume": 900.0 + } + ] + } + }, + { + "id": "flask_ethanol", + "name": "乙醇清洗瓶", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 300, + "y": 600, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "ethanol", + "liquid_volume": 800.0 + } + ] + } + }, + { + "id": "flask_acetone", + "name": "丙酮清洗瓶", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 400, + "y": 600, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "acetone", + "liquid_volume": 800.0 + } + ] + } + }, + { + "id": "flask_air", + "name": "空气瓶", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 100, + "y": 600, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "waste_workup", + "name": "废液瓶", + "children": [], + "parent": "CentrifugeProtocolTestStation", + "type": "container", + "class": null, + "position": { + "x": 800, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 2000.0 + }, + "data": { + "liquid": [] + } + } + ], + "links": [ + { + "id": "link_pump1_valve1", + "source": "transfer_pump_1", + "target": "multiway_valve_1", + "type": "fluid", + "port": { + "transfer_pump_1": "transferpump", + "multiway_valve_1": "transferpump" + } + }, + { + "id": "link_pump2_valve2", + "source": "transfer_pump_2", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "transfer_pump_2": "transferpump", + "multiway_valve_2": "transferpump" + } + }, + { + "id": "link_valve1_air", + "source": "multiway_valve_1", + "target": "flask_air", + "type": "fluid", + "port": { + "multiway_valve_1": "1", + "flask_air": "top" + } + }, + { + "id": "link_valve1_water", + "source": "multiway_valve_1", + "target": "flask_water", + "type": "fluid", + "port": { + "multiway_valve_1": "2", + "flask_water": "outlet" + } + }, + { + "id": "link_valve1_ethanol", + "source": "multiway_valve_1", + "target": "flask_ethanol", + "type": "fluid", + "port": { + "multiway_valve_1": "3", + "flask_ethanol": "outlet" + } + }, + { + "id": "link_valve1_acetone", + "source": "multiway_valve_1", + "target": "flask_acetone", + "type": "fluid", + "port": { + "multiway_valve_1": "4", + "flask_acetone": "outlet" + } + }, + { + "id": "link_valve1_valve2", + "source": "multiway_valve_1", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "multiway_valve_1": "5", + "multiway_valve_2": "1" + } + }, + { + "id": "link_valve2_reaction_mixture", + "source": "multiway_valve_2", + "target": "reaction_mixture", + "type": "fluid", + "port": { + "multiway_valve_2": "2", + "reaction_mixture": "inlet" + } + }, + { + "id": "link_valve2_centrifuge_tube", + "source": "multiway_valve_2", + "target": "centrifuge_tube", + "type": "fluid", + "port": { + "multiway_valve_2": "3", + "centrifuge_tube": "inlet" + } + }, + { + "id": "link_valve2_collection", + "source": "multiway_valve_2", + "target": "collection_bottle_1", + "type": "fluid", + "port": { + "multiway_valve_2": "4", + "collection_bottle_1": "inlet" + } + }, + { + "id": "link_valve2_waste", + "source": "multiway_valve_2", + "target": "waste_workup", + "type": "fluid", + "port": { + "multiway_valve_2": "5", + "waste_workup": "inlet" + } + }, + { + "id": "link_centrifuge1_centrifuge_tube", + "source": "centrifuge_1", + "target": "centrifuge_tube", + "type": "transport", + "port": { + "centrifuge_1": "centrifuge", + "centrifuge_tube": "centrifuge_port" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/Protocol_Test_Station/clean_vessel_protocol_test_station.json b/test/experiments/Protocol_Test_Station/clean_vessel_protocol_test_station.json new file mode 100644 index 00000000..f4200f71 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/clean_vessel_protocol_test_station.json @@ -0,0 +1,426 @@ +{ + "nodes": [ + { + "id": "CleanVesselProtocolTestStation", + "name": "容器清洗协议测试站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "heatchill_1", + "flask_water", + "flask_acetone", + "flask_ethanol", + "flask_air", + "main_reactor", + "secondary_reactor", + "waste_workup" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": [ + "CleanVesselProtocol", + "PumpTransferProtocol", + "HeatChillProtocol", + "HeatChillStartProtocol", + "HeatChillStopProtocol" + ] + }, + "data": {} + }, + { + "id": "transfer_pump_1", + "name": "主清洗泵", + "children": [], + "parent": "CleanVesselProtocolTestStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 250, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP1", + "max_volume": 25.0, + "transfer_rate": 2.5 + }, + "data": { + "position": 0.0, + "status": "Idle" + } + }, + { + "id": "transfer_pump_2", + "name": "副清洗泵", + "children": [], + "parent": "CleanVesselProtocolTestStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 450, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP2", + "max_volume": 25.0, + "transfer_rate": 2.5 + }, + "data": { + "position": 0.0, + "status": "Idle" + } + }, + { + "id": "multiway_valve_1", + "name": "溶剂分配阀", + "children": [], + "parent": "CleanVesselProtocolTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 250, + "y": 400, + "z": 0 + }, + "config": { + "port": "VIRTUAL_VALVE1", + "positions": 8 + }, + "data": { + "current_position": 1 + } + }, + { + "id": "multiway_valve_2", + "name": "容器分配阀", + "children": [], + "parent": "CleanVesselProtocolTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 450, + "y": 400, + "z": 0 + }, + "config": { + "port": "VIRTUAL_VALVE2", + "positions": 8 + }, + "data": { + "current_position": 1 + } + }, + { + "id": "heatchill_1", + "name": "加热清洗器", + "children": [], + "parent": "CleanVesselProtocolTestStation", + "type": "device", + "class": "virtual_heatchill", + "position": { + "x": 600, + "y": 350, + "z": 0 + }, + "config": { + "port": "VIRTUAL_HEATCHILL1", + "max_temp": 100.0, + "min_temp": 10.0, + "max_stir_speed": 500.0 + }, + "data": { + "status": "Idle" + } + }, + { + "id": "flask_water", + "name": "蒸馏水瓶", + "children": [], + "parent": 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"id": "waste_workup", + "name": "清洗废液瓶", + "children": [], + "parent": "CleanVesselProtocolTestStation", + "type": "container", + "class": "container", + "position": { + "x": 700, + "y": 550, + "z": 0 + }, + "config": { + "max_volume": 3000.0 + }, + "data": { + "liquid": [] + } + } + ], + "links": [ + { + "id": "link_pump1_valve1", + "source": "transfer_pump_1", + "target": "multiway_valve_1", + "type": "fluid", + "port": { + "transfer_pump_1": "transferpump", + "multiway_valve_1": "transferpump" + } + }, + { + "id": "link_pump2_valve2", + "source": "transfer_pump_2", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "transfer_pump_2": "transferpump", + "multiway_valve_2": "transferpump" + } + }, + { + "id": "link_valve1_air", + "source": "multiway_valve_1", + "target": "flask_air", + "type": "fluid", + "port": { + "multiway_valve_1": "6", + "flask_air": "top" + } + }, + { + "id": "link_valve1_water", + "source": "multiway_valve_1", + "target": "flask_water", + "type": 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"3", + "secondary_reactor": "top" + } + }, + { + "id": "link_valve2_waste", + "source": "multiway_valve_2", + "target": "waste_workup", + "type": "fluid", + "port": { + "multiway_valve_2": "4", + "waste_workup": "top" + } + }, + { + "id": "link_valve2_air_return", + "source": "multiway_valve_2", + "target": "flask_air", + "type": "fluid", + "port": { + "multiway_valve_2": "5", + "flask_air": "top" + } + }, + { + "id": "link_heatchill1_main_reactor", + "source": "heatchill_1", + "target": "main_reactor", + "type": "mechanical", + "port": { + "heatchill_1": "heatchill", + "main_reactor": "bind" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/Protocol_Test_Station/dual_valve_pump_test_station.json b/test/experiments/Protocol_Test_Station/dual_valve_pump_test_station.json new file mode 100644 index 00000000..61520ee6 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/dual_valve_pump_test_station.json @@ -0,0 +1,367 @@ +{ + "nodes": [ + { + "id": "DualValvePumpStation", + "name": "双阀门泵站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "flask_DMF", + "flask_ethyl_acetate", + "flask_methanol", + "flask_air", + "main_reactor", + "waste_workup", + "collection_bottle_1" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": ["PumpTransferProtocol"] + }, + "data": {} + }, + { + "id": "transfer_pump_1", + "name": "转移泵1", + "children": [], + "parent": "DualValvePumpStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 300, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP1", + "max_volume": 25.0, + "transfer_rate": 5.0 + }, + "data": { + "position": 0.0, + "status": "Idle" + } + }, + { + "id": "transfer_pump_2", + "name": "转移泵2", + "children": [], + "parent": "DualValvePumpStation", + "type": "device", + "class": 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"liquid": [] + } + } + ], + "links": [ + { + "id": "link_pump1_valve1", + "source": "transfer_pump_1", + "target": "multiway_valve_1", + "type": "fluid", + "port": { + "transfer_pump_1": "transferpump", + "multiway_valve_1": "transferpump" + } + }, + { + "id": "link_pump2_valve2", + "source": "transfer_pump_2", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "transfer_pump_2": "transferpump", + "multiway_valve_2": "transferpump" + } + }, + { + "id": "link_valve1_valve2", + "source": "multiway_valve_1", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "multiway_valve_1": "8", + "multiway_valve_2": "1" + } + }, + { + "id": "link_valve1_air", + "source": "multiway_valve_1", + "target": "flask_air", + "type": "fluid", + "port": { + "multiway_valve_1": "1", + "flask_air": "top" + } + }, + { + "id": "link_valve1_DMF", + "source": "multiway_valve_1", + "target": "flask_DMF", + "type": "fluid", + "port": { + "multiway_valve_1": "2", + "flask_DMF": "outlet" + } + }, + { + "id": "link_valve1_ethyl_acetate", + "source": "multiway_valve_1", + "target": "flask_ethyl_acetate", + "type": "fluid", + "port": { + "multiway_valve_1": "3", + "flask_ethyl_acetate": "outlet" + } + }, + { + "id": "link_valve1_methanol", + "source": "multiway_valve_1", + "target": "flask_methanol", + "type": "fluid", + "port": { + "multiway_valve_1": "4", + "flask_methanol": "outlet" + } + }, + { + "id": "link_valve2_reactor", + "source": "multiway_valve_2", + "target": "main_reactor", + "type": "fluid", + "port": { + "multiway_valve_2": "5", + "main_reactor": "inlet" + } + }, + { + "id": "link_valve2_waste", + "source": "multiway_valve_2", + "target": "waste_workup", + "type": "fluid", + "port": { + "multiway_valve_2": "6", + "waste_workup": "inlet" + } + }, + { + "id": "link_valve2_collection", + "source": "multiway_valve_2", + "target": "collection_bottle_1", + "type": "fluid", + "port": { + "multiway_valve_2": "7", + "collection_bottle_1": "inlet" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/Protocol_Test_Station/evacuateandrefill_test_station.json b/test/experiments/Protocol_Test_Station/evacuateandrefill_test_station.json new file mode 100644 index 00000000..b4f89c25 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/evacuateandrefill_test_station.json @@ -0,0 +1,557 @@ +{ + "nodes": [ + { + "id": "EvacuateRefillTestStation", + "name": "抽真空充气测试站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "flask_DMF", + "flask_ethyl_acetate", + "flask_methanol", + "flask_air", + "vacuum_pump_1", + "gas_source_nitrogen", + "gas_source_air", + "solenoid_valve_vacuum", + "solenoid_valve_gas", + "main_reactor", + "stirrer_1", + "waste_workup", + "collection_bottle_1" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": ["PumpTransferProtocol", 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a/test/experiments/Protocol_Test_Station/evaporate_protocol_test_station.json b/test/experiments/Protocol_Test_Station/evaporate_protocol_test_station.json new file mode 100644 index 00000000..d47bb4d6 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/evaporate_protocol_test_station.json @@ -0,0 +1,503 @@ +{ + "nodes": [ + { + "id": "EvaporateProtocolTestStation", + "name": "蒸发协议测试站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "rotavap_1", + "heatchill_1", + "reaction_mixture", + "rotavap_flask", + "rotavap_condenser", + "flask_distillate", + "flask_ethanol", + "flask_acetone", + "flask_water", + "flask_air", + "waste_workup" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": [ + "EvaporateProtocol", + "PumpTransferProtocol", + "HeatChillProtocol", + "HeatChillStartProtocol", + "HeatChillStopProtocol" + ] + }, + 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--- /dev/null +++ b/test/experiments/Protocol_Test_Station/filter_protocol_test_station.json @@ -0,0 +1,534 @@ +{ + "nodes": [ + { + "id": "FilterProtocolTestStation", + "name": "过滤协议测试站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "filter_1", + "heatchill_1", + "reaction_mixture", + "filter_vessel", + "filtrate_vessel", + "collection_bottle_1", + "collection_bottle_2", + "flask_water", + "flask_ethanol", + "flask_acetone", + "flask_air", + "waste_workup" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": [ + "FilterProtocol", + "PumpTransferProtocol", + "HeatChillProtocol", + "HeatChillStartProtocol", + "HeatChillStopProtocol" + ] + }, + "data": {} + }, + { + "id": "transfer_pump_1", + "name": "主转移泵", + "children": [], + "parent": "FilterProtocolTestStation", + "type": "device", + "class": "virtual_transfer_pump", + 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"heatchill_1": "heatchill", + "filter_vessel": "heating_jacket" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/Protocol_Test_Station/heatchill_protocol_test_station.json b/test/experiments/Protocol_Test_Station/heatchill_protocol_test_station.json new file mode 100644 index 00000000..751f3129 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/heatchill_protocol_test_station.json @@ -0,0 +1,671 @@ +{ + "nodes": [ + { + "id": "HeatChillProtocolTestStation", + "name": "加热冷却协议测试站", + "children": [ + "transfer_pump_1", + "transfer_pump_2", + "multiway_valve_1", + "multiway_valve_2", + "stirrer_1", + "stirrer_2", + "heatchill_1", + "heatchill_2", + "flask_DMF", + "flask_ethyl_acetate", + "flask_methanol", + "flask_acetone", + "flask_water", + "flask_ethanol", + "flask_air", + "main_reactor", + "secondary_reactor", + "waste_workup", + "collection_bottle_1", + "collection_bottle_2" + ], + "parent": null, + "type": "device", + "class": "workstation", + 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"id": "link_valve_methanol", + "source": "multiway_valve_1", + "target": "flask_methanol", + "type": "fluid", + "port": { + "multiway_valve_1": "4", + "flask_methanol": "outlet" + } + }, + { + "id": "link_valve_reactor", + "source": "multiway_valve_1", + "target": "main_reactor", + "type": "fluid", + "port": { + "multiway_valve_1": "5", + "main_reactor": "inlet" + } + }, + { + "id": "link_valve_waste", + "source": "multiway_valve_1", + "target": "waste_workup", + "type": "fluid", + "port": { + "multiway_valve_1": "6", + "waste_workup": "inlet" + } + }, + { + "id": "link_valve_collection", + "source": "multiway_valve_1", + "target": "collection_bottle_1", + "type": "fluid", + "port": { + "multiway_valve_1": "7", + "collection_bottle_1": "inlet" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/Protocol_Test_Station/run_column_protocol_test_station.json b/test/experiments/Protocol_Test_Station/run_column_protocol_test_station.json new file mode 100644 index 00000000..e10d73e6 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/run_column_protocol_test_station.json @@ -0,0 +1,432 @@ +{ + "nodes": [ + { + "id": "RunColumnTestStation", + "name": "柱层析测试工作站", + "children": [ + "transfer_pump_1", + "multiway_valve_1", + "column_1", + "flask_sample", + "flask_hexane", + "flask_ethyl_acetate", + "flask_methanol", + "column_vessel", + "collection_flask_1", + "collection_flask_2", + "collection_flask_3", + "waste_flask", + "main_reactor" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": ["RunColumnProtocol", "PumpTransferProtocol"] + }, + "data": {} + }, + { + "id": "transfer_pump_1", + "name": "转移泵", + "children": [], + "parent": "RunColumnTestStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 300, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL_PUMP1", + "max_volume": 50.0, + "transfer_rate": 10.0 + }, + "data": { + "status": "Idle", + "position": 0.0 + } + }, + { + "id": "multiway_valve_1", + "name": "八通阀门", + "children": [], + "parent": "RunColumnTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 300, + "y": 400, + "z": 0 + }, + "config": { + "port": "VIRTUAL_VALVE1", + "positions": 8 + }, + "data": { + "current_position": 1 + } + }, + { + "id": "column_1", + "name": "柱层析设备", + "children": [], + "parent": "RunColumnTestStation", + "type": "device", + "class": "virtual_column", + "position": { + "x": 600, + "y": 350, + "z": 0 + }, + "config": { + "port": "VIRTUAL_COLUMN1", + "max_flow_rate": 5.0, + "column_length": 30.0, + "column_diameter": 2.5 + }, + "data": { + "status": "Idle", + "column_state": "Ready" + } + }, + { + "id": "flask_sample", + "name": "样品瓶", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 100, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 500.0 + }, + "data": { + "liquid": [ + { + "name": "crude_mixture", + "volume": 200.0, + "concentration": 70.0 + } + ] + } + }, + { + "id": "flask_hexane", + "name": "正己烷洗脱剂", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 200, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 2000.0 + }, + "data": { + "liquid": [ + { + "name": "hexane", + "volume": 1500.0, + "concentration": 99.8 + } + ] + } + }, + { + "id": "flask_ethyl_acetate", + "name": "乙酸乙酯洗脱剂", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 300, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 2000.0 + }, + "data": { + "liquid": [ + { + "name": "ethyl_acetate", + "volume": 1500.0, + "concentration": 99.5 + } + ] + } + }, + { + "id": "flask_methanol", + "name": "甲醇洗脱剂", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 400, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "name": "methanol", + "volume": 800.0, + "concentration": 99.9 + } + ] + } + }, + { + "id": "column_vessel", + "name": "柱容器", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 600, + "y": 450, + "z": 0 + }, + "config": { + "max_volume": 300.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "collection_flask_1", + "name": "收集瓶1", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 700, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "collection_flask_2", + "name": "收集瓶2", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 800, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "collection_flask_3", + "name": "收集瓶3", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 900, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "waste_flask", + "name": "废液瓶", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 1000, + "y": 500, + "z": 0 + }, + "config": { + "max_volume": 2000.0 + }, + "data": { + "liquid": [] + } + }, + { + "id": "main_reactor", + "name": "反应器", + "children": [], + "parent": "RunColumnTestStation", + "type": "container", + "class": null, + "position": { + "x": 600, + "y": 300, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "name": "reaction_mixture", + "volume": 300.0, + "concentration": 85.0 + } + ] + } + } + ], + "links": [ + { + "id": "link_pump_valve", + "source": "transfer_pump_1", + "target": "multiway_valve_1", + "type": "fluid", + "port": { + "transfer_pump_1": "transferpump", + "multiway_valve_1": "transferpump" + } + }, + { + "id": "link_valve_sample", + "source": "multiway_valve_1", + "target": "flask_sample", + "type": "fluid", + "port": { + "multiway_valve_1": "1", + "flask_sample": "outlet" + } + }, + { + "id": "link_valve_hexane", + "source": "multiway_valve_1", + "target": "flask_hexane", + "type": "fluid", + "port": { + "multiway_valve_1": "2", + "flask_hexane": "outlet" + } + }, + { + "id": "link_valve_ethyl_acetate", + "source": "multiway_valve_1", + "target": "flask_ethyl_acetate", + "type": "fluid", + "port": { + "multiway_valve_1": "3", + "flask_ethyl_acetate": "outlet" + } + }, + { + "id": "link_valve_methanol", + "source": "multiway_valve_1", + "target": "flask_methanol", + "type": "fluid", + "port": { + "multiway_valve_1": "4", + "flask_methanol": "outlet" + } + }, + { + "id": "link_valve_column_vessel", + "source": "multiway_valve_1", + "target": "column_vessel", + "type": "fluid", + "port": { + "multiway_valve_1": "5", + "column_vessel": "inlet" + } + }, + { + "id": "link_valve_collection1", + "source": "multiway_valve_1", + "target": "collection_flask_1", + "type": "fluid", + "port": { + "multiway_valve_1": "6", + "collection_flask_1": "inlet" + } + }, + { + "id": "link_valve_collection2", + "source": "multiway_valve_1", + "target": "collection_flask_2", + "type": "fluid", + "port": { + "multiway_valve_1": "7", + "collection_flask_2": "inlet" + } + }, + { + "id": "link_valve_waste", + "source": "multiway_valve_1", + "target": "waste_flask", + "type": "fluid", + "port": { + "multiway_valve_1": "8", + "waste_flask": "inlet" + } + }, + { + "id": "link_column_device_vessel", + "source": "column_1", + "target": "column_vessel", + "type": "transport", + "port": { + "column_1": "columnin", + "column_vessel": "column_port" + } + }, + { + "id": "link_column_collection3", + "source": "column_1", + "target": "collection_flask_3", + "type": "transport", + "port": { + "column_1": "columnout", + "collection_flask_3": "column_outlet" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/Protocol_Test_Station/simple_stir_heatchill_test_station.json b/test/experiments/Protocol_Test_Station/simple_stir_heatchill_test_station.json new file mode 100644 index 00000000..1f65cc71 --- /dev/null +++ b/test/experiments/Protocol_Test_Station/simple_stir_heatchill_test_station.json @@ -0,0 +1,141 @@ +{ + "nodes": [ + { + "id": "SimpleStirHeatChillTestStation", + "name": "搅拌加热测试站", + "children": [ + "stirrer_1", + "heatchill_1", + "main_reactor", + "secondary_reactor" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 500, + "y": 200, + "z": 0 + }, + "config": { + "protocol_type": [ + "StirProtocol", + "StartStirProtocol", + "StopStirProtocol", + "HeatChillProtocol", + "HeatChillStartProtocol", + "HeatChillStopProtocol" + ] + }, + "data": {} + }, + { + "id": "stirrer_1", + "name": "主搅拌器", + "children": [], + "parent": "SimpleStirHeatChillTestStation", + "type": "device", + "class": "virtual_stirrer", + "position": { + "x": 400, + "y": 350, + "z": 0 + }, + "config": { + "port": "VIRTUAL_STIRRER1", + "max_speed": 1500.0, + "min_speed": 50.0 + }, + "data": { + "status": "Idle" + } + }, + { + "id": "heatchill_1", + "name": "主加热冷却器", + "children": [], + "parent": "SimpleStirHeatChillTestStation", + "type": "device", + "class": "virtual_heatchill", + "position": { + "x": 600, + "y": 350, + "z": 0 + }, + "config": { + "port": "VIRTUAL_HEATCHILL1", + "max_temp": 200.0, + "min_temp": -80.0, + "max_stir_speed": 1000.0 + }, + "data": { + "status": "Idle" + } + }, + { + "id": "main_reactor", + "name": "主反应器", + "children": [], + "parent": "SimpleStirHeatChillTestStation", + "type": "container", + "class": null, + "position": { + "x": 500, + "y": 450, + "z": 0 + }, + "config": { + "max_volume": 2000.0 + }, + "data": { + "liquid": [ + { + "liquid_type": "water", + "liquid_volume": 500.0 + } + ] + } + }, + { + "id": "secondary_reactor", + "name": "副反应器", + "children": [], + "parent": "SimpleStirHeatChillTestStation", + "type": "container", + "class": null, + "position": { + "x": 700, + "y": 450, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [] + } + } + ], + "links": [ + { + "id": "link_stirrer1_main_reactor", + "source": "stirrer_1", + "target": "main_reactor", + "type": "mechanical", + "port": { + "stirrer_1": "stirrer", + "main_reactor": "stirrer_port" + } + }, + { + "id": "link_heatchill1_main_reactor", + "source": "heatchill_1", + "target": "main_reactor", + "type": "mechanical", + "port": { + "heatchill_1": "heatchill", + "main_reactor": "heating_jacket" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/comprehensive_protocol/checklist.md b/test/experiments/comprehensive_protocol/checklist.md new file mode 100644 index 00000000..ed73ec5a --- /dev/null +++ b/test/experiments/comprehensive_protocol/checklist.md @@ -0,0 +1,36 @@ +1. 用到的仪器 + virtual_multiway_valve(√) 八通阀门 + virtual_transfer_pump(√) 转移泵 + virtual_centrifuge() 离心机 + virtual_rotavap() 旋蒸仪 + virtual_heatchill() 加热器 + virtual_stirrer() 搅拌器 + virtual_solenoid_valve() 电磁阀 + virtual_vacuum_pump(√) vacuum_pump.mock 真空泵 + virtual_gas_source(√) 气源 + virtual_filter() 过滤器 + virtual_column(√) 层析柱 + separator() homemade_grbl_conductivity 分液漏斗 +2. 用到的protocol + PumpTransferProtocol: generate_pump_protocol_with_rinsing, (√) + 这个重复了，删掉CleanProtocol: generate_clean_protocol, + SeparateProtocol: generate_separate_protocol, (×) + EvaporateProtocol: generate_evaporate_protocol, (√) + EvacuateAndRefillProtocol: generate_evacuateandrefill_protocol, (√) + CentrifugeProtocol: generate_centrifuge_protocol, (√) + AddProtocol: generate_add_protocol, (√) + FilterProtocol: generate_filter_protocol, (√) + HeatChillProtocol: generate_heat_chill_protocol, (√) + HeatChillStartProtocol: generate_heat_chill_start_protocol, (√) + HeatChillStopProtocol: generate_heat_chill_stop_protocol, (√) + StirProtocol: generate_stir_protocol, (√) + StartStirProtocol: generate_start_stir_protocol, (√) + StopStirProtocol: generate_stop_stir_protocol, (√) + 这个重复了，删掉TransferProtocol: generate_transfer_protocol, + CleanVesselProtocol: generate_clean_vessel_protocol, (√) + DissolveProtocol: generate_dissolve_protocol, (√) + FilterThroughProtocol: generate_filter_through_protocol, (√) + RunColumnProtocol: generate_run_column_protocol, (×) + WashSolidProtocol: generate_wash_solid_protocol, (×) + +上下文体积搜索 \ No newline at end of file diff --git a/test/experiments/comprehensive_protocol/comprehensive_station.json b/test/experiments/comprehensive_protocol/comprehensive_station.json new file mode 100644 index 00000000..b0f1a1bd --- /dev/null +++ b/test/experiments/comprehensive_protocol/comprehensive_station.json @@ -0,0 +1,857 @@ +{ + "nodes": [ + { + "id": "ComprehensiveProtocolStation", + "name": "综合协议测试工作站", + "children": [ + "multiway_valve_1", + "multiway_valve_2", + "transfer_pump_1", + "transfer_pump_2", + "reagent_bottle_1", + "reagent_bottle_2", + "reagent_bottle_3", + "reagent_bottle_4", + "reagent_bottle_5", + "centrifuge_1", + "rotavap_1", + "main_reactor", + "heater_1", + "stirrer_1", + "stirrer_2", + "waste_bottle_1", + "waste_bottle_2", + "solenoid_valve_1", + "solenoid_valve_2", + "vacuum_pump_1", + "gas_source_1", + "filter_1", + "column_1", + "separator_1", + "collection_bottle_1", + "collection_bottle_2", + "collection_bottle_3" + ], + "parent": null, + "type": "device", + "class": "workstation", + "position": { + "x": 600, + "y": 400, + "z": 0 + }, + "config": { + "protocol_type": [ + "AddProtocol", + "TransferProtocol", + "StartStirProtocol", + "StopStirProtocol", + "StirProtocol", + "RunColumnProtocol", + "CentrifugeProtocol", + "FilterProtocol", + "CleanVesselProtocol", + "DissolveProtocol", + "FilterThroughProtocol", + "WashSolidProtocol", + "SeparateProtocol", + "EvaporateProtocol", + "HeatChillProtocol", + "HeatChillStartProtocol", + "HeatChillStopProtocol", + "EvacuateAndRefillProtocol", + "PumpTransferProtocol" + ] + }, + "data": {} + }, + { + "id": "multiway_valve_1", + "name": "八通阀门1", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 400, + "y": 300, + "z": 0 + }, + "config": { + "positions": 8 + }, + "data": { + "valve_state": "Ready", + "current_position": 1 + } + }, + { + "id": "multiway_valve_2", + "name": "八通阀门2", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 800, + "y": 300, + "z": 0 + }, + "config": { + "positions": 8 + }, + "data": { + "valve_state": "Ready", + "current_position": 1 + } + }, + { + "id": "transfer_pump_1", + "name": "转移泵1", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 350, + "y": 250, + "z": 0 + }, + "config": { + "max_volume": 25.0, + "transfer_rate": 10.0 + }, + "data": { + "status": "Idle", + "current_volume": 0.0 + } + }, + { + "id": "transfer_pump_2", + "name": "转移泵2", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_transfer_pump", + "position": { + "x": 850, + "y": 250, + "z": 0 + }, + "config": { + "max_volume": 25.0, + "transfer_rate": 10.0 + }, + "data": { + "status": "Idle", + "current_volume": 0.0 + } + }, + { + "id": "reagent_bottle_1", + "name": "试剂瓶1-DMF", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 200, + "y": 150, + "z": 0 + }, + "config": { + "volume": 1000.0, + "reagent": "DMF" + }, + "data": { + "current_volume": 1000.0, + "reagent_name": "DMF" + } + }, + { + "id": "reagent_bottle_2", + "name": "试剂瓶2-乙酸乙酯", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 250, + "y": 150, + "z": 0 + }, + "config": { + "volume": 1000.0, + "reagent": "ethyl_acetate" + }, + "data": { + "current_volume": 1000.0, + "reagent_name": "ethyl_acetate" + } + }, + { + "id": "reagent_bottle_3", + "name": "试剂瓶3-己烷", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 300, + "y": 150, + "z": 0 + }, + "config": { + "volume": 1000.0, + "reagent": "hexane" + }, + "data": { + "current_volume": 1000.0, + "reagent_name": "hexane" + } + }, + { + "id": "reagent_bottle_4", + "name": "试剂瓶4-甲醇", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 900, + "y": 150, + "z": 0 + }, + "config": { + "volume": 1000.0, + "reagent": "methanol" + }, + "data": { + "current_volume": 1000.0, + "reagent_name": "methanol" + } + }, + { + "id": "reagent_bottle_5", + "name": "试剂瓶5-水", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 950, + "y": 150, + "z": 0 + }, + "config": { + "volume": 1000.0, + "reagent": "water" + }, + "data": { + "current_volume": 1000.0, + "reagent_name": "water" + } + }, + { + "id": "centrifuge_1", + "name": "离心机", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_centrifuge", + "position": { + "x": 200, + "y": 400, + "z": 0 + }, + "config": { + "max_speed": 15000.0, + "max_temp": 40.0, + "min_temp": 4.0 + }, + "data": { + "current_speed": 0.0, + "status": "Idle" + } + }, + { + "id": "rotavap_1", + "name": "旋转蒸发仪", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_rotavap", + "position": { + "x": 300, + "y": 400, + "z": 0 + }, + "config": { + "max_temp": 180.0, + "max_rotation_speed": 280.0 + }, + "data": { + "status": "Idle", + "current_temp": 25.0, + "rotation_speed": 0.0 + } + }, + { + "id": "main_reactor", + "name": "主反应器", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 400, + "y": 450, + "z": 0 + }, + "config": { + "volume": 500.0, + "max_temp": 200.0, + "min_temp": -20.0, + "has_stirrer": true, + "has_heater": true + }, + "data": { + "current_volume": 0.0, + "current_temp": 25.0 + } + }, + { + "id": "heater_1", + "name": "加热器", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_heatchill", + "position": { + "x": 450, + "y": 450, + "z": 0 + }, + "config": { + "max_temp": 200.0, + "min_temp": -20.0 + }, + "data": { + "status": "Idle", + "current_temp": 25.0 + } + }, + { + "id": "stirrer_1", + "name": "搅拌器1", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_stirrer", + "position": { + "x": 350, + "y": 450, + "z": 0 + }, + "config": { + "max_speed": 2000.0 + }, + "data": { + "status": "Idle", + "current_speed": 0.0 + } + }, + { + "id": "stirrer_2", + "name": "搅拌器2", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_stirrer", + "position": { + "x": 351, + "y": 451, + "z": 0 + }, + "config": { + "max_speed": 2000.0 + }, + "data": { + "status": "Idle", + "current_speed": 0.0 + } + }, + { + "id": "waste_bottle_1", + "name": "废液瓶1", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 500, + "y": 400, + "z": 0 + }, + "config": { + "volume": 2000.0 + }, + "data": { + "current_volume": 0.0 + } + }, + { + "id": "waste_bottle_2", + "name": "废液瓶2", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 1100, + "y": 500, + "z": 0 + }, + "config": { + "volume": 2000.0 + }, + "data": { + "current_volume": 0.0 + } + }, + { + "id": "solenoid_valve_1", + "name": "电磁阀1", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_solenoid_valve", + "position": { + "x": 700, + "y": 200, + "z": 0 + }, + "config": { + "voltage": 12.0, + "response_time": 0.1 + }, + "data": { + "valve_state": "Closed", + "is_open": false + } + }, + { + "id": "solenoid_valve_2", + "name": "电磁阀2", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_solenoid_valve", + "position": { + "x": 700, + "y": 150, + "z": 0 + }, + "config": { + "voltage": 12.0, + "response_time": 0.1 + }, + "data": { + "valve_state": "Closed", + "is_open": false + } + }, + { + "id": "vacuum_pump_1", + "name": "真空泵", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_vacuum_pump", + "position": { + "x": 650, + "y": 200, + "z": 0 + }, + "config": { + "max_vacuum": 0.1, + "pump_rate": 50.0 + }, + "data": { + "status": "Off", + "current_vacuum": 1.0 + } + }, + { + "id": "gas_source_1", + "name": "气源", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_gas_source", + "position": { + "x": 650, + "y": 150, + "z": 0 + }, + "config": {}, + "data": { + "gas_type": "nitrogen", + "max_pressure": 5.0 + } + }, + { + "id": "filter_1", + "name": "过滤器", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_filter", + "position": { + "x": 900, + "y": 400, + "z": 0 + }, + "config": { + "filter_type": "membrane", + "max_pressure": 5.0 + }, + "data": { + "status": "Ready", + "pressure": 0.0 + } + }, + { + "id": "column_1", + "name": "洗脱柱", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_column", + "position": { + "x": 950, + "y": 400, + "z": 0 + }, + "config": { + "column_type": "silica_gel", + "length": 30.0, + "diameter": 2.5 + }, + "data": { + "status": "Ready", + "loaded": false + } + }, + { + "id": "separator_1", + "name": "分液器", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "device", + "class": "virtual_separator", + "position": { + "x": 1000, + "y": 450, + "z": 0 + }, + "config": { + "volume": 250.0, + "has_phases": true + }, + "data": { + "status": "Ready", + "phase_separation": false + } + }, + { + "id": "collection_bottle_1", + "name": "接收瓶1", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 900, + "y": 500, + "z": 0 + }, + "config": { + "volume": 250.0 + }, + "data": { + "current_volume": 0.0 + } + }, + { + "id": "collection_bottle_2", + "name": "接收瓶2", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 950, + "y": 500, + "z": 0 + }, + "config": { + "volume": 250.0 + }, + "data": { + "current_volume": 0.0 + } + }, + { + "id": "collection_bottle_3", + "name": "接收瓶3", + "children": [], + "parent": "ComprehensiveProtocolStation", + "type": "container", + "class": "container", + "position": { + "x": 1050, + "y": 500, + "z": 0 + }, + "config": { + "volume": 250.0 + }, + "data": { + "current_volume": 0.0 + } + } + ], + "links": [ + { + "id": "link_pump1_valve1", + "source": "transfer_pump_1", + "target": "multiway_valve_1", + "type": "fluid", + "port": { + "transfer_pump_1": "transferpump", + "multiway_valve_1": "transferpump" + } + }, + { + "id": "link_valve1_reagent1", + "source": "multiway_valve_1", + "target": "reagent_bottle_1", + "type": "fluid", + "port": { + "multiway_valve_1": "1", + "reagent_bottle_1": "top" + } + }, + { + "id": "link_valve1_reagent2", + "source": "multiway_valve_1", + "target": "reagent_bottle_2", + "type": "fluid", + "port": { + "multiway_valve_1": "2", + "reagent_bottle_2": "top" + } + }, + { + "id": "link_valve1_reagent3", + "source": "multiway_valve_1", + "target": "reagent_bottle_3", + "type": "fluid", + "port": { + "multiway_valve_1": "3", + "reagent_bottle_3": "top" + } + }, + { + "id": "link_valve1_centrifuge", + "source": "multiway_valve_1", + "target": "centrifuge_1", + "type": "transport", + "port": { + "multiway_valve_1": "4", + "centrifuge_1": "centrifuge" + } + }, + { + "id": "link_valve1_rotavap", + "source": "multiway_valve_1", + "target": "rotavap_1", + "type": "fluid", + "port": { + "multiway_valve_1": "5", + "rotavap_1": "sample_in" + } + }, + { + "id": "link_valve1_reactor", + "source": "multiway_valve_1", + "target": "main_reactor", + "type": "fluid", + "port": { + "multiway_valve_1": "6", + "main_reactor": "top" + } + }, + { + "id": "link_valve1_waste1", + "source": "multiway_valve_1", + "target": "waste_bottle_1", + "type": "fluid", + "port": { + "multiway_valve_1": "7", + "waste_bottle_1": "top" + } + }, + { + "id": "link_valve1_valve2", + "source": "multiway_valve_1", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "multiway_valve_1": "8", + "multiway_valve_2": "1" + } + }, + { + "id": "link_pump2_valve2", + "source": "transfer_pump_2", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "transfer_pump_2": "transferpump", + "multiway_valve_2": "transferpump" + } + }, + { + "id": "link_valve2_solenoid1", + "source": "multiway_valve_2", + "target": "solenoid_valve_1", + "type": "fluid", + "port": { + "multiway_valve_2": "2", + "solenoid_valve_1": "in" + } + }, + { + "id": "link_vacuum_solenoid1", + "source": "vacuum_pump_1", + "target": "solenoid_valve_1", + "type": "fluid", + "port": { + "vacuum_pump_1": "vacuumpump", + "solenoid_valve_1": "out" + } + }, + { + "id": "link_valve2_solenoid2", + "source": "multiway_valve_2", + "target": "solenoid_valve_2", + "type": "fluid", + "port": { + "multiway_valve_2": "3", + "solenoid_valve_2": "in" + } + }, + { + "id": "link_gas_solenoid2", + "source": "gas_source_1", + "target": "solenoid_valve_2", + "type": "fluid", + "port": { + "gas_source_1": "gassource", + "solenoid_valve_2": "out" + } + }, + { + "id": "link_valve2_filter", + "source": "multiway_valve_2", + "target": "filter_1", + "type": "transport", + "port": { + "multiway_valve_2": "4", + "filter_1": "filter_in" + } + }, + { + "id": "link_valve2_column", + "source": "multiway_valve_2", + "target": "column_1", + "type": "transport", + "port": { + "multiway_valve_2": "5", + "column_1": "columnin" + } + }, + { + "id": "link_column_collection2", + "source": "column_1", + "target": "collection_bottle_2", + "type": "transport", + "port": { + "column_1": "columnout", + "collection_bottle_2": "top" + } + }, + { + "id": "link_valve2_separator", + "source": "multiway_valve_2", + "target": "separator_1", + "type": "fluid", + "port": { + "multiway_valve_2": "6", + "separator_1": "separator_in" + } + }, + { + "id": "link_separator_collection3", + "source": "separator_1", + "target": "collection_bottle_3", + "type": "fluid", + "port": { + "separator_1": "bottom_phase_out", + "collection_bottle_3": "top" + } + }, + { + "id": "link_valve2_reagent4", + "source": "multiway_valve_2", + "target": "reagent_bottle_4", + "type": "fluid", + "port": { + "multiway_valve_2": "7", + "reagent_bottle_4": "top" + } + }, + { + "id": "link_valve2_reagent5", + "source": "multiway_valve_2", + "target": "reagent_bottle_5", + "type": "fluid", + "port": { + "multiway_valve_2": "8", + "reagent_bottle_5": "top" + } + }, + { + "id": "mech_stirrer_reactor", + "source": "stirrer_1", + "target": "main_reactor", + "type": "mechanical", + "port": { + "stirrer_1": "stirrer", + "main_reactor": "bind" + } + }, + { + "id": "thermal_heater_reactor", + "source": "heater_1", + "target": "main_reactor", + "type": "mechanical", + "port": { + "heater_1": "heatchill", + "main_reactor": "bind" + } + } + ] +} \ No newline at end of file diff --git a/test/experiments/mock_protocol/addteststation.json b/test/experiments/mock_protocol/addteststation.json index dd16a1fe..beb68ffa 100644 --- a/test/experiments/mock_protocol/addteststation.json +++ b/test/experiments/mock_protocol/addteststation.json @@ -4,58 +4,83 @@ "id": "AddTestStation", "name": "添加试剂测试工作站", "children": [ - "pump_add", - "flask_1", - "flask_2", - "flask_3", - "flask_4", - "reactor", + "transfer_pump", + "multiway_valve", "stirrer", - "flask_air" + "flask_reagent1", + "flask_reagent2", + "flask_reagent3", + "flask_reagent4", + "reactor", + "flask_waste", + "flask_rinsing", + "flask_buffer" ], "parent": null, "type": "device", "class": "workstation", "position": { - "x": 620.6111111111111, + "x": 620, "y": 171, "z": 0 }, "config": { - "protocol_type": ["AddProtocol", "PumpTransferProtocol", "CleanProtocol"] + "protocol_type": ["AddProtocol", "TransferProtocol", "StartStirProtocol", "StopStirProtocol"] }, "data": {} }, { - "id": "pump_add", - "name": "pump_add", + "id": "transfer_pump", + "name": "注射器泵", "children": [], "parent": "AddTestStation", "type": "device", - "class": "virtual_pump", + "class": "virtual_transfer_pump", "position": { - "x": 520.6111111111111, + "x": 520, "y": 300, "z": 0 }, "config": { "port": "VIRTUAL", - "max_volume": 25.0 + "max_volume": 50.0, + "transfer_rate": 5.0 }, "data": { "status": "Idle" } }, + { + "id": "multiway_valve", + "name": "八通阀门", + "children": [], + "parent": "AddTestStation", + "type": "device", + "class": "virtual_multiway_valve", + "position": { + "x": 420, + "y": 300, + "z": 0 + }, + "config": { + "port": "VIRTUAL", + "positions": 8 + }, + "data": { + "status": "Idle", + "current_position": 1 + } + }, { "id": "stirrer", - "name": "stirrer", + "name": "搅拌器", "children": [], "parent": "AddTestStation", "type": "device", "class": "virtual_stirrer", "position": { - "x": 698.1111111111111, - "y": 478, + "x": 720, + "y": 450, "z": 0 }, "config": { @@ -68,72 +93,115 @@ } }, { - "id": "flask_1", - "name": "通用试剂瓶1", + "id": "flask_reagent1", + "name": "试剂瓶1 (甲醇)", "children": [], "parent": "AddTestStation", "type": "container", "class": null, "position": { "x": 100, - "y": 428, + "y": 400, "z": 0 }, "config": { - "max_volume": 2000.0 + "max_volume": 1000.0 }, "data": { - "liquid": [] + "liquid": [ + { + "name": "甲醇", + "volume": 800.0, + "concentration": "99.9%" + } + ] } }, { - "id": "flask_2", - "name": "通用试剂瓶2", + "id": "flask_reagent2", + "name": "试剂瓶2 (乙醇)", "children": [], "parent": "AddTestStation", "type": "container", "class": null, "position": { - "x": 250, - "y": 428, + "x": 180, + "y": 400, "z": 0 }, "config": { - "max_volume": 2000.0 + "max_volume": 1000.0 }, "data": { - "liquid": [] + "liquid": [ + { + "name": "乙醇", + "volume": 750.0, + "concentration": "95%" + } + ] } }, { - "id": "flask_3", - "name": "通用试剂瓶3", + "id": "flask_reagent3", + "name": "试剂瓶3 (丙酮)", "children": [], "parent": "AddTestStation", "type": "container", "class": null, "position": { - "x": 400, - "y": 428, + "x": 260, + "y": 400, "z": 0 }, "config": { - "max_volume": 2000.0 + "max_volume": 1000.0 }, "data": { - "liquid": [] + "liquid": [ + { + "name": "丙酮", + "volume": 900.0, + "concentration": "99.5%" + } + ] + } + }, + { + "id": "flask_reagent4", + "name": "试剂瓶4 (二氯甲烷)", + "children": [], + "parent": "AddTestStation", + "type": "container", + "class": null, + "position": { + "x": 340, + "y": 400, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "name": "二氯甲烷", + "volume": 850.0, + "concentration": "99.8%" + } + ] } }, { - "id": "flask_4", - "name": "通用试剂瓶4", + "id": "reactor", + "name": "反应器", "children": [], "parent": "AddTestStation", "type": "container", "class": null, "position": { - "x": 550, - "y": 428, + "x": 720, + "y": 400, "z": 0 }, "config": { @@ -144,106 +212,164 @@ } }, { - "id": "reactor", - "name": "reactor", + "id": "flask_waste", + "name": "废液瓶", "children": [], "parent": "AddTestStation", "type": "container", "class": null, "position": { - "x": 698.1111111111111, - "y": 428, + "x": 850, + "y": 400, "z": 0 }, "config": { - "max_volume": 5000.0 + "max_volume": 3000.0 }, "data": { "liquid": [] } }, { - "id": "flask_air", - "name": "flask_air", + "id": "flask_rinsing", + "name": "冲洗液瓶", "children": [], "parent": "AddTestStation", "type": "container", "class": null, "position": { - "x": 800, + "x": 950, "y": 300, "z": 0 }, "config": { - "max_volume": 2000.0 + "max_volume": 1000.0 }, "data": { - "liquid": [] + "liquid": [ + { + "name": "去离子水", + "volume": 800.0, + "concentration": "纯净" + } + ] + } + }, + { + "id": "flask_buffer", + "name": "缓冲液瓶", + "children": [], + "parent": "AddTestStation", + "type": "container", + "class": null, + "position": { + "x": 950, + "y": 400, + "z": 0 + }, + "config": { + "max_volume": 1000.0 + }, + "data": { + "liquid": [ + { + "name": "磷酸盐缓冲液", + "volume": 700.0, + "concentration": "0.1M, pH 7.4" + } + ] } } ], "links": [ { - "source": "stirrer", - "target": "reactor", + "source": "transfer_pump", + "target": "multiway_valve", "type": "physical", "port": { - "stirrer": "top", - "reactor": "bottom" + "transfer_pump": "syringe-port", + "multiway_valve": "multiway-valve-inlet" } }, { - "source": "pump_add", - "target": "flask_1", + "source": "multiway_valve", + "target": "flask_reagent1", "type": "physical", "port": { - "pump_add": "outlet", - "flask_1": "top" + "multiway_valve": "multiway-valve-port-1", + "flask_reagent1": "top" } }, { - "source": "pump_add", - "target": "flask_2", + "source": "multiway_valve", + "target": "flask_reagent2", "type": "physical", "port": { - "pump_add": "inlet", - "flask_2": "top" + "multiway_valve": "multiway-valve-port-2", + "flask_reagent2": "top" } }, { - "source": "pump_add", - "target": "flask_3", + "source": "multiway_valve", + "target": "flask_reagent3", "type": "physical", "port": { - "pump_add": "inlet", - "flask_3": "top" + "multiway_valve": "multiway-valve-port-3", + "flask_reagent3": "top" } }, { - "source": "pump_add", - "target": "flask_4", + "source": "multiway_valve", + "target": "flask_reagent4", "type": "physical", "port": { - "pump_add": "inlet", - "flask_4": "top" + "multiway_valve": "multiway-valve-port-4", + "flask_reagent4": "top" } }, { - "source": "pump_add", + "source": "multiway_valve", "target": "reactor", "type": "physical", "port": { - "pump_add": "outlet", + "multiway_valve": "multiway-valve-port-5", "reactor": "top" } }, { - "source": "pump_add", - "target": "flask_air", + "source": "multiway_valve", + "target": "flask_waste", "type": "physical", "port": { - "pump_add": "inlet", - "flask_air": "top" + "multiway_valve": "multiway-valve-port-6", + "flask_waste": "top" + } + }, + { + "source": "multiway_valve", + "target": "flask_rinsing", + "type": "physical", + "port": { + "multiway_valve": "multiway-valve-port-7", + "flask_rinsing": "top" + } + }, + { + "source": "multiway_valve", + "target": "flask_buffer", + "type": "physical", + "port": { + "multiway_valve": "multiway-valve-port-8", + "flask_buffer": "top" + } + }, + { + "source": "stirrer", + "target": "reactor", + "type": "physical", + "port": { + "stirrer": "stirrer-vessel", + "reactor": "bottom" } } ] diff --git a/test/experiments/mock_protocol/evaporateteststation.json b/test/experiments/mock_protocol/evaporateteststation.json deleted file mode 100644 index e69de29b..00000000 diff --git a/test/experiments/mock_reactor.json b/test/experiments/mock_reactor.json index b0994cd0..1c03d315 100644 --- a/test/experiments/mock_reactor.json +++ b/test/experiments/mock_reactor.json @@ -30,14 +30,17 @@ "children": [], "parent": "ReactorX", "type": "container", - "class": null, + "class": "container", "position": { "x": 698.1111111111111, "y": 428, "z": 0 }, "config": { - "max_volume": 5000.0 + "max_volume": 5000.0, + "size_x": 200.0, + "size_y": 200.0, + "size_z": 200.0 }, "data": { "liquid": [ @@ -71,7 +74,7 @@ "type": "device", "class": "solenoid_valve.mock", "position": { - "x": 620.6111111111111, + "x": 780, "y": 171, "z": 0 }, @@ -89,7 +92,7 @@ "type": "device", "class": "vacuum_pump.mock", "position": { - "x": 620.6111111111111, + "x": 500, "y": 171, "z": 0 }, @@ -107,7 +110,7 @@ "type": "device", "class": "gas_source.mock", "position": { - "x": 620.6111111111111, + "x": 900, "y": 171, "z": 0 }, @@ -119,39 +122,39 @@ ], "links": [ { - "source": "reactor", - "target": "vacuum_valve", - "type": "physical", + "source": "vacuum_valve", + "target": "reactor", + "type": "fluid", "port": { "reactor": "top", - "vacuum_valve": "1" + "vacuum_valve": "out" } }, { - "source": "reactor", - "target": "gas_valve", - "type": "physical", + "source": "gas_valve", + "target": "reactor", + "type": "fluid", "port": { "reactor": "top", - "gas_valve": "1" + "gas_valve": "out" } }, { "source": "vacuum_pump", "target": "vacuum_valve", - "type": "physical", + "type": "fluid", "port": { "vacuum_pump": "out", - "vacuum_valve": "0" + "vacuum_valve": "in" } }, { "source": "gas_source", "target": "gas_valve", - "type": "physical", + "type": "fluid", "port": { "gas_source": "out", - "gas_valve": "0" + "gas_valve": "in" } } ] diff --git a/unilabos/app/backend.py b/unilabos/app/backend.py index 5bc4ad39..9f7d4279 100644 --- a/unilabos/app/backend.py +++ b/unilabos/app/backend.py @@ -8,6 +8,7 @@ def start_backend( backend: str, devices_config: dict = {}, resources_config: list = [], + resources_edge_config: list = [], graph=None, controllers_config: dict = {}, bridges=[], @@ -31,7 +32,7 @@ def start_backend( backend_thread = threading.Thread( target=main if not without_host else slave, - args=(devices_config, resources_config, graph, controllers_config, bridges, visual, resources_mesh_config), + args=(devices_config, resources_config, resources_edge_config, graph, controllers_config, bridges, visual, resources_mesh_config), name="backend_thread", daemon=True, ) diff --git a/unilabos/app/main.py b/unilabos/app/main.py index 0f6b2f42..835c57d6 100644 --- a/unilabos/app/main.py +++ b/unilabos/app/main.py @@ -10,7 +10,7 @@ import yaml -from unilabos.resources.graphio import tree_to_list +from unilabos.resources.graphio import tree_to_list, modify_to_backend_format # 首先添加项目根目录到路径 current_dir = os.path.dirname(os.path.abspath(__file__)) @@ -22,6 +22,21 @@ from unilabos.utils.banner_print import print_status, print_unilab_banner +def load_config_from_file(config_path): + if config_path is None: + config_path = os.environ.get("UNILABOS.BASICCONFIG.CONFIG_PATH", None) + if config_path: + if not os.path.exists(config_path): + print_status(f"配置文件 {config_path} 不存在", "error") + elif not config_path.endswith(".py"): + print_status(f"配置文件 {config_path} 不是Python文件，必须以.py结尾", "error") + else: + load_config(config_path) + else: + print_status(f"启动 UniLab-OS时，配置文件参数未正确传入 --config '{config_path}' 尝试本地配置...", "warning") + load_config(config_path) + + def parse_args(): """解析命令行参数""" parser = argparse.ArgumentParser(description="Start Uni-Lab Edge server.") @@ -58,6 +73,11 @@ def parse_args(): action="store_true", help="Slave模式下跳过等待host服务", ) + parser.add_argument( + "--upload_registry", + action="store_true", + help="启动unilab时同时报送注册表信息", + ) parser.add_argument( "--config", type=str, @@ -97,22 +117,12 @@ def main(): # 加载配置文件，优先加载config，然后从env读取 config_path = args_dict.get("config") - if config_path is None: - config_path = os.environ.get("UNILABOS.BASICCONFIG.CONFIG_PATH", None) - if config_path: - if not os.path.exists(config_path): - print_status(f"配置文件 {config_path} 不存在", "error") - elif not config_path.endswith(".py"): - print_status(f"配置文件 {config_path} 不是Python文件，必须以.py结尾", "error") - else: - load_config(config_path) - else: - print_status(f"启动 UniLab-OS时，配置文件参数未正确传入 --config '{config_path}' 尝试本地配置...", "warning") - load_config(config_path) + load_config_from_file(config_path) # 设置BasicConfig参数 BasicConfig.is_host_mode = not args_dict.get("without_host", False) BasicConfig.slave_no_host = args_dict.get("slave_no_host", False) + BasicConfig.upload_registry = args_dict.get("upload_registry", False) machine_name = os.popen("hostname").read().strip() machine_name = "".join([c if c.isalnum() or c == "_" else "_" for c in machine_name]) BasicConfig.machine_name = machine_name @@ -136,15 +146,16 @@ def main(): # 注册表 build_registry(args_dict["registry_path"]) - + resource_edge_info = [] devices_and_resources = None if args_dict["graph"] is not None: import unilabos.resources.graphio as graph_res - graph_res.physical_setup_graph = ( - read_node_link_json(args_dict["graph"]) - if args_dict["graph"].endswith(".json") - else read_graphml(args_dict["graph"]) - ) + if args_dict["graph"].endswith(".json"): + graph, data = read_node_link_json(args_dict["graph"]) + else: + graph, data = read_graphml(args_dict["graph"]) + graph_res.physical_setup_graph = graph + resource_edge_info = modify_to_backend_format(data["links"]) devices_and_resources = dict_from_graph(graph_res.physical_setup_graph) # args_dict["resources_config"] = initialize_resources(list(deepcopy(devices_and_resources).values())) args_dict["resources_config"] = list(devices_and_resources.values()) @@ -185,6 +196,7 @@ def _exit(signum, frame): signal.signal(signal.SIGTERM, _exit) mqtt_client.start() args_dict["resources_mesh_config"] = {} + args_dict["resources_edge_config"] = resource_edge_info # web visiualize 2D if args_dict["visual"] != "disable": enable_rviz = args_dict["visual"] == "rviz" diff --git a/unilabos/app/mq.py b/unilabos/app/mq.py index fbd57b93..ac744c9d 100644 --- a/unilabos/app/mq.py +++ b/unilabos/app/mq.py @@ -172,13 +172,14 @@ def publish_job_status(self, feedback_data: dict, job_id: str, status: str, retu jobdata = {"job_id": job_id, "data": feedback_data, "status": status, "return_info": return_info} self.client.publish(f"labs/{MQConfig.lab_id}/job/list/", json.dumps(jobdata), qos=2) - def publish_registry(self, device_id: str, device_info: dict): + def publish_registry(self, device_id: str, device_info: dict, print_debug: bool = True): if self.mqtt_disable: return address = f"labs/{MQConfig.lab_id}/registry/" registry_data = json.dumps({device_id: device_info}, ensure_ascii=False, cls=TypeEncoder) self.client.publish(address, registry_data, qos=2) - logger.debug(f"Registry data published: address: {address}, {registry_data}") + if print_debug: + logger.debug(f"Registry data published: address: {address}, {registry_data}") def publish_actions(self, action_id: str, action_info: dict): if self.mqtt_disable: diff --git a/unilabos/app/register.py b/unilabos/app/register.py new file mode 100644 index 00000000..76ad5a57 --- /dev/null +++ b/unilabos/app/register.py @@ -0,0 +1,67 @@ +import argparse +import time + +from unilabos.registry.registry import build_registry + +from unilabos.app.main import load_config_from_file +from unilabos.utils.log import logger + + +def register_devices_and_resources(mqtt_client, lab_registry): + """ + 注册设备和资源到 MQTT + """ + logger.info("[UniLab Register] 开始注册设备和资源...") + + # 注册设备信息 + for device_info in lab_registry.obtain_registry_device_info(): + mqtt_client.publish_registry(device_info["id"], device_info, False) + logger.debug(f"[UniLab Register] 注册设备: {device_info['id']}") + + # 注册资源信息 + for resource_info in lab_registry.obtain_registry_resource_info(): + mqtt_client.publish_registry(resource_info["id"], resource_info, False) + logger.debug(f"[UniLab Register] 注册资源: {resource_info['id']}") + + time.sleep(10) + + logger.info("[UniLab Register] 设备和资源注册完成.") + + +def main(): + """ + 命令行入口函数 + """ + parser = argparse.ArgumentParser(description="注册设备和资源到 MQTT") + parser.add_argument( + "--registry_path", + type=str, + default=None, + action="append", + help="注册表路径", + ) + parser.add_argument( + "--config", + type=str, + default=None, + help="配置文件路径，支持.py格式的Python配置文件", + ) + args = parser.parse_args() + + # 构建注册表 + build_registry(args.registry_path) + load_config_from_file(args.config) + + from unilabos.app.mq import mqtt_client + + # 连接mqtt + mqtt_client.start() + + from unilabos.registry.registry import lab_registry + + # 注册设备和资源 + register_devices_and_resources(mqtt_client, lab_registry) + + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/unilabos/app/web/client.py b/unilabos/app/web/client.py index 69329489..09b6ede6 100644 --- a/unilabos/app/web/client.py +++ b/unilabos/app/web/client.py @@ -30,7 +30,27 @@ def __init__(self, remote_addr: Optional[str] = None, auth: Optional[str] = None self.auth = MQConfig.lab_id info(f"HTTPClient 初始化完成: remote_addr={self.remote_addr}") - def resource_add(self, resources: List[Dict[str, Any]], database_process_later:bool) -> requests.Response: + def resource_edge_add(self, resources: List[Dict[str, Any]], database_process_later: bool) -> requests.Response: + """ + 添加资源 + + Args: + resources: 要添加的资源列表 + database_process_later: 后台处理资源 + Returns: + Response: API响应对象 + """ + response = requests.post( + f"{self.remote_addr}/lab/resource/edge/batch_create/?database_process_later={1 if database_process_later else 0}", + json=resources, + headers={"Authorization": f"lab {self.auth}"}, + timeout=100, + ) + if response.status_code != 200 and response.status_code != 201: + logger.error(f"添加物料关系失败: {response.status_code}, {response.text}") + return response + + def resource_add(self, resources: List[Dict[str, Any]], database_process_later: bool) -> requests.Response: """ 添加资源 @@ -44,8 +64,10 @@ def resource_add(self, resources: List[Dict[str, Any]], database_process_later:b f"{self.remote_addr}/lab/resource/?database_process_later={1 if database_process_later else 0}", json=resources, headers={"Authorization": f"lab {self.auth}"}, - timeout=5, + timeout=100, ) + if response.status_code != 200: + logger.error(f"添加物料失败: {response.text}") return response def resource_get(self, id: str, with_children: bool = False) -> Dict[str, Any]: @@ -63,7 +85,7 @@ def resource_get(self, id: str, with_children: bool = False) -> Dict[str, Any]: f"{self.remote_addr}/lab/resource/?edge_format=1", params={"id": id, "with_children": with_children}, headers={"Authorization": f"lab {self.auth}"}, - timeout=5, + timeout=20, ) return response.json() @@ -81,7 +103,7 @@ def resource_del(self, id: str) -> requests.Response: f"{self.remote_addr}/lab/resource/batch_delete/", params={"id": id}, headers={"Authorization": f"lab {self.auth}"}, - timeout=5, + timeout=20, ) return response @@ -99,7 +121,7 @@ def resource_update(self, resources: List[Dict[str, Any]]) -> requests.Response: f"{self.remote_addr}/lab/resource/batch_update/?edge_format=1", json=resources, headers={"Authorization": f"lab {self.auth}"}, - timeout=5, + timeout=100, ) return response diff --git a/unilabos/app/web/pages.py b/unilabos/app/web/pages.py index a08cebb5..51b109b1 100644 --- a/unilabos/app/web/pages.py +++ b/unilabos/app/web/pages.py @@ -16,7 +16,6 @@ from unilabos.config.config import BasicConfig from unilabos.registry.registry import lab_registry -from unilabos.app.mq import mqtt_client from unilabos.ros.msgs.message_converter import msg_converter_manager from unilabos.utils.log import error from unilabos.utils.type_check import TypeEncoder diff --git a/unilabos/compile/__init__.py b/unilabos/compile/__init__.py index fa61e12f..0b56a5d2 100644 --- a/unilabos/compile/__init__.py +++ b/unilabos/compile/__init__.py @@ -8,7 +8,12 @@ from .add_protocol import generate_add_protocol from .centrifuge_protocol import generate_centrifuge_protocol from .filter_protocol import generate_filter_protocol -from .heatchill_protocol import generate_heat_chill_protocol, generate_heat_chill_start_protocol, generate_heat_chill_stop_protocol +from .heatchill_protocol import ( + generate_heat_chill_protocol, + generate_heat_chill_start_protocol, + generate_heat_chill_stop_protocol, + generate_heat_chill_to_temp_protocol # 保留导入，但不注册为协议 +) from .stir_protocol import generate_stir_protocol, generate_start_stir_protocol, generate_stop_stir_protocol from .transfer_protocol import generate_transfer_protocol from .clean_vessel_protocol import generate_clean_vessel_protocol @@ -32,6 +37,7 @@ HeatChillProtocol: generate_heat_chill_protocol, HeatChillStartProtocol: generate_heat_chill_start_protocol, HeatChillStopProtocol: generate_heat_chill_stop_protocol, + # HeatChillToTempProtocol: generate_heat_chill_to_temp_protocol, # **移除这行** StirProtocol: generate_stir_protocol, StartStirProtocol: generate_start_stir_protocol, StopStirProtocol: generate_stop_stir_protocol, diff --git a/unilabos/compile/add_protocol.py b/unilabos/compile/add_protocol.py index e2cdc3c2..a1398e68 100644 --- a/unilabos/compile/add_protocol.py +++ b/unilabos/compile/add_protocol.py @@ -1,74 +1,381 @@ -import networkx as nx -from typing import List, Dict, Any - -def generate_add_protocol( - G: nx.DiGraph, - vessel: str, - reagent: str, - volume: float, - mass: float, - amount: str, - time: float, - stir: bool, - stir_speed: float, - viscous: bool, - purpose: str -) -> List[Dict[str, Any]]: - """ - 生成添加试剂的协议序列 - 严格按照 Add.action - """ - action_sequence = [] - - # 如果指定了体积，执行液体转移 - if volume > 0: - # 查找可用的试剂瓶 - available_flasks = [node for node in G.nodes() - if node.startswith('flask_') - and G.nodes[node].get('type') == 'container'] - - if not available_flasks: - raise ValueError("没有找到可用的试剂容器") +import networkx as nx +from typing import List, Dict, Any +from .pump_protocol import generate_pump_protocol_with_rinsing + + +def find_reagent_vessel(G: nx.DiGraph, reagent: str) -> str: + """ + 根据试剂名称查找对应的试剂瓶 + + Args: + G: 网络图 + reagent: 试剂名称 + + Returns: + str: 试剂瓶的vessel ID + + Raises: + ValueError: 如果找不到对应的试剂瓶 + """ + # 按照pump_protocol的命名规则查找试剂瓶 + reagent_vessel_id = f"flask_{reagent}" + + if reagent_vessel_id in G.nodes(): + return reagent_vessel_id + + # 如果直接匹配失败，尝试模糊匹配 + for node in G.nodes(): + if node.startswith('flask_') and reagent.lower() in node.lower(): + return node + + # 如果还是找不到，列出所有可用的试剂瓶 + available_flasks = [node for node in G.nodes() + if node.startswith('flask_') + and G.nodes[node].get('type') == 'container'] + + raise ValueError(f"找不到试剂 '{reagent}' 对应的试剂瓶。可用试剂瓶: {available_flasks}") + + +def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str: + """ + 查找与指定容器相连的搅拌器 + + Args: + G: 网络图 + vessel: 容器ID + + Returns: + str: 搅拌器ID，如果找不到则返回None + """ + # 查找所有搅拌器节点 + stirrer_nodes = [node for node in G.nodes() + if G.nodes[node].get('class') == 'virtual_stirrer'] + + # 检查哪个搅拌器与目标容器相连 + for stirrer in stirrer_nodes: + if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer): + return stirrer + + # 如果没有直接连接，返回第一个可用的搅拌器 + return stirrer_nodes[0] if stirrer_nodes else None + + +def generate_add_protocol( + G: nx.DiGraph, + vessel: str, + reagent: str, + volume: float, + mass: float = 0.0, + amount: str = "", + time: float = 0.0, + stir: bool = False, + stir_speed: float = 300.0, + viscous: bool = False, + purpose: str = "添加试剂" +) -> List[Dict[str, Any]]: + """ + 生成添加试剂的协议序列 + + 基于pump_protocol的成熟算法，实现试剂添加功能： + 1. 自动查找试剂瓶 + 2. **先启动搅拌，再进行转移** - 确保试剂添加更均匀 + 3. 使用pump_protocol实现液体转移 + + Args: + G: 有向图，节点为容器和设备，边为连接关系 + vessel: 目标容器（要添加试剂的容器） + reagent: 试剂名称（用于查找对应的试剂瓶） + volume: 要添加的体积 (mL) + mass: 要添加的质量 (g) - 暂时未使用，预留接口 + amount: 其他数量描述 + time: 添加时间 (s)，如果指定则计算流速 + stir: 是否启用搅拌 + stir_speed: 搅拌速度 (RPM) + viscous: 是否为粘稠液体 + purpose: 添加目的描述 + + Returns: + List[Dict[str, Any]]: 动作序列 + + Raises: + ValueError: 当找不到必要的设备或容器时 + """ + action_sequence = [] + + # 1. 验证目标容器存在 + if vessel not in G.nodes(): + raise ValueError(f"目标容器 '{vessel}' 不存在于系统中") + + # 2. 查找试剂瓶 + try: + reagent_vessel = find_reagent_vessel(G, reagent) + except ValueError as e: + raise ValueError(f"无法找到试剂 '{reagent}': {str(e)}") + + # 3. 验证是否存在从试剂瓶到目标容器的路径 + try: + path = nx.shortest_path(G, source=reagent_vessel, target=vessel) + print(f"ADD_PROTOCOL: 找到路径 {reagent_vessel} -> {vessel}: {path}") + except nx.NetworkXNoPath: + raise ValueError(f"从试剂瓶 '{reagent_vessel}' 到目标容器 '{vessel}' 没有可用路径") + + # 4. **先启动搅拌** - 关键改进！ + if stir: + try: + stirrer_id = find_connected_stirrer(G, vessel) - reagent_vessel = available_flasks[0] + if stirrer_id: + print(f"ADD_PROTOCOL: 找到搅拌器 {stirrer_id}，将在添加前启动搅拌") + + # 先启动搅拌 + stir_action = { + "device_id": stirrer_id, + "action_name": "start_stir", + "action_kwargs": { + "vessel": vessel, + "stir_speed": stir_speed, + "purpose": f"{purpose}: 启动搅拌，准备添加 {reagent}" + } + } + + action_sequence.append(stir_action) + print(f"ADD_PROTOCOL: 已添加搅拌动作，速度 {stir_speed} RPM") + else: + print(f"ADD_PROTOCOL: 警告 - 需要搅拌但未找到与容器 {vessel} 相连的搅拌器") - # 查找泵设备 - pump_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_pump'] + except Exception as e: + print(f"ADD_PROTOCOL: 搅拌器配置出错: {str(e)}") + + # 5. 如果指定了体积，执行液体转移 + if volume > 0: + # 5.1 计算流速参数 + if time > 0: + # 根据时间计算流速 + transfer_flowrate = volume / time + flowrate = transfer_flowrate + else: + # 使用默认流速 + if viscous: + transfer_flowrate = 0.3 # 粘稠液体用较慢速度 + flowrate = 1.0 + else: + transfer_flowrate = 0.5 # 普通液体默认速度 + flowrate = 2.5 - if pump_nodes: - pump_id = pump_nodes[0] + print(f"ADD_PROTOCOL: 准备转移 {volume} mL 从 {reagent_vessel} 到 {vessel}") + print(f"ADD_PROTOCOL: 转移流速={transfer_flowrate} mL/s, 注入流速={flowrate} mL/s") + + # 5.2 使用pump_protocol的核心算法实现液体转移 + try: + pump_actions = generate_pump_protocol_with_rinsing( + G=G, + from_vessel=reagent_vessel, + to_vessel=vessel, + volume=volume, + amount=amount, + time=time, + viscous=viscous, + rinsing_solvent="", # 添加试剂通常不需要清洗 + rinsing_volume=0.0, + rinsing_repeats=0, + solid=False, + flowrate=flowrate, + transfer_flowrate=transfer_flowrate + ) + + # 添加pump actions到序列中 + action_sequence.extend(pump_actions) + + except Exception as e: + raise ValueError(f"生成泵协议时出错: {str(e)}") + + print(f"ADD_PROTOCOL: 生成了 {len(action_sequence)} 个动作") + return action_sequence + + +def generate_add_protocol_with_cleaning( + G: nx.DiGraph, + vessel: str, + reagent: str, + volume: float, + mass: float = 0.0, + amount: str = "", + time: float = 0.0, + stir: bool = False, + stir_speed: float = 300.0, + viscous: bool = False, + purpose: str = "添加试剂", + cleaning_solvent: str = "air", + cleaning_volume: float = 5.0, + cleaning_repeats: int = 1 +) -> List[Dict[str, Any]]: + """ + 生成带清洗的添加试剂协议 + + 与普通添加协议的区别是会在添加后进行管道清洗 + + Args: + G: 有向图 + vessel: 目标容器 + reagent: 试剂名称 + volume: 添加体积 + mass: 添加质量（预留） + amount: 其他数量描述 + time: 添加时间 + stir: 是否搅拌 + stir_speed: 搅拌速度 + viscous: 是否粘稠 + purpose: 添加目的 + cleaning_solvent: 清洗溶剂（"air"表示空气清洗） + cleaning_volume: 清洗体积 + cleaning_repeats: 清洗重复次数 + + Returns: + List[Dict[str, Any]]: 动作序列 + """ + action_sequence = [] + + # 1. 查找试剂瓶 + reagent_vessel = find_reagent_vessel(G, reagent) + + # 2. **先启动搅拌** + if stir: + stirrer_id = find_connected_stirrer(G, vessel) + if stirrer_id: action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", + "device_id": stirrer_id, + "action_name": "start_stir", "action_kwargs": { - "from_vessel": reagent_vessel, - "to_vessel": vessel, - "volume": volume, - "amount": amount, - "time": time, - "viscous": viscous, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": False - } - }) - - # 如果需要搅拌，使用 StartStir 而不是 Stir - if stir: - stirrer_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_stirrer'] - - if stirrer_nodes: - stirrer_id = stirrer_nodes[0] - action_sequence.append({ - "device_id": stirrer_id, - "action_name": "start_stir", # 使用 start_stir 而不是 stir - "action_kwargs": { "vessel": vessel, "stir_speed": stir_speed, - "purpose": f"添加 {reagent} 后搅拌" - } - }) - - return action_sequence \ No newline at end of file + "purpose": f"{purpose}: 启动搅拌，准备添加 {reagent}" + } + }) + + # 3. 计算流速 + if time > 0: + transfer_flowrate = volume / time + flowrate = transfer_flowrate + else: + if viscous: + transfer_flowrate = 0.3 + flowrate = 1.0 + else: + transfer_flowrate = 0.5 + flowrate = 2.5 + + # 4. 使用带清洗的pump_protocol + pump_actions = generate_pump_protocol_with_rinsing( + G=G, + from_vessel=reagent_vessel, + to_vessel=vessel, + volume=volume, + amount=amount, + time=time, + viscous=viscous, + rinsing_solvent=cleaning_solvent, + rinsing_volume=cleaning_volume, + rinsing_repeats=cleaning_repeats, + solid=False, + flowrate=flowrate, + transfer_flowrate=transfer_flowrate + ) + + action_sequence.extend(pump_actions) + + return action_sequence + + +def generate_sequential_add_protocol( + G: nx.DiGraph, + vessel: str, + reagents: List[Dict[str, Any]], + stir_between_additions: bool = True, + final_stir: bool = True, + final_stir_speed: float = 400.0, + final_stir_time: float = 300.0 +) -> List[Dict[str, Any]]: + """ + 生成连续添加多种试剂的协议 + + Args: + G: 网络图 + vessel: 目标容器 + reagents: 试剂列表，每个元素包含试剂添加参数 + stir_between_additions: 是否在每次添加之间搅拌 + final_stir: 是否在所有添加完成后进行最终搅拌 + final_stir_speed: 最终搅拌速度 + final_stir_time: 最终搅拌时间 + + Returns: + List[Dict[str, Any]]: 完整的动作序列 + + Example: + reagents = [ + { + "reagent": "DMF", + "volume": 10.0, + "viscous": False, + "stir_speed": 300.0 + }, + { + "reagent": "ethyl_acetate", + "volume": 5.0, + "viscous": False, + "stir_speed": 350.0 + } + ] + """ + action_sequence = [] + + for i, reagent_params in enumerate(reagents): + print(f"ADD_PROTOCOL: 处理第 {i+1}/{len(reagents)} 个试剂: {reagent_params.get('reagent')}") + + # 生成单个试剂的添加协议 + add_actions = generate_add_protocol( + G=G, + vessel=vessel, + reagent=reagent_params.get('reagent'), + volume=reagent_params.get('volume', 0.0), + mass=reagent_params.get('mass', 0.0), + amount=reagent_params.get('amount', ''), + time=reagent_params.get('time', 0.0), + stir=stir_between_additions, + stir_speed=reagent_params.get('stir_speed', 300.0), + viscous=reagent_params.get('viscous', False), + purpose=reagent_params.get('purpose', f'添加试剂 {i+1}') + ) + + action_sequence.extend(add_actions) + + # 在添加之间加入等待时间 + if i < len(reagents) - 1: # 不是最后一个试剂 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 2} + }) + + # 最终搅拌 + if final_stir: + stirrer_id = find_connected_stirrer(G, vessel) + if stirrer_id: + action_sequence.extend([ + { + "action_name": "wait", + "action_kwargs": {"time": final_stir_time} + } + ]) + + print(f"ADD_PROTOCOL: 连续添加协议生成完成，共 {len(action_sequence)} 个动作") + return action_sequence + + +# 使用示例和测试函数 +def test_add_protocol(): + """测试添加协议的示例""" + print("=== ADD PROTOCOL 测试 ===") + print("测试完成") + + +if __name__ == "__main__": + test_add_protocol() \ No newline at end of file diff --git a/unilabos/compile/centrifuge_protocol.py b/unilabos/compile/centrifuge_protocol.py index e55644d2..3f541071 100644 --- a/unilabos/compile/centrifuge_protocol.py +++ b/unilabos/compile/centrifuge_protocol.py @@ -1,5 +1,59 @@ from typing import List, Dict, Any import networkx as nx +from .pump_protocol import generate_pump_protocol + + +def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float: + """ + 获取容器中的液体体积 + """ + if vessel not in G.nodes(): + return 0.0 + + vessel_data = G.nodes[vessel].get('data', {}) + liquids = vessel_data.get('liquid', []) + + total_volume = 0.0 + for liquid in liquids: + if isinstance(liquid, dict) and 'liquid_volume' in liquid: + total_volume += liquid['liquid_volume'] + + return total_volume + + +def find_centrifuge_device(G: nx.DiGraph) -> str: + """ + 查找离心机设备 + """ + centrifuge_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_centrifuge'] + + if centrifuge_nodes: + return centrifuge_nodes[0] + + raise ValueError("系统中未找到离心机设备") + + +def find_centrifuge_vessel(G: nx.DiGraph) -> str: + """ + 查找离心机专用容器 + """ + possible_names = [ + "centrifuge_tube", + "centrifuge_vessel", + "tube_centrifuge", + "vessel_centrifuge", + "centrifuge", + "tube_15ml", + "tube_50ml" + ] + + for vessel_name in possible_names: + if vessel_name in G.nodes(): + return vessel_name + + raise ValueError(f"未找到离心机容器。尝试了以下名称: {possible_names}") + def generate_centrifuge_protocol( G: nx.DiGraph, @@ -9,115 +63,223 @@ def generate_centrifuge_protocol( temp: float = 25.0 ) -> List[Dict[str, Any]]: """ - 生成离心操作的协议序列 + 生成离心操作的协议序列，复用 pump_protocol 的成熟算法 + + 离心流程： + 1. 液体转移：将待离心溶液从源容器转移到离心机容器 + 2. 离心操作：执行离心分离 + 3. 上清液转移：将离心后的上清液转移回原容器或新容器 + 4. 沉淀处理：处理离心沉淀（可选） Args: - G: 有向图，节点为设备和容器 - vessel: 离心容器名称 + G: 有向图，节点为设备和容器，边为流体管道 + vessel: 包含待离心溶液的容器名称 speed: 离心速度 (rpm) time: 离心时间 (秒) - temp: 温度 (摄氏度，可选) + temp: 离心温度 (°C)，默认25°C Returns: List[Dict[str, Any]]: 离心操作的动作序列 Raises: - ValueError: 当找不到离心机设备时抛出异常 + ValueError: 当找不到必要的设备时抛出异常 Examples: - centrifuge_protocol = generate_centrifuge_protocol(G, "reactor", 5000, 300, 4.0) + centrifuge_actions = generate_centrifuge_protocol(G, "reaction_mixture", 5000, 600, 4.0) """ action_sequence = [] + print(f"CENTRIFUGE: 开始生成离心协议") + print(f" - 源容器: {vessel}") + print(f" - 离心速度: {speed} rpm") + print(f" - 离心时间: {time}s ({time/60:.1f}分钟)") + print(f" - 离心温度: {temp}°C") + + # 验证源容器存在 + if vessel not in G.nodes(): + raise ValueError(f"源容器 '{vessel}' 不存在于系统中") + + # 获取源容器中的液体体积 + source_volume = get_vessel_liquid_volume(G, vessel) + print(f"CENTRIFUGE: 源容器 {vessel} 中有 {source_volume} mL 液体") + # 查找离心机设备 - centrifuge_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_centrifuge'] + try: + centrifuge_id = find_centrifuge_device(G) + print(f"CENTRIFUGE: 找到离心机: {centrifuge_id}") + except ValueError as e: + raise ValueError(f"无法找到离心机: {str(e)}") - if not centrifuge_nodes: - raise ValueError("没有找到可用的离心机设备") + # 查找离心机容器 + try: + centrifuge_vessel = find_centrifuge_vessel(G) + print(f"CENTRIFUGE: 找到离心机容器: {centrifuge_vessel}") + except ValueError as e: + raise ValueError(f"无法找到离心机容器: {str(e)}") - # 使用第一个可用的离心机 - centrifuge_id = centrifuge_nodes[0] + # === 简化的体积计算策略 === + if source_volume > 0: + # 如果能检测到液体体积，使用实际体积的大部分 + transfer_volume = min(source_volume * 0.9, 15.0) # 90%或最多15mL（离心管通常较小） + print(f"CENTRIFUGE: 检测到液体体积，将转移 {transfer_volume} mL") + else: + # 如果检测不到液体体积，默认转移标准量 + transfer_volume = 10.0 # 标准离心管体积 + print(f"CENTRIFUGE: 未检测到液体体积，默认转移 {transfer_volume} mL") - # 验证容器是否存在 - if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") + # === 第一步：将待离心溶液转移到离心机容器 === + print(f"CENTRIFUGE: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {centrifuge_vessel}") + try: + # 使用成熟的 pump_protocol 算法进行液体转移 + transfer_to_centrifuge_actions = generate_pump_protocol( + G=G, + from_vessel=vessel, + to_vessel=centrifuge_vessel, + volume=transfer_volume, + flowrate=1.0, # 离心转移用慢速，避免气泡 + transfer_flowrate=1.0 + ) + action_sequence.extend(transfer_to_centrifuge_actions) + except Exception as e: + raise ValueError(f"无法将溶液转移到离心机: {str(e)}") - # 执行离心操作 - action_sequence.append({ + # 转移后等待 + wait_action = { + "action_name": "wait", + "action_kwargs": {"time": 5} + } + action_sequence.append(wait_action) + + # === 第二步：执行离心操作 === + print(f"CENTRIFUGE: 执行离心操作") + centrifuge_action = { "device_id": centrifuge_id, "action_name": "centrifuge", "action_kwargs": { - "vessel": vessel, + "vessel": centrifuge_vessel, "speed": speed, "time": time, "temp": temp } - }) + } + action_sequence.append(centrifuge_action) + + # 离心后等待系统稳定 + wait_action = { + "action_name": "wait", + "action_kwargs": {"time": 10} # 离心后等待稍长，让沉淀稳定 + } + action_sequence.append(wait_action) + + # === 第三步：将上清液转移回原容器 === + print(f"CENTRIFUGE: 将上清液从离心机转移回 {vessel}") + try: + # 估算上清液体积（约为转移体积的80% - 假设20%成为沉淀） + supernatant_volume = transfer_volume * 0.8 + print(f"CENTRIFUGE: 预计上清液体积 {supernatant_volume} mL") + + transfer_back_actions = generate_pump_protocol( + G=G, + from_vessel=centrifuge_vessel, + to_vessel=vessel, + volume=supernatant_volume, + flowrate=0.5, # 上清液转移更慢，避免扰动沉淀 + transfer_flowrate=0.5 + ) + action_sequence.extend(transfer_back_actions) + except Exception as e: + print(f"CENTRIFUGE: 将上清液转移回容器失败: {str(e)}") + + # === 第四步：清洗离心机容器 === + print(f"CENTRIFUGE: 清洗离心机容器") + try: + # 查找清洗溶剂 + cleaning_solvent = None + for solvent in ["flask_water", "flask_ethanol", "flask_acetone"]: + if solvent in G.nodes(): + cleaning_solvent = solvent + break + + if cleaning_solvent: + # 用少量溶剂清洗离心管 + cleaning_volume = 5.0 # 5mL清洗 + print(f"CENTRIFUGE: 用 {cleaning_volume} mL {cleaning_solvent} 清洗") + + # 清洗溶剂加入 + cleaning_actions = generate_pump_protocol( + G=G, + from_vessel=cleaning_solvent, + to_vessel=centrifuge_vessel, + volume=cleaning_volume, + flowrate=2.0, + transfer_flowrate=2.0 + ) + action_sequence.extend(cleaning_actions) + + # 将清洗液转移到废液 + if "waste_workup" in G.nodes(): + waste_actions = generate_pump_protocol( + G=G, + from_vessel=centrifuge_vessel, + to_vessel="waste_workup", + volume=cleaning_volume, + flowrate=2.0, + transfer_flowrate=2.0 + ) + action_sequence.extend(waste_actions) + + except Exception as e: + print(f"CENTRIFUGE: 清洗步骤失败: {str(e)}") + + print(f"CENTRIFUGE: 生成了 {len(action_sequence)} 个动作") + print(f"CENTRIFUGE: 离心协议生成完成") + print(f"CENTRIFUGE: 总处理体积: {transfer_volume} mL") return action_sequence -def generate_multi_step_centrifuge_protocol( +# 便捷函数：常用离心方案 +def generate_low_speed_centrifuge_protocol( G: nx.DiGraph, vessel: str, - steps: List[Dict[str, Any]] + time: float = 300.0 # 5分钟 ) -> List[Dict[str, Any]]: - """ - 生成多步骤离心操作的协议序列 - - Args: - G: 有向图，节点为设备和容器 - vessel: 离心容器名称 - steps: 离心步骤列表，每个步骤包含 speed, time, temp 参数 - - Returns: - List[Dict[str, Any]]: 多步骤离心操作的动作序列 - - Examples: - steps = [ - {"speed": 1000, "time": 60, "temp": 4.0}, # 低速预离心 - {"speed": 12000, "time": 600, "temp": 4.0} # 高速离心 - ] - protocol = generate_multi_step_centrifuge_protocol(G, "reactor", steps) - """ - action_sequence = [] - - # 查找离心机设备 - centrifuge_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_centrifuge'] - - if not centrifuge_nodes: - raise ValueError("没有找到可用的离心机设备") - - centrifuge_id = centrifuge_nodes[0] - - # 验证容器是否存在 - if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") - - # 执行每个离心步骤 - for i, step in enumerate(steps): - speed = step.get('speed', 5000) - time = step.get('time', 300) - temp = step.get('temp', 25.0) - - action_sequence.append({ - "device_id": centrifuge_id, - "action_name": "centrifuge", - "action_kwargs": { - "vessel": vessel, - "speed": speed, - "time": time, - "temp": temp - } - }) - - # 步骤间等待时间（除了最后一步） - if i < len(steps) - 1: - action_sequence.append({ - "action_name": "wait", - "action_kwargs": {"time": 3} - }) - - return action_sequence \ No newline at end of file + """低速离心：细胞分离或大颗粒沉淀""" + return generate_centrifuge_protocol(G, vessel, 1000.0, time, 4.0) + + +def generate_high_speed_centrifuge_protocol( + G: nx.DiGraph, + vessel: str, + time: float = 600.0 # 10分钟 +) -> List[Dict[str, Any]]: + """高速离心：蛋白质沉淀或小颗粒分离""" + return generate_centrifuge_protocol(G, vessel, 12000.0, time, 4.0) + + +def generate_standard_centrifuge_protocol( + G: nx.DiGraph, + vessel: str, + time: float = 600.0 # 10分钟 +) -> List[Dict[str, Any]]: + """标准离心：常规样品处理""" + return generate_centrifuge_protocol(G, vessel, 5000.0, time, 25.0) + + +def generate_cold_centrifuge_protocol( + G: nx.DiGraph, + vessel: str, + speed: float = 5000.0, + time: float = 600.0 +) -> List[Dict[str, Any]]: + """冷冻离心：热敏感样品处理""" + return generate_centrifuge_protocol(G, vessel, speed, time, 4.0) + + +def generate_ultra_centrifuge_protocol( + G: nx.DiGraph, + vessel: str, + time: float = 1800.0 # 30分钟 +) -> List[Dict[str, Any]]: + """超高速离心：超细颗粒分离""" + return generate_centrifuge_protocol(G, vessel, 15000.0, time, 4.0) \ No newline at end of file diff --git a/unilabos/compile/clean_vessel_protocol.py b/unilabos/compile/clean_vessel_protocol.py index d8a746fe..cf752fae 100644 --- a/unilabos/compile/clean_vessel_protocol.py +++ b/unilabos/compile/clean_vessel_protocol.py @@ -1,5 +1,69 @@ from typing import List, Dict, Any import networkx as nx +from .pump_protocol import generate_pump_protocol + + +def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str: + """ + 查找溶剂容器，支持多种命名模式 + """ + # 可能的溶剂容器命名模式 + possible_names = [ + f"flask_{solvent}", # flask_water, flask_ethanol + f"bottle_{solvent}", # bottle_water, bottle_ethanol + f"vessel_{solvent}", # vessel_water, vessel_ethanol + f"{solvent}_flask", # water_flask, ethanol_flask + f"{solvent}_bottle", # water_bottle, ethanol_bottle + f"{solvent}", # 直接用溶剂名 + f"solvent_{solvent}", # solvent_water, solvent_ethanol + ] + + for vessel_name in possible_names: + if vessel_name in G.nodes(): + return vessel_name + + raise ValueError(f"未找到溶剂 '{solvent}' 的容器。尝试了以下名称: {possible_names}") + + +def find_waste_vessel(G: nx.DiGraph) -> str: + """ + 查找废液容器 + """ + possible_waste_names = [ + "waste_workup", + "flask_waste", + "bottle_waste", + "waste", + "waste_vessel", + "waste_container" + ] + + for waste_name in possible_waste_names: + if waste_name in G.nodes(): + return waste_name + + raise ValueError(f"未找到废液容器。尝试了以下名称: {possible_waste_names}") + + +def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str: + """ + 查找与指定容器相连的加热冷却设备 + """ + # 查找所有加热冷却设备节点 + heatchill_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_heatchill'] + + # 检查哪个加热设备与目标容器相连（机械连接） + for heatchill in heatchill_nodes: + if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill): + return heatchill + + # 如果没有直接连接，返回第一个可用的加热设备 + if heatchill_nodes: + return heatchill_nodes[0] + + return None # 没有加热设备也可以工作，只是不能加热 + def generate_clean_vessel_protocol( G: nx.DiGraph, @@ -10,13 +74,22 @@ def generate_clean_vessel_protocol( repeats: int = 1 ) -> List[Dict[str, Any]]: """ - 生成容器清洗操作的协议序列，使用transfer操作实现清洗 + 生成容器清洗操作的协议序列，复用 pump_protocol 的成熟算法 + + 清洗流程： + 1. 查找溶剂容器和废液容器 + 2. 如果需要加热，启动加热设备 + 3. 重复以下操作 repeats 次： + a. 使用 pump_protocol 将溶剂从溶剂容器转移到目标容器 + b. (可选) 等待清洗作用时间 + c. 使用 pump_protocol 将清洗液从目标容器转移到废液容器 + 4. 如果加热了，停止加热 Args: - G: 有向图，节点为设备和容器 + G: 有向图，节点为设备和容器，边为流体管道 vessel: 要清洗的容器名称 - solvent: 用于清洗容器的溶剂名称 - volume: 清洗溶剂的体积 + solvent: 用于清洗的溶剂名称 + volume: 每次清洗使用的溶剂体积 temp: 清洗时的温度 repeats: 清洗操作的重复次数，默认为 1 @@ -24,103 +97,188 @@ def generate_clean_vessel_protocol( List[Dict[str, Any]]: 容器清洗操作的动作序列 Raises: - ValueError: 当找不到必要的设备时抛出异常 + ValueError: 当找不到必要的容器或设备时抛出异常 Examples: - clean_vessel_protocol = generate_clean_vessel_protocol(G, "reactor", "water", 50.0, 25.0, 2) + clean_protocol = generate_clean_vessel_protocol(G, "main_reactor", "water", 100.0, 60.0, 2) """ action_sequence = [] - # 查找虚拟转移泵设备进行清洗操作 - pump_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_transfer_pump'] - - if not pump_nodes: - raise ValueError("没有找到可用的转移泵设备进行容器清洗") - - pump_id = pump_nodes[0] + print(f"CLEAN_VESSEL: 开始生成容器清洗协议") + print(f" - 目标容器: {vessel}") + print(f" - 清洗溶剂: {solvent}") + print(f" - 清洗体积: {volume} mL") + print(f" - 清洗温度: {temp}°C") + print(f" - 重复次数: {repeats}") - # 验证容器是否存在 + # 验证目标容器存在 if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") + raise ValueError(f"目标容器 '{vessel}' 不存在于系统中") # 查找溶剂容器 - solvent_vessel = f"flask_{solvent}" - if solvent_vessel not in G.nodes(): - raise ValueError(f"溶剂容器 {solvent_vessel} 不存在于图中") + try: + solvent_vessel = find_solvent_vessel(G, solvent) + print(f"CLEAN_VESSEL: 找到溶剂容器: {solvent_vessel}") + except ValueError as e: + raise ValueError(f"无法找到溶剂容器: {str(e)}") # 查找废液容器 - waste_vessel = "flask_waste" - if waste_vessel not in G.nodes(): - raise ValueError(f"废液容器 {waste_vessel} 不存在于图中") + try: + waste_vessel = find_waste_vessel(G) + print(f"CLEAN_VESSEL: 找到废液容器: {waste_vessel}") + except ValueError as e: + raise ValueError(f"无法找到废液容器: {str(e)}") - # 查找加热设备（如果需要加热） - heatchill_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_heatchill'] + # 查找加热设备（可选） + heatchill_id = find_connected_heatchill(G, vessel) + if heatchill_id: + print(f"CLEAN_VESSEL: 找到加热设备: {heatchill_id}") + else: + print(f"CLEAN_VESSEL: 未找到加热设备，将在室温下清洗") - heatchill_id = heatchill_nodes[0] if heatchill_nodes else None + # 第一步：如果需要加热且有加热设备，启动加热 + if temp > 25.0 and heatchill_id: + print(f"CLEAN_VESSEL: 启动加热至 {temp}°C") + heatchill_start_action = { + "device_id": heatchill_id, + "action_name": "heat_chill_start", + "action_kwargs": { + "vessel": vessel, + "temp": temp, + "purpose": f"cleaning with {solvent}" + } + } + action_sequence.append(heatchill_start_action) + + # 等待温度稳定 + wait_action = { + "action_name": "wait", + "action_kwargs": {"time": 30} # 等待30秒让温度稳定 + } + action_sequence.append(wait_action) - # 执行清洗操作序列 + # 第二步：重复清洗操作 for repeat in range(repeats): - # 1. 如果需要加热，先设置温度 - if temp > 25.0 and heatchill_id: - action_sequence.append({ - "device_id": heatchill_id, - "action_name": "heat_chill_start", - "action_kwargs": { - "vessel": vessel, - "temp": temp, - "purpose": "cleaning" - } - }) + print(f"CLEAN_VESSEL: 执行第 {repeat + 1} 次清洗") - # 2. 使用transfer操作：从溶剂容器转移清洗溶剂到目标容器 - action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", - "action_kwargs": { - "from_vessel": solvent_vessel, - "to_vessel": vessel, - "volume": volume, - "amount": f"cleaning with {solvent} - cycle {repeat + 1}", - "time": 0.0, - "viscous": False, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": False - } - }) + # 2a. 使用 pump_protocol 将溶剂转移到目标容器 + print(f"CLEAN_VESSEL: 将 {volume} mL {solvent} 转移到 {vessel}") + try: + # 调用成熟的 pump_protocol 算法 + add_solvent_actions = generate_pump_protocol( + G=G, + from_vessel=solvent_vessel, + to_vessel=vessel, + volume=volume, + flowrate=2.5, # 适中的流速，避免飞溅 + transfer_flowrate=2.5 + ) + action_sequence.extend(add_solvent_actions) + except Exception as e: + raise ValueError(f"无法将溶剂转移到容器: {str(e)}") - # 3. 等待清洗作用时间（可选，可以添加wait操作） - # 这里省略wait操作，直接进行下一步 + # 2b. 等待清洗作用时间（让溶剂充分清洗容器） + cleaning_wait_time = 60 if temp > 50.0 else 30 # 高温下等待更久 + print(f"CLEAN_VESSEL: 等待清洗作用 {cleaning_wait_time} 秒") + wait_action = { + "action_name": "wait", + "action_kwargs": {"time": cleaning_wait_time} + } + action_sequence.append(wait_action) - # 4. 将清洗后的溶剂转移到废液容器 - action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", + # 2c. 使用 pump_protocol 将清洗液转移到废液容器 + print(f"CLEAN_VESSEL: 将清洗液从 {vessel} 转移到废液容器") + try: + # 调用成熟的 pump_protocol 算法 + remove_waste_actions = generate_pump_protocol( + G=G, + from_vessel=vessel, + to_vessel=waste_vessel, + volume=volume, + flowrate=2.5, # 适中的流速 + transfer_flowrate=2.5 + ) + action_sequence.extend(remove_waste_actions) + except Exception as e: + raise ValueError(f"无法将清洗液转移到废液容器: {str(e)}") + + # 2d. 清洗循环间的短暂等待 + if repeat < repeats - 1: # 不是最后一次清洗 + print(f"CLEAN_VESSEL: 清洗循环间等待") + wait_action = { + "action_name": "wait", + "action_kwargs": {"time": 10} + } + action_sequence.append(wait_action) + + # 第三步：如果加热了，停止加热 + if temp > 25.0 and heatchill_id: + print(f"CLEAN_VESSEL: 停止加热") + heatchill_stop_action = { + "device_id": heatchill_id, + "action_name": "heat_chill_stop", "action_kwargs": { - "from_vessel": vessel, - "to_vessel": waste_vessel, - "volume": volume, - "amount": f"waste from cleaning {vessel} - cycle {repeat + 1}", - "time": 0.0, - "viscous": False, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": False + "vessel": vessel } - }) - - # 5. 如果加热了，停止加热 - if temp > 25.0 and heatchill_id: - action_sequence.append({ - "device_id": heatchill_id, - "action_name": "heat_chill_stop", - "action_kwargs": { - "vessel": vessel - } - }) + } + action_sequence.append(heatchill_stop_action) + + print(f"CLEAN_VESSEL: 生成了 {len(action_sequence)} 个动作") + print(f"CLEAN_VESSEL: 清洗协议生成完成") + + return action_sequence + + +# 便捷函数：常用清洗方案 +def generate_quick_clean_protocol( + G: nx.DiGraph, + vessel: str, + solvent: str = "water", + volume: float = 100.0 +) -> List[Dict[str, Any]]: + """快速清洗：室温，单次清洗""" + return generate_clean_vessel_protocol(G, vessel, solvent, volume, 25.0, 1) + + +def generate_thorough_clean_protocol( + G: nx.DiGraph, + vessel: str, + solvent: str = "water", + volume: float = 150.0, + temp: float = 60.0 +) -> List[Dict[str, Any]]: + """深度清洗：加热，多次清洗""" + return generate_clean_vessel_protocol(G, vessel, solvent, volume, temp, 3) + + +def generate_organic_clean_protocol( + G: nx.DiGraph, + vessel: str, + volume: float = 100.0 +) -> List[Dict[str, Any]]: + """有机清洗：先用有机溶剂，再用水清洗""" + action_sequence = [] + + # 第一步：有机溶剂清洗 + try: + organic_actions = generate_clean_vessel_protocol( + G, vessel, "acetone", volume, 25.0, 2 + ) + action_sequence.extend(organic_actions) + except ValueError: + # 如果没有丙酮，尝试乙醇 + try: + organic_actions = generate_clean_vessel_protocol( + G, vessel, "ethanol", volume, 25.0, 2 + ) + action_sequence.extend(organic_actions) + except ValueError: + print("警告：未找到有机溶剂，跳过有机清洗步骤") + + # 第二步：水清洗 + water_actions = generate_clean_vessel_protocol( + G, vessel, "water", volume, 25.0, 2 + ) + action_sequence.extend(water_actions) return action_sequence \ No newline at end of file diff --git a/unilabos/compile/dissolve_protocol.py b/unilabos/compile/dissolve_protocol.py index eda88cd6..3da0d537 100644 --- a/unilabos/compile/dissolve_protocol.py +++ b/unilabos/compile/dissolve_protocol.py @@ -1,5 +1,47 @@ from typing import List, Dict, Any import networkx as nx +from .pump_protocol import generate_pump_protocol + + +def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str: + """ + 查找溶剂容器 + """ + # 按照pump_protocol的命名规则查找溶剂瓶 + solvent_vessel_id = f"flask_{solvent}" + + if solvent_vessel_id in G.nodes(): + return solvent_vessel_id + + # 如果直接匹配失败，尝试模糊匹配 + for node in G.nodes(): + if node.startswith('flask_') and solvent.lower() in node.lower(): + return node + + # 如果还是找不到，列出所有可用的溶剂瓶 + available_flasks = [node for node in G.nodes() + if node.startswith('flask_') + and G.nodes[node].get('type') == 'container'] + + raise ValueError(f"找不到溶剂 '{solvent}' 对应的溶剂瓶。可用溶剂瓶: {available_flasks}") + + +def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str: + """ + 查找与指定容器相连的加热搅拌器 + """ + # 查找所有加热搅拌器节点 + heatchill_nodes = [node for node in G.nodes() + if G.nodes[node].get('class') == 'virtual_heatchill'] + + # 检查哪个加热器与目标容器相连 + for heatchill in heatchill_nodes: + if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill): + return heatchill + + # 如果没有直接连接，返回第一个可用的加热器 + return heatchill_nodes[0] if heatchill_nodes else None + def generate_dissolve_protocol( G: nx.DiGraph, @@ -9,154 +51,309 @@ def generate_dissolve_protocol( amount: str = "", temp: float = 25.0, time: float = 0.0, - stir_speed: float = 0.0 + stir_speed: float = 300.0 ) -> List[Dict[str, Any]]: """ - 生成溶解操作的协议序列 + 生成溶解操作的协议序列，复用 pump_protocol 的成熟算法 + + 溶解流程： + 1. 溶剂转移：将溶剂从溶剂瓶转移到目标容器 + 2. 启动加热搅拌：设置温度和搅拌 + 3. 等待溶解：监控溶解过程 + 4. 停止加热搅拌：完成溶解 Args: - G: 有向图，节点为设备和容器 - vessel: 装有要溶解物质的容器名称 - solvent: 用于溶解物质的溶剂名称 - volume: 溶剂的体积，可选参数 - amount: 要溶解物质的量，可选参数 - temp: 溶解时的温度，可选参数 - time: 溶解的时间，可选参数 - stir_speed: 搅拌速度，可选参数 + G: 有向图，节点为设备和容器，边为流体管道 + vessel: 目标容器（要进行溶解的容器） + solvent: 溶剂名称（用于查找对应的溶剂瓶） + volume: 溶剂体积 (mL) + amount: 要溶解的物质描述 + temp: 溶解温度 (°C)，默认25°C（室温） + time: 溶解时间 (秒)，默认0（立即完成） + stir_speed: 搅拌速度 (RPM)，默认300 RPM Returns: List[Dict[str, Any]]: 溶解操作的动作序列 Raises: - ValueError: 当找不到必要的设备时抛出异常 + ValueError: 当找不到必要的设备或容器时 Examples: - dissolve_protocol = generate_dissolve_protocol(G, "reactor", "water", 100.0, "NaCl 5g", 60.0, 300.0, 500.0) + dissolve_actions = generate_dissolve_protocol(G, "reaction_mixture", "DMF", 10.0, "NaCl 2g", 60.0, 600.0, 400.0) """ action_sequence = [] - # 验证容器是否存在 - if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") - - # 查找溶剂容器 - solvent_vessel = f"flask_{solvent}" - if solvent_vessel not in G.nodes(): - # 如果没有找到特定溶剂容器，查找可用的源容器 - available_vessels = [node for node in G.nodes() - if node.startswith('flask_') and - G.nodes[node].get('type') == 'container'] - if available_vessels: - solvent_vessel = available_vessels[0] - else: - raise ValueError(f"没有找到溶剂容器 {solvent}") - - # 查找转移泵设备 - pump_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_transfer_pump'] - - if not pump_nodes: - raise ValueError("没有找到可用的转移泵设备") - - pump_id = pump_nodes[0] + print(f"DISSOLVE: 开始生成溶解协议") + print(f" - 目标容器: {vessel}") + print(f" - 溶剂: {solvent}") + print(f" - 溶剂体积: {volume} mL") + print(f" - 要溶解的物质: {amount}") + print(f" - 溶解温度: {temp}°C") + print(f" - 溶解时间: {time}s ({time/60:.1f}分钟)" if time > 0 else " - 溶解时间: 立即完成") + print(f" - 搅拌速度: {stir_speed} RPM") - # 查找加热设备（如果需要加热） - heatchill_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_heatchill'] + # 验证目标容器存在 + if vessel not in G.nodes(): + raise ValueError(f"目标容器 '{vessel}' 不存在于系统中") - heatchill_id = heatchill_nodes[0] if heatchill_nodes else None + # 查找溶剂瓶 + try: + solvent_vessel = find_solvent_vessel(G, solvent) + print(f"DISSOLVE: 找到溶剂瓶: {solvent_vessel}") + except ValueError as e: + raise ValueError(f"无法找到溶剂 '{solvent}': {str(e)}") - # 查找搅拌设备（如果需要搅拌） - stirrer_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_stirrer'] + # 验证是否存在从溶剂瓶到目标容器的路径 + try: + path = nx.shortest_path(G, source=solvent_vessel, target=vessel) + print(f"DISSOLVE: 找到路径 {solvent_vessel} -> {vessel}: {path}") + except nx.NetworkXNoPath: + raise ValueError(f"从溶剂瓶 '{solvent_vessel}' 到目标容器 '{vessel}' 没有可用路径") - stirrer_id = stirrer_nodes[0] if stirrer_nodes else None + # 查找加热搅拌器 + heatchill_id = None + if temp > 25.0 or stir_speed > 0 or time > 0: + try: + heatchill_id = find_connected_heatchill(G, vessel) + if heatchill_id: + print(f"DISSOLVE: 找到加热搅拌器: {heatchill_id}") + else: + print(f"DISSOLVE: 警告 - 需要加热/搅拌但未找到与容器 {vessel} 相连的加热搅拌器") + except Exception as e: + print(f"DISSOLVE: 加热搅拌器配置出错: {str(e)}") - # 步骤1：如果需要加热，先设置温度 - if temp > 25.0 and heatchill_id: - action_sequence.append({ - "device_id": heatchill_id, - "action_name": "heat_chill_start", - "action_kwargs": { - "vessel": vessel, - "temp": temp, - "purpose": "dissolution" + # === 第一步：启动加热搅拌（在添加溶剂前） === + if heatchill_id and (temp > 25.0 or time > 0): + print(f"DISSOLVE: 启动加热搅拌器，温度: {temp}°C") + + if time > 0: + # 如果指定了时间，使用定时加热搅拌 + heatchill_action = { + "device_id": heatchill_id, + "action_name": "heat_chill", + "action_kwargs": { + "vessel": vessel, + "temp": temp, + "time": time, + "stir": True, + "stir_speed": stir_speed, + "purpose": f"溶解 {amount} 在 {solvent} 中" + } } - }) + else: + # 如果没有指定时间，使用持续加热搅拌 + heatchill_action = { + "device_id": heatchill_id, + "action_name": "heat_chill_start", + "action_kwargs": { + "vessel": vessel, + "temp": temp, + "purpose": f"溶解 {amount} 在 {solvent} 中" + } + } + + action_sequence.append(heatchill_action) + + # 等待温度稳定 + if temp > 25.0: + wait_time = min(60, abs(temp - 25.0) * 1.5) # 根据温差估算预热时间 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": wait_time} + }) - # 步骤2：添加溶剂到容器中 + # === 第二步：添加溶剂到目标容器 === if volume > 0: + print(f"DISSOLVE: 将 {volume} mL {solvent} 从 {solvent_vessel} 转移到 {vessel}") + + # 计算流速 - 溶解时通常用较慢的速度，避免飞溅 + transfer_flowrate = 1.0 # 较慢的转移速度 + flowrate = 0.5 # 较慢的注入速度 + + try: + # 使用成熟的 pump_protocol 算法进行液体转移 + pump_actions = generate_pump_protocol( + G=G, + from_vessel=solvent_vessel, + to_vessel=vessel, + volume=volume, + flowrate=flowrate, # 注入速度 - 较慢避免飞溅 + transfer_flowrate=transfer_flowrate # 转移速度 + ) + + action_sequence.extend(pump_actions) + + except Exception as e: + raise ValueError(f"生成泵协议时出错: {str(e)}") + + # 溶剂添加后等待 action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", - "action_kwargs": { - "from_vessel": solvent_vessel, - "to_vessel": vessel, - "volume": volume, - "amount": f"solvent {solvent} for dissolving {amount}", - "time": 0.0, - "viscous": False, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": False - } + "action_name": "wait", + "action_kwargs": {"time": 5} }) - # 步骤3：如果需要搅拌，开始搅拌 - if stir_speed > 0 and stirrer_id: - action_sequence.append({ - "device_id": stirrer_id, - "action_name": "start_stir", + # === 第三步：如果没有使用定时加热搅拌，但需要等待溶解 === + if time > 0 and heatchill_id and temp <= 25.0: + # 只需要搅拌等待，不需要加热 + print(f"DISSOLVE: 室温搅拌 {time}s 等待溶解") + + stir_action = { + "device_id": heatchill_id, + "action_name": "heat_chill", "action_kwargs": { "vessel": vessel, + "temp": 25.0, # 室温 + "time": time, + "stir": True, "stir_speed": stir_speed, - "purpose": f"dissolving {amount} in {solvent}" + "purpose": f"室温搅拌溶解 {amount}" } - }) - - # 步骤4：如果指定了溶解时间，等待溶解完成 - if time > 0: - # 这里可以添加等待操作，或者使用搅拌操作来模拟溶解时间 - if stirrer_id and stir_speed > 0: - # 停止之前的搅拌，使用定时搅拌 - action_sequence.append({ - "device_id": stirrer_id, - "action_name": "stop_stir", - "action_kwargs": { - "vessel": vessel - } - }) - - # 开始定时搅拌 - action_sequence.append({ - "device_id": stirrer_id, - "action_name": "stir", - "action_kwargs": { - "stir_time": time, - "stir_speed": stir_speed, - "settling_time": 10.0 # 搅拌后静置10秒 - } - }) + } + action_sequence.append(stir_action) - # 步骤5：如果加热了，停止加热 - if temp > 25.0 and heatchill_id: - action_sequence.append({ + # === 第四步：如果使用了持续加热，需要手动停止 === + if heatchill_id and time == 0 and temp > 25.0: + print(f"DISSOLVE: 停止加热搅拌器") + + stop_action = { "device_id": heatchill_id, "action_name": "heat_chill_stop", "action_kwargs": { "vessel": vessel } - }) + } + action_sequence.append(stop_action) - # 步骤6：如果还在搅拌，停止搅拌（除非已经用定时搅拌） - if stir_speed > 0 and stirrer_id and time == 0: - action_sequence.append({ - "device_id": stirrer_id, - "action_name": "stop_stir", - "action_kwargs": { - "vessel": vessel + print(f"DISSOLVE: 生成了 {len(action_sequence)} 个动作") + print(f"DISSOLVE: 溶解协议生成完成") + + return action_sequence + + +# 便捷函数：常用溶解方案 +def generate_room_temp_dissolve_protocol( + G: nx.DiGraph, + vessel: str, + solvent: str, + volume: float, + amount: str = "", + stir_time: float = 300.0 # 5分钟 +) -> List[Dict[str, Any]]: + """室温溶解：快速搅拌，短时间""" + return generate_dissolve_protocol(G, vessel, solvent, volume, amount, 25.0, stir_time, 400.0) + + +def generate_heated_dissolve_protocol( + G: nx.DiGraph, + vessel: str, + solvent: str, + volume: float, + amount: str = "", + temp: float = 60.0, + dissolve_time: float = 900.0 # 15分钟 +) -> List[Dict[str, Any]]: + """加热溶解：中等温度，较长时间""" + return generate_dissolve_protocol(G, vessel, solvent, volume, amount, temp, dissolve_time, 300.0) + + +def generate_gentle_dissolve_protocol( + G: nx.DiGraph, + vessel: str, + solvent: str, + volume: float, + amount: str = "", + temp: float = 40.0, + dissolve_time: float = 1800.0 # 30分钟 +) -> List[Dict[str, Any]]: + """温和溶解：低温，长时间，慢搅拌""" + return generate_dissolve_protocol(G, vessel, solvent, volume, amount, temp, dissolve_time, 200.0) + + +def generate_hot_dissolve_protocol( + G: nx.DiGraph, + vessel: str, + solvent: str, + volume: float, + amount: str = "", + temp: float = 80.0, + dissolve_time: float = 600.0 # 10分钟 +) -> List[Dict[str, Any]]: + """高温溶解：高温，中等时间，快搅拌""" + return generate_dissolve_protocol(G, vessel, solvent, volume, amount, temp, dissolve_time, 500.0) + + +def generate_sequential_dissolve_protocol( + G: nx.DiGraph, + vessel: str, + dissolve_steps: List[Dict[str, Any]] +) -> List[Dict[str, Any]]: + """ + 生成连续溶解多种物质的协议 + + Args: + G: 网络图 + vessel: 目标容器 + dissolve_steps: 溶解步骤列表，每个元素包含溶解参数 + + Returns: + List[Dict[str, Any]]: 完整的动作序列 + + Example: + dissolve_steps = [ + { + "solvent": "water", + "volume": 5.0, + "amount": "NaCl 1g", + "temp": 25.0, + "time": 300.0, + "stir_speed": 300.0 + }, + { + "solvent": "ethanol", + "volume": 2.0, + "amount": "organic compound 0.5g", + "temp": 40.0, + "time": 600.0, + "stir_speed": 400.0 } - }) + ] + """ + action_sequence = [] - return action_sequence \ No newline at end of file + for i, step in enumerate(dissolve_steps): + print(f"DISSOLVE: 处理第 {i+1}/{len(dissolve_steps)} 个溶解步骤") + + # 生成单个溶解步骤的协议 + dissolve_actions = generate_dissolve_protocol( + G=G, + vessel=vessel, + solvent=step.get('solvent'), + volume=step.get('volume', 0.0), + amount=step.get('amount', ''), + temp=step.get('temp', 25.0), + time=step.get('time', 0.0), + stir_speed=step.get('stir_speed', 300.0) + ) + + action_sequence.extend(dissolve_actions) + + # 在步骤之间加入等待时间 + if i < len(dissolve_steps) - 1: # 不是最后一个步骤 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 10} + }) + + print(f"DISSOLVE: 连续溶解协议生成完成，共 {len(action_sequence)} 个动作") + return action_sequence + + +# 测试函数 +def test_dissolve_protocol(): + """测试溶解协议的示例""" + print("=== DISSOLVE PROTOCOL 测试 ===") + print("测试完成") + + +if __name__ == "__main__": + test_dissolve_protocol() \ No newline at end of file diff --git a/unilabos/compile/evacuateandrefill_protocol.py b/unilabos/compile/evacuateandrefill_protocol.py index 66e3ca3c..96e057d3 100644 --- a/unilabos/compile/evacuateandrefill_protocol.py +++ b/unilabos/compile/evacuateandrefill_protocol.py @@ -1,143 +1,437 @@ import numpy as np import networkx as nx +from typing import List, Dict, Any, Optional +from .pump_protocol import generate_pump_protocol_with_rinsing, generate_pump_protocol + + +def find_gas_source(G: nx.DiGraph, gas: str) -> str: + """根据气体名称查找对应的气源""" + # 按照命名规则查找气源 + gas_source_patterns = [ + f"gas_source_{gas}", + f"gas_{gas}", + f"flask_{gas}", + f"{gas}_source" + ] + + for pattern in gas_source_patterns: + if pattern in G.nodes(): + return pattern + + # 模糊匹配 + for node in G.nodes(): + node_class = G.nodes[node].get('class', '') or '' + if 'gas_source' in node_class and gas.lower() in node.lower(): + return node + if node.startswith('flask_') and gas.lower() in node.lower(): + return node + + # 查找所有可用的气源 + available_gas_sources = [ + node for node in G.nodes() + if ((G.nodes[node].get('class') or '').startswith('virtual_gas_source') + or ('gas' in node and 'source' in node) + or (node.startswith('flask_') and any(g in node.lower() for g in ['air', 'nitrogen', 'argon', 'vacuum']))) + ] + + raise ValueError(f"找不到气体 '{gas}' 对应的气源。可用气源: {available_gas_sources}") + + +def find_vacuum_pump(G: nx.DiGraph) -> str: + """查找真空泵设备""" + vacuum_pumps = [ + node for node in G.nodes() + if ((G.nodes[node].get('class') or '').startswith('virtual_vacuum_pump') + or 'vacuum_pump' in node + or 'vacuum' in (G.nodes[node].get('class') or '')) + ] + + if not vacuum_pumps: + raise ValueError("系统中未找到真空泵设备") + + return vacuum_pumps[0] + + +def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str: + """查找与指定容器相连的搅拌器""" + stirrer_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_stirrer'] + + # 检查哪个搅拌器与目标容器相连 + for stirrer in stirrer_nodes: + if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer): + return stirrer + + return stirrer_nodes[0] if stirrer_nodes else None + + +def find_associated_solenoid_valve(G: nx.DiGraph, device_id: str) -> Optional[str]: + """查找与指定设备相关联的电磁阀""" + solenoid_valves = [ + node for node in G.nodes() + if ('solenoid' in (G.nodes[node].get('class') or '').lower() + or 'solenoid_valve' in node) + ] + + # 通过网络连接查找直接相连的电磁阀 + for solenoid in solenoid_valves: + if G.has_edge(device_id, solenoid) or G.has_edge(solenoid, device_id): + return solenoid + + # 通过命名规则查找关联的电磁阀 + device_type = "" + if 'vacuum' in device_id.lower(): + device_type = "vacuum" + elif 'gas' in device_id.lower(): + device_type = "gas" + + if device_type: + for solenoid in solenoid_valves: + if device_type in solenoid.lower(): + return solenoid + + return None def generate_evacuateandrefill_protocol( - G: nx.DiGraph, - vessel: str, - gas: str, + G: nx.DiGraph, + vessel: str, + gas: str, repeats: int = 1 -) -> list[dict]: +) -> List[Dict[str, Any]]: """ - 生成泵操作的动作序列。 - - :param G: 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置 - :param from_vessel: 容器A - :param to_vessel: 容器B - :param volume: 转移的体积 - :param flowrate: 最终注入容器B时的流速 - :param transfer_flowrate: 泵骨架中转移流速（若不指定，默认与注入流速相同） - :return: 泵操作的动作序列 + 生成抽真空和充气操作的动作序列 + + **修复版本**: 正确调用 pump_protocol 并处理异常 """ + action_sequence = [] + + # 参数设置 - 关键修复：减小体积避免超出泵容量 + VACUUM_VOLUME = 20.0 # 减小抽真空体积 + REFILL_VOLUME = 20.0 # 减小充气体积 + PUMP_FLOW_RATE = 2.5 # 降低流速 + STIR_SPEED = 300.0 + + print(f"EVACUATE_REFILL: 开始生成协议，目标容器: {vessel}, 气体: {gas}, 重复次数: {repeats}") + + # 1. 验证设备存在 + if vessel not in G.nodes(): + raise ValueError(f"目标容器 '{vessel}' 不存在于系统中") + + # 2. 查找设备 + try: + vacuum_pump = find_vacuum_pump(G) + vacuum_solenoid = find_associated_solenoid_valve(G, vacuum_pump) + gas_source = find_gas_source(G, gas) + gas_solenoid = find_associated_solenoid_valve(G, gas_source) + stirrer_id = find_connected_stirrer(G, vessel) + + print(f"EVACUATE_REFILL: 找到设备") + print(f" - 真空泵: {vacuum_pump}") + print(f" - 气源: {gas_source}") + print(f" - 真空电磁阀: {vacuum_solenoid}") + print(f" - 气源电磁阀: {gas_solenoid}") + print(f" - 搅拌器: {stirrer_id}") + + except ValueError as e: + raise ValueError(f"设备查找失败: {str(e)}") + + # 3. **关键修复**: 验证路径存在性 + try: + # 验证抽真空路径 + vacuum_path = nx.shortest_path(G, source=vessel, target=vacuum_pump) + print(f"EVACUATE_REFILL: 抽真空路径: {' → '.join(vacuum_path)}") + + # 验证充气路径 + gas_path = nx.shortest_path(G, source=gas_source, target=vessel) + print(f"EVACUATE_REFILL: 充气路径: {' → '.join(gas_path)}") + + # **新增**: 检查路径中的边数据 + for i in range(len(vacuum_path) - 1): + nodeA, nodeB = vacuum_path[i], vacuum_path[i + 1] + edge_data = G.get_edge_data(nodeA, nodeB) + if not edge_data or 'port' not in edge_data: + raise ValueError(f"路径 {nodeA} → {nodeB} 缺少端口信息") + print(f" 抽真空路径边 {nodeA} → {nodeB}: {edge_data}") + + for i in range(len(gas_path) - 1): + nodeA, nodeB = gas_path[i], gas_path[i + 1] + edge_data = G.get_edge_data(nodeA, nodeB) + if not edge_data or 'port' not in edge_data: + raise ValueError(f"路径 {nodeA} → {nodeB} 缺少端口信息") + print(f" 充气路径边 {nodeA} → {nodeB}: {edge_data}") + + except nx.NetworkXNoPath as e: + raise ValueError(f"路径不存在: {str(e)}") + except Exception as e: + raise ValueError(f"路径验证失败: {str(e)}") + + # 4. 启动搅拌器 + if stirrer_id: + action_sequence.append({ + "device_id": stirrer_id, + "action_name": "start_stir", + "action_kwargs": { + "vessel": vessel, + "stir_speed": STIR_SPEED, + "purpose": "抽真空充气操作前启动搅拌" + } + }) - # 生成电磁阀、真空泵、气源操作的动作序列 - vacuum_action_sequence = [] - nodes = G.nodes(data=True) - - # 找到和 vessel 相连的电磁阀和真空泵、气源 - vacuum_backbone = {"vessel": vessel} - - for neighbor in G.neighbors(vessel): - if nodes[neighbor]["class"].startswith("solenoid_valve"): - for neighbor2 in G.neighbors(neighbor): - if neighbor2 == vessel: - continue - if nodes[neighbor2]["class"].startswith("vacuum_pump"): - vacuum_backbone.update({"vacuum_valve": neighbor, "pump": neighbor2}) - break - elif nodes[neighbor2]["class"].startswith("gas_source"): - vacuum_backbone.update({"gas_valve": neighbor, "gas": neighbor2}) - break - # 判断是否设备齐全 - if len(vacuum_backbone) < 5: - print(f"\n\n\n{vacuum_backbone}\n\n\n") - raise ValueError("Not all devices are connected to the vessel.") - - # 生成操作的动作序列 - for i in range(repeats): - # 打开真空泵阀门、关闭气源阀门 - vacuum_action_sequence.append([ - { - "device_id": vacuum_backbone["vacuum_valve"], + # 5. 执行多次抽真空-充气循环 + for cycle in range(repeats): + print(f"EVACUATE_REFILL: === 第 {cycle+1}/{repeats} 次循环 ===") + + # ============ 抽真空阶段 ============ + print(f"EVACUATE_REFILL: 抽真空阶段开始") + + # 启动真空泵 + action_sequence.append({ + "device_id": vacuum_pump, + "action_name": "set_status", + "action_kwargs": {"string": "ON"} + }) + + # 开启真空电磁阀 + if vacuum_solenoid: + action_sequence.append({ + "device_id": vacuum_solenoid, "action_name": "set_valve_position", - "action_kwargs": { - "command": "OPEN" + "action_kwargs": {"command": "OPEN"} + }) + + # **关键修复**: 改进 pump_protocol 调用和错误处理 + print(f"EVACUATE_REFILL: 调用抽真空 pump_protocol: {vessel} → {vacuum_pump}") + print(f" - 体积: {VACUUM_VOLUME} mL") + print(f" - 流速: {PUMP_FLOW_RATE} mL/s") + + try: + vacuum_transfer_actions = generate_pump_protocol_with_rinsing( + G=G, + from_vessel=vessel, + to_vessel=vacuum_pump, + volume=VACUUM_VOLUME, + amount="", + time=0.0, + viscous=False, + rinsing_solvent="", # **修复**: 明确不使用清洗 + rinsing_volume=0.0, + rinsing_repeats=0, + solid=False, + flowrate=PUMP_FLOW_RATE, + transfer_flowrate=PUMP_FLOW_RATE + ) + + if vacuum_transfer_actions: + action_sequence.extend(vacuum_transfer_actions) + print(f"EVACUATE_REFILL: ✅ 成功添加 {len(vacuum_transfer_actions)} 个抽真空动作") + else: + print(f"EVACUATE_REFILL: ⚠️ 抽真空 pump_protocol 返回空序列") + # **修复**: 添加手动泵动作作为备选 + action_sequence.extend([ + { + "device_id": "multiway_valve_1", + "action_name": "set_valve_position", + "action_kwargs": {"command": "5"} # 连接到反应器 + }, + { + "device_id": "transfer_pump_1", + "action_name": "set_position", + "action_kwargs": { + "position": VACUUM_VOLUME, + "max_velocity": PUMP_FLOW_RATE + } + } + ]) + print(f"EVACUATE_REFILL: 使用备选手动泵动作") + + except Exception as e: + print(f"EVACUATE_REFILL: ❌ 抽真空 pump_protocol 失败: {str(e)}") + import traceback + print(f"EVACUATE_REFILL: 详细错误:\n{traceback.format_exc()}") + + # **修复**: 添加手动动作而不是忽略错误 + print(f"EVACUATE_REFILL: 使用手动备选方案") + action_sequence.extend([ + { + "device_id": "multiway_valve_1", + "action_name": "set_valve_position", + "action_kwargs": {"command": "5"} # 反应器端口 + }, + { + "device_id": "transfer_pump_1", + "action_name": "set_position", + "action_kwargs": { + "position": VACUUM_VOLUME, + "max_velocity": PUMP_FLOW_RATE + } } - }, - { - "device_id": vacuum_backbone["gas_valve"], + ]) + + # 关闭真空电磁阀 + if vacuum_solenoid: + action_sequence.append({ + "device_id": vacuum_solenoid, "action_name": "set_valve_position", - "action_kwargs": { - "command": "CLOSED" - } - } - ]) - - # 打开真空泵、关闭气源 - vacuum_action_sequence.append([ - { - "device_id": vacuum_backbone["pump"], - "action_name": "set_status", - "action_kwargs": { - "string": "ON" - } - }, - { - "device_id": vacuum_backbone["gas"], - "action_name": "set_status", - "action_kwargs": { - "string": "OFF" - } - } - ]) - vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}}) + "action_kwargs": {"command": "CLOSED"} + }) + + # 关闭真空泵 + action_sequence.append({ + "device_id": vacuum_pump, + "action_name": "set_status", + "action_kwargs": {"string": "OFF"} + }) + + # ============ 充气阶段 ============ + print(f"EVACUATE_REFILL: 充气阶段开始") - # 关闭真空泵阀门、打开气源阀门 - vacuum_action_sequence.append([ - { - "device_id": vacuum_backbone["vacuum_valve"], + # 启动气源 + action_sequence.append({ + "device_id": gas_source, + "action_name": "set_status", + "action_kwargs": {"string": "ON"} + }) + + # 开启气源电磁阀 + if gas_solenoid: + action_sequence.append({ + "device_id": gas_solenoid, "action_name": "set_valve_position", - "action_kwargs": { - "command": "CLOSED" + "action_kwargs": {"command": "OPEN"} + }) + + # **关键修复**: 改进充气 pump_protocol 调用 + print(f"EVACUATE_REFILL: 调用充气 pump_protocol: {gas_source} → {vessel}") + + try: + gas_transfer_actions = generate_pump_protocol_with_rinsing( + G=G, + from_vessel=gas_source, + to_vessel=vessel, + volume=REFILL_VOLUME, + amount="", + time=0.0, + viscous=False, + rinsing_solvent="", # **修复**: 明确不使用清洗 + rinsing_volume=0.0, + rinsing_repeats=0, + solid=False, + flowrate=PUMP_FLOW_RATE, + transfer_flowrate=PUMP_FLOW_RATE + ) + + if gas_transfer_actions: + action_sequence.extend(gas_transfer_actions) + print(f"EVACUATE_REFILL: ✅ 成功添加 {len(gas_transfer_actions)} 个充气动作") + else: + print(f"EVACUATE_REFILL: ⚠️ 充气 pump_protocol 返回空序列") + # **修复**: 添加手动充气动作 + action_sequence.extend([ + { + "device_id": "multiway_valve_2", + "action_name": "set_valve_position", + "action_kwargs": {"command": "8"} # 氮气端口 + }, + { + "device_id": "transfer_pump_2", + "action_name": "set_position", + "action_kwargs": { + "position": REFILL_VOLUME, + "max_velocity": PUMP_FLOW_RATE + } + }, + { + "device_id": "multiway_valve_2", + "action_name": "set_valve_position", + "action_kwargs": {"command": "5"} # 反应器端口 + }, + { + "device_id": "transfer_pump_2", + "action_name": "set_position", + "action_kwargs": { + "position": 0.0, + "max_velocity": PUMP_FLOW_RATE + } + } + ]) + + except Exception as e: + print(f"EVACUATE_REFILL: ❌ 充气 pump_protocol 失败: {str(e)}") + import traceback + print(f"EVACUATE_REFILL: 详细错误:\n{traceback.format_exc()}") + + # **修复**: 使用手动充气动作 + print(f"EVACUATE_REFILL: 使用手动充气方案") + action_sequence.extend([ + { + "device_id": "multiway_valve_2", + "action_name": "set_valve_position", + "action_kwargs": {"command": "8"} # 连接气源 + }, + { + "device_id": "transfer_pump_2", + "action_name": "set_position", + "action_kwargs": { + "position": REFILL_VOLUME, + "max_velocity": PUMP_FLOW_RATE + } + }, + { + "device_id": "multiway_valve_2", + "action_name": "set_valve_position", + "action_kwargs": {"command": "5"} # 连接反应器 + }, + { + "device_id": "transfer_pump_2", + "action_name": "set_position", + "action_kwargs": { + "position": 0.0, + "max_velocity": PUMP_FLOW_RATE + } } - }, - { - "device_id": vacuum_backbone["gas_valve"], + ]) + + # 关闭气源电磁阀 + if gas_solenoid: + action_sequence.append({ + "device_id": gas_solenoid, "action_name": "set_valve_position", - "action_kwargs": { - "command": "OPEN" - } - } - ]) - - # 关闭真空泵、打开气源 - vacuum_action_sequence.append([ - { - "device_id": vacuum_backbone["pump"], - "action_name": "set_status", - "action_kwargs": { - "string": "OFF" - } - }, - { - "device_id": vacuum_backbone["gas"], - "action_name": "set_status", - "action_kwargs": { - "string": "ON" - } - } - ]) - vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}}) + "action_kwargs": {"command": "CLOSED"} + }) # 关闭气源 - vacuum_action_sequence.append( - { - "device_id": vacuum_backbone["gas"], - "action_name": "set_status", - "action_kwargs": { - "string": "OFF" - } - } - ) + action_sequence.append({ + "device_id": gas_source, + "action_name": "set_status", + "action_kwargs": {"string": "OFF"} + }) - # 关闭阀门 - vacuum_action_sequence.append( - { - "device_id": vacuum_backbone["gas_valve"], - "action_name": "set_valve_position", - "action_kwargs": { - "command": "CLOSED" - } - } - ) - return vacuum_action_sequence + # 等待下一次循环 + if cycle < repeats - 1: + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 2.0} + }) + + # 停止搅拌器 + if stirrer_id: + action_sequence.append({ + "device_id": stirrer_id, + "action_name": "stop_stir", + "action_kwargs": {"vessel": vessel} + }) + + print(f"EVACUATE_REFILL: 协议生成完成，共 {len(action_sequence)} 个动作") + return action_sequence + + +# 测试函数 +def test_evacuateandrefill_protocol(): + """测试抽真空充气协议""" + print("=== EVACUATE AND REFILL PROTOCOL 测试 ===") + print("测试完成") + + +if __name__ == "__main__": + test_evacuateandrefill_protocol() \ No newline at end of file diff --git a/unilabos/compile/evacuateandrefill_protocol_old.py b/unilabos/compile/evacuateandrefill_protocol_old.py new file mode 100644 index 00000000..9f891ea2 --- /dev/null +++ b/unilabos/compile/evacuateandrefill_protocol_old.py @@ -0,0 +1,143 @@ +# import numpy as np +# import networkx as nx + + +# def generate_evacuateandrefill_protocol( +# G: nx.DiGraph, +# vessel: str, +# gas: str, +# repeats: int = 1 +# ) -> list[dict]: +# """ +# 生成泵操作的动作序列。 + +# :param G: 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置 +# :param from_vessel: 容器A +# :param to_vessel: 容器B +# :param volume: 转移的体积 +# :param flowrate: 最终注入容器B时的流速 +# :param transfer_flowrate: 泵骨架中转移流速（若不指定，默认与注入流速相同） +# :return: 泵操作的动作序列 +# """ + +# # 生成电磁阀、真空泵、气源操作的动作序列 +# vacuum_action_sequence = [] +# nodes = G.nodes(data=True) + +# # 找到和 vessel 相连的电磁阀和真空泵、气源 +# vacuum_backbone = {"vessel": vessel} + +# for neighbor in G.neighbors(vessel): +# if nodes[neighbor]["class"].startswith("solenoid_valve"): +# for neighbor2 in G.neighbors(neighbor): +# if neighbor2 == vessel: +# continue +# if nodes[neighbor2]["class"].startswith("vacuum_pump"): +# vacuum_backbone.update({"vacuum_valve": neighbor, "pump": neighbor2}) +# break +# elif nodes[neighbor2]["class"].startswith("gas_source"): +# vacuum_backbone.update({"gas_valve": neighbor, "gas": neighbor2}) +# break +# # 判断是否设备齐全 +# if len(vacuum_backbone) < 5: +# print(f"\n\n\n{vacuum_backbone}\n\n\n") +# raise ValueError("Not all devices are connected to the vessel.") + +# # 生成操作的动作序列 +# for i in range(repeats): +# # 打开真空泵阀门、关闭气源阀门 +# vacuum_action_sequence.append([ +# { +# "device_id": vacuum_backbone["vacuum_valve"], +# "action_name": "set_valve_position", +# "action_kwargs": { +# "command": "OPEN" +# } +# }, +# { +# "device_id": vacuum_backbone["gas_valve"], +# "action_name": "set_valve_position", +# "action_kwargs": { +# "command": "CLOSED" +# } +# } +# ]) + +# # 打开真空泵、关闭气源 +# vacuum_action_sequence.append([ +# { +# "device_id": vacuum_backbone["pump"], +# "action_name": "set_status", +# "action_kwargs": { +# "string": "ON" +# } +# }, +# { +# "device_id": vacuum_backbone["gas"], +# "action_name": "set_status", +# "action_kwargs": { +# "string": "OFF" +# } +# } +# ]) +# vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}}) + +# # 关闭真空泵阀门、打开气源阀门 +# vacuum_action_sequence.append([ +# { +# "device_id": vacuum_backbone["vacuum_valve"], +# "action_name": "set_valve_position", +# "action_kwargs": { +# "command": "CLOSED" +# } +# }, +# { +# "device_id": vacuum_backbone["gas_valve"], +# "action_name": "set_valve_position", +# "action_kwargs": { +# "command": "OPEN" +# } +# } +# ]) + +# # 关闭真空泵、打开气源 +# vacuum_action_sequence.append([ +# { +# "device_id": vacuum_backbone["pump"], +# "action_name": "set_status", +# "action_kwargs": { +# "string": "OFF" +# } +# }, +# { +# "device_id": vacuum_backbone["gas"], +# "action_name": "set_status", +# "action_kwargs": { +# "string": "ON" +# } +# } +# ]) +# vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}}) + +# # 关闭气源 +# vacuum_action_sequence.append( +# { +# "device_id": vacuum_backbone["gas"], +# "action_name": "set_status", +# "action_kwargs": { +# "string": "OFF" +# } +# } +# ) + +# # 关闭阀门 +# vacuum_action_sequence.append( +# { +# "device_id": vacuum_backbone["gas_valve"], +# "action_name": "set_valve_position", +# "action_kwargs": { +# "command": "CLOSED" +# } +# } +# ) +# return vacuum_action_sequence diff --git a/unilabos/compile/evaporate_protocol.py b/unilabos/compile/evaporate_protocol.py index 15af5e11..4cee78d9 100644 --- a/unilabos/compile/evaporate_protocol.py +++ b/unilabos/compile/evaporate_protocol.py @@ -1,81 +1,326 @@ -import numpy as np +from typing import List, Dict, Any import networkx as nx +from .pump_protocol import generate_pump_protocol + + +def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float: + """ + 获取容器中的液体体积 + """ + if vessel not in G.nodes(): + return 0.0 + + vessel_data = G.nodes[vessel].get('data', {}) + liquids = vessel_data.get('liquid', []) + + total_volume = 0.0 + for liquid in liquids: + if isinstance(liquid, dict) and 'liquid_volume' in liquid: + total_volume += liquid['liquid_volume'] + + return total_volume + + +def find_rotavap_device(G: nx.DiGraph) -> str: + """查找旋转蒸发仪设备""" + rotavap_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_rotavap'] + + if rotavap_nodes: + return rotavap_nodes[0] + + raise ValueError("系统中未找到旋转蒸发仪设备") + + +def find_solvent_recovery_vessel(G: nx.DiGraph) -> str: + """查找溶剂回收容器""" + possible_names = [ + "flask_distillate", + "bottle_distillate", + "vessel_distillate", + "distillate", + "solvent_recovery", + "flask_solvent_recovery", + "collection_flask" + ] + + for vessel_name in possible_names: + if vessel_name in G.nodes(): + return vessel_name + + # 如果找不到专门的回收容器，使用废液容器 + waste_names = ["waste_workup", "flask_waste", "bottle_waste", "waste"] + for vessel_name in waste_names: + if vessel_name in G.nodes(): + return vessel_name + + raise ValueError(f"未找到溶剂回收容器。尝试了以下名称: {possible_names + waste_names}") def generate_evaporate_protocol( - G: nx.DiGraph, + G: nx.DiGraph, vessel: str, - pressure: float, - temp: float, - time: float, - stir_speed: float -) -> list[dict]: + pressure: float = 0.1, + temp: float = 60.0, + time: float = 1800.0, + stir_speed: float = 100.0 +) -> List[Dict[str, Any]]: """ - Generate a protocol to evaporate a solution from a vessel. - - :param G: Directed graph. Nodes are containers and pumps, edges are fluidic connections. - :param vessel: Vessel to clean. - :param solvent: Solvent to clean vessel with. - :param volume: Volume of solvent to clean vessel with. - :param temp: Temperature to heat vessel to while cleaning. - :param repeats: Number of cleaning cycles to perform. - :return: List of actions to clean vessel. + 生成蒸发操作的协议序列 + + 蒸发流程： + 1. 液体转移：将待蒸发溶液从源容器转移到旋转蒸发仪 + 2. 蒸发操作：执行旋转蒸发 + 3. (可选) 溶剂回收：将冷凝的溶剂转移到回收容器 + 4. 残留物转移：将浓缩物从旋转蒸发仪转移回原容器或新容器 + + Args: + G: 有向图，节点为设备和容器，边为流体管道 + vessel: 包含待蒸发溶液的容器名称 + pressure: 蒸发时的真空度 (bar)，默认0.1 bar + temp: 蒸发时的加热温度 (°C)，默认60°C + time: 蒸发时间 (秒)，默认1800秒(30分钟) + stir_speed: 旋转速度 (RPM)，默认100 RPM + + Returns: + List[Dict[str, Any]]: 蒸发操作的动作序列 + + Raises: + ValueError: 当找不到必要的设备时抛出异常 + + Examples: + evaporate_actions = generate_evaporate_protocol(G, "reaction_mixture", 0.05, 80.0, 3600.0) """ + action_sequence = [] - # 生成泵操作的动作序列 - pump_action_sequence = [] - reactor_volume = 500.0 - transfer_flowrate = flowrate = 2.5 + print(f"EVAPORATE: 开始生成蒸发协议") + print(f" - 源容器: {vessel}") + print(f" - 真空度: {pressure} bar") + print(f" - 温度: {temp}°C") + print(f" - 时间: {time}s ({time/60:.1f}分钟)") + print(f" - 旋转速度: {stir_speed} RPM") - # 开启冷凝器 - pump_action_sequence.append({ - "device_id": "rotavap_chiller", - "action_name": "set_temperature", - "action_kwargs": { - "command": "-40" - } - }) - # TODO: 通过温度反馈改为 HeatChillToTemp，而非等待固定时间 - pump_action_sequence.append({ - "action_name": "wait", - "action_kwargs": { - "time": 1800 - } - }) + # 验证源容器存在 + if vessel not in G.nodes(): + raise ValueError(f"源容器 '{vessel}' 不存在于系统中") - # 开启旋蒸真空泵、旋转，在液体转移后运行time时间 - pump_action_sequence.append({ - "device_id": "rotavap_controller", - "action_name": "set_pump_time", - "action_kwargs": { - "command": str(time + reactor_volume / flowrate * 3) - } - }) - pump_action_sequence.append({ - "device_id": "rotavap_controller", - "action_name": "set_pump_time", - "action_kwargs": { - "command": str(time + reactor_volume / flowrate * 3) - } - }) + # 获取源容器中的液体体积 + source_volume = get_vessel_liquid_volume(G, vessel) + print(f"EVAPORATE: 源容器 {vessel} 中有 {source_volume} mL 液体") - # 液体转入旋转蒸发器 - pump_action_sequence.append({ - "device_id": "", - "action_name": "PumpTransferProtocol", - "action_kwargs": { - "from_vessel": vessel, - "to_vessel": "rotavap", - "volume": reactor_volume, - "time": reactor_volume / flowrate, - # "transfer_flowrate": transfer_flowrate, - } - }) + # 查找旋转蒸发仪 + try: + rotavap_id = find_rotavap_device(G) + print(f"EVAPORATE: 找到旋转蒸发仪: {rotavap_id}") + except ValueError as e: + raise ValueError(f"无法找到旋转蒸发仪: {str(e)}") + + # 查找旋转蒸发仪样品容器 + rotavap_vessel = None + possible_rotavap_vessels = ["rotavap_flask", "rotavap", "flask_rotavap", "evaporation_flask"] + for rv in possible_rotavap_vessels: + if rv in G.nodes(): + rotavap_vessel = rv + break + + if not rotavap_vessel: + raise ValueError(f"未找到旋转蒸发仪样品容器。尝试了: {possible_rotavap_vessels}") + + print(f"EVAPORATE: 找到旋转蒸发仪样品容器: {rotavap_vessel}") + + # 查找溶剂回收容器 + try: + distillate_vessel = find_solvent_recovery_vessel(G) + print(f"EVAPORATE: 找到溶剂回收容器: {distillate_vessel}") + except ValueError as e: + print(f"EVAPORATE: 警告 - {str(e)}") + distillate_vessel = None - pump_action_sequence.append({ + # === 简化的体积计算策略 === + if source_volume > 0: + # 如果能检测到液体体积，使用实际体积的大部分 + transfer_volume = min(source_volume * 0.9, 250.0) # 90%或最多250mL + print(f"EVAPORATE: 检测到液体体积，将转移 {transfer_volume} mL") + else: + # 如果检测不到液体体积，默认转移一整瓶 250mL + transfer_volume = 250.0 + print(f"EVAPORATE: 未检测到液体体积，默认转移整瓶 {transfer_volume} mL") + + # === 第一步：将待蒸发溶液转移到旋转蒸发仪 === + print(f"EVAPORATE: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {rotavap_vessel}") + try: + transfer_to_rotavap_actions = generate_pump_protocol( + G=G, + from_vessel=vessel, + to_vessel=rotavap_vessel, + volume=transfer_volume, + flowrate=2.0, + transfer_flowrate=2.0 + ) + action_sequence.extend(transfer_to_rotavap_actions) + except Exception as e: + raise ValueError(f"无法将溶液转移到旋转蒸发仪: {str(e)}") + + # 转移后等待 + wait_action = { "action_name": "wait", + "action_kwargs": {"time": 10} + } + action_sequence.append(wait_action) + + # === 第二步：执行旋转蒸发 === + print(f"EVAPORATE: 执行旋转蒸发操作") + evaporate_action = { + "device_id": rotavap_id, + "action_name": "evaporate", "action_kwargs": { - "time": time + "vessel": rotavap_vessel, + "pressure": pressure, + "temp": temp, + "time": time, + "stir_speed": stir_speed } - }) - return pump_action_sequence + } + action_sequence.append(evaporate_action) + + # 蒸发后等待系统稳定 + wait_action = { + "action_name": "wait", + "action_kwargs": {"time": 30} + } + action_sequence.append(wait_action) + + # === 第三步：溶剂回收（如果有回收容器）=== + if distillate_vessel: + print(f"EVAPORATE: 回收冷凝溶剂到 {distillate_vessel}") + try: + condenser_vessel = "rotavap_condenser" + if condenser_vessel in G.nodes(): + # 估算回收体积（约为转移体积的70% - 大部分溶剂被蒸发回收） + recovery_volume = transfer_volume * 0.7 + print(f"EVAPORATE: 预计回收 {recovery_volume} mL 溶剂") + + recovery_actions = generate_pump_protocol( + G=G, + from_vessel=condenser_vessel, + to_vessel=distillate_vessel, + volume=recovery_volume, + flowrate=3.0, + transfer_flowrate=3.0 + ) + action_sequence.extend(recovery_actions) + else: + print("EVAPORATE: 未找到冷凝器容器，跳过溶剂回收") + except Exception as e: + print(f"EVAPORATE: 溶剂回收失败: {str(e)}") + + # === 第四步：将浓缩物转移回原容器 === + print(f"EVAPORATE: 将浓缩物从旋转蒸发仪转移回 {vessel}") + try: + # 估算浓缩物体积（约为转移体积的20% - 大部分溶剂已蒸发） + concentrate_volume = transfer_volume * 0.2 + print(f"EVAPORATE: 预计浓缩物体积 {concentrate_volume} mL") + + transfer_back_actions = generate_pump_protocol( + G=G, + from_vessel=rotavap_vessel, + to_vessel=vessel, + volume=concentrate_volume, + flowrate=1.0, # 浓缩物可能粘稠，用较慢流速 + transfer_flowrate=1.0 + ) + action_sequence.extend(transfer_back_actions) + except Exception as e: + print(f"EVAPORATE: 将浓缩物转移回容器失败: {str(e)}") + + # === 第五步：清洗旋转蒸发仪 === + print(f"EVAPORATE: 清洗旋转蒸发仪") + try: + # 查找清洗溶剂 + cleaning_solvent = None + for solvent in ["flask_ethanol", "flask_acetone", "flask_water"]: + if solvent in G.nodes(): + cleaning_solvent = solvent + break + + if cleaning_solvent and distillate_vessel: + # 用固定量溶剂清洗（不依赖检测体积） + cleaning_volume = 50.0 # 固定50mL清洗 + print(f"EVAPORATE: 用 {cleaning_volume} mL {cleaning_solvent} 清洗") + + # 清洗溶剂加入 + cleaning_actions = generate_pump_protocol( + G=G, + from_vessel=cleaning_solvent, + to_vessel=rotavap_vessel, + volume=cleaning_volume, + flowrate=2.0, + transfer_flowrate=2.0 + ) + action_sequence.extend(cleaning_actions) + + # 将清洗液转移到废液/回收容器 + waste_actions = generate_pump_protocol( + G=G, + from_vessel=rotavap_vessel, + to_vessel=distillate_vessel, # 使用回收容器作为废液 + volume=cleaning_volume, + flowrate=2.0, + transfer_flowrate=2.0 + ) + action_sequence.extend(waste_actions) + + except Exception as e: + print(f"EVAPORATE: 清洗步骤失败: {str(e)}") + + print(f"EVAPORATE: 生成了 {len(action_sequence)} 个动作") + print(f"EVAPORATE: 蒸发协议生成完成") + print(f"EVAPORATE: 总处理体积: {transfer_volume} mL") + + return action_sequence + + +# 便捷函数：常用蒸发方案 - 都使用250mL标准瓶体积 +def generate_quick_evaporate_protocol( + G: nx.DiGraph, + vessel: str, + temp: float = 40.0, + time: float = 900.0 # 15分钟 +) -> List[Dict[str, Any]]: + """快速蒸发：低温、短时间、整瓶处理""" + return generate_evaporate_protocol(G, vessel, 0.2, temp, time, 80.0) + + +def generate_gentle_evaporate_protocol( + G: nx.DiGraph, + vessel: str, + temp: float = 50.0, + time: float = 2700.0 # 45分钟 +) -> List[Dict[str, Any]]: + """温和蒸发：中等条件、较长时间、整瓶处理""" + return generate_evaporate_protocol(G, vessel, 0.1, temp, time, 60.0) + + +def generate_high_vacuum_evaporate_protocol( + G: nx.DiGraph, + vessel: str, + temp: float = 35.0, + time: float = 3600.0 # 1小时 +) -> List[Dict[str, Any]]: + """高真空蒸发：低温、高真空、长时间、整瓶处理""" + return generate_evaporate_protocol(G, vessel, 0.01, temp, time, 120.0) + + +def generate_standard_evaporate_protocol( + G: nx.DiGraph, + vessel: str +) -> List[Dict[str, Any]]: + """标准蒸发：常用参数、整瓶250mL处理""" + return generate_evaporate_protocol( + G=G, + vessel=vessel, + pressure=0.1, # 标准真空度 + temp=60.0, # 适中温度 + time=1800.0, # 30分钟 + stir_speed=100.0 # 适中旋转速度 + ) diff --git a/unilabos/compile/filter_protocol.py b/unilabos/compile/filter_protocol.py index 2847c5dc..7e3ca6b4 100644 --- a/unilabos/compile/filter_protocol.py +++ b/unilabos/compile/filter_protocol.py @@ -1,5 +1,89 @@ from typing import List, Dict, Any import networkx as nx +from .pump_protocol import generate_pump_protocol + + +def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float: + """获取容器中的液体体积""" + if vessel not in G.nodes(): + return 0.0 + + vessel_data = G.nodes[vessel].get('data', {}) + liquids = vessel_data.get('liquid', []) + + total_volume = 0.0 + for liquid in liquids: + if isinstance(liquid, dict) and 'liquid_volume' in liquid: + total_volume += liquid['liquid_volume'] + + return total_volume + + +def find_filter_device(G: nx.DiGraph) -> str: + """查找过滤器设备""" + filter_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_filter'] + + if filter_nodes: + return filter_nodes[0] + + raise ValueError("系统中未找到过滤器设备") + + +def find_filter_vessel(G: nx.DiGraph) -> str: + """查找过滤器专用容器""" + possible_names = [ + "filter_vessel", # 标准过滤器容器 + "filtration_vessel", # 备选名称 + "vessel_filter", # 备选名称 + "filter_unit", # 备选名称 + "filter" # 简单名称 + ] + + for vessel_name in possible_names: + if vessel_name in G.nodes(): + return vessel_name + + raise ValueError(f"未找到过滤器容器。尝试了以下名称: {possible_names}") + + +def find_filtrate_vessel(G: nx.DiGraph, filtrate_vessel: str = "") -> str: + """查找滤液收集容器""" + if filtrate_vessel and filtrate_vessel in G.nodes(): + return filtrate_vessel + + # 自动查找滤液容器 + possible_names = [ + "filtrate_vessel", + "collection_bottle_1", + "collection_bottle_2", + "waste_workup" + ] + + for vessel_name in possible_names: + if vessel_name in G.nodes(): + return vessel_name + + raise ValueError(f"未找到滤液收集容器。尝试了以下名称: {possible_names}") + + +def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str: + """查找与指定容器相连的加热搅拌器""" + # 查找所有加热搅拌器节点 + heatchill_nodes = [node for node in G.nodes() + if G.nodes[node].get('class') == 'virtual_heatchill'] + + # 检查哪个加热器与目标容器相连 + for heatchill in heatchill_nodes: + if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill): + return heatchill + + # 如果没有直接连接，返回第一个可用的加热器 + if heatchill_nodes: + return heatchill_nodes[0] + + raise ValueError(f"未找到与容器 {vessel} 相连的加热搅拌器") + def generate_filter_protocol( G: nx.DiGraph, @@ -12,59 +96,209 @@ def generate_filter_protocol( volume: float = 0.0 ) -> List[Dict[str, Any]]: """ - 生成过滤操作的协议序列 + 生成过滤操作的协议序列，复用 pump_protocol 的成熟算法 + + 过滤流程： + 1. 液体转移：将待过滤溶液从源容器转移到过滤器 + 2. 启动加热搅拌：设置温度和搅拌 + 3. 执行过滤：通过过滤器分离固液 + 4. (可选) 继续或停止加热搅拌 Args: - G: 有向图，节点为设备和容器 - vessel: 过滤容器 - filtrate_vessel: 滤液容器（可选） - stir: 是否搅拌 - stir_speed: 搅拌速度（可选） - temp: 温度（可选，摄氏度） - continue_heatchill: 是否继续加热冷却 - volume: 过滤体积（可选） + G: 有向图，节点为设备和容器，边为流体管道 + vessel: 包含待过滤溶液的容器名称 + filtrate_vessel: 滤液收集容器（可选，自动查找） + stir: 是否在过滤过程中搅拌 + stir_speed: 搅拌速度 (RPM) + temp: 过滤温度 (°C) + continue_heatchill: 过滤后是否继续加热搅拌 + volume: 预期过滤体积 (mL)，0表示全部过滤 Returns: List[Dict[str, Any]]: 过滤操作的动作序列 - - Raises: - ValueError: 当找不到过滤设备时抛出异常 - - Examples: - filter_protocol = generate_filter_protocol(G, "reactor", "filtrate_vessel", stir=True, volume=100.0) """ action_sequence = [] - # 查找过滤设备 - filter_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_filter'] + print(f"FILTER: 开始生成过滤协议") + print(f" - 源容器: {vessel}") + print(f" - 滤液容器: {filtrate_vessel}") + print(f" - 搅拌: {stir} ({stir_speed} RPM)" if stir else " - 搅拌: 否") + print(f" - 过滤温度: {temp}°C") + print(f" - 预期过滤体积: {volume} mL" if volume > 0 else " - 预期过滤体积: 全部") + print(f" - 继续加热搅拌: {continue_heatchill}") - if not filter_nodes: - raise ValueError("没有找到可用的过滤设备") + # 验证源容器存在 + if vessel not in G.nodes(): + raise ValueError(f"源容器 '{vessel}' 不存在于系统中") - # 使用第一个可用的过滤器 - filter_id = filter_nodes[0] + # 获取源容器中的液体体积 + source_volume = get_vessel_liquid_volume(G, vessel) + print(f"FILTER: 源容器 {vessel} 中有 {source_volume} mL 液体") - # 验证容器是否存在 - if vessel not in G.nodes(): - raise ValueError(f"过滤容器 {vessel} 不存在于图中") + # 查找过滤器设备 + try: + filter_id = find_filter_device(G) + print(f"FILTER: 找到过滤器: {filter_id}") + except ValueError as e: + raise ValueError(f"无法找到过滤器: {str(e)}") + + # 查找过滤器容器 + try: + filter_vessel_id = find_filter_vessel(G) + print(f"FILTER: 找到过滤器容器: {filter_vessel_id}") + except ValueError as e: + raise ValueError(f"无法找到过滤器容器: {str(e)}") + + # 查找滤液收集容器 + try: + actual_filtrate_vessel = find_filtrate_vessel(G, filtrate_vessel) + print(f"FILTER: 找到滤液收集容器: {actual_filtrate_vessel}") + except ValueError as e: + raise ValueError(f"无法找到滤液收集容器: {str(e)}") - if filtrate_vessel and filtrate_vessel not in G.nodes(): - raise ValueError(f"滤液容器 {filtrate_vessel} 不存在于图中") + # 查找加热搅拌器（如果需要温度控制或搅拌） + heatchill_id = None + if temp != 25.0 or stir or continue_heatchill: + try: + heatchill_id = find_connected_heatchill(G, filter_vessel_id) + print(f"FILTER: 找到加热搅拌器: {heatchill_id}") + except ValueError as e: + print(f"FILTER: 警告 - {str(e)}") - # 执行过滤操作 + # === 简化的体积计算策略 === + if volume > 0: + transfer_volume = min(volume, source_volume if source_volume > 0 else volume) + print(f"FILTER: 指定过滤体积 {transfer_volume} mL") + elif source_volume > 0: + transfer_volume = source_volume * 0.9 # 90% + print(f"FILTER: 检测到液体体积，将过滤 {transfer_volume} mL") + else: + transfer_volume = 50.0 # 默认过滤量 + print(f"FILTER: 未检测到液体体积，默认过滤 {transfer_volume} mL") + + # === 第一步：启动加热搅拌器（在转移前预热） === + if heatchill_id and (temp != 25.0 or stir): + print(f"FILTER: 启动加热搅拌器，温度: {temp}°C，搅拌: {stir}") + + heatchill_action = { + "device_id": heatchill_id, + "action_name": "heat_chill_start", + "action_kwargs": { + "vessel": filter_vessel_id, + "temp": temp, + "purpose": f"过滤过程温度控制和搅拌" + } + } + action_sequence.append(heatchill_action) + + # 等待温度稳定 + if temp != 25.0: + wait_time = min(30, abs(temp - 25.0) * 1.0) # 根据温差估算预热时间 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": wait_time} + }) + + # === 第二步：将待过滤溶液转移到过滤器 === + print(f"FILTER: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {filter_vessel_id}") + try: + # 使用成熟的 pump_protocol 算法进行液体转移 + transfer_to_filter_actions = generate_pump_protocol( + G=G, + from_vessel=vessel, + to_vessel=filter_vessel_id, + volume=transfer_volume, + flowrate=1.0, # 过滤转移用较慢速度，避免扰动 + transfer_flowrate=1.5 + ) + action_sequence.extend(transfer_to_filter_actions) + except Exception as e: + raise ValueError(f"无法将溶液转移到过滤器: {str(e)}") + + # 转移后等待 action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 5} + }) + + # === 第三步：执行过滤操作（完全按照 Filter.action 参数） === + print(f"FILTER: 执行过滤操作") + filter_action = { "device_id": filter_id, - "action_name": "filter_sample", + "action_name": "filter", "action_kwargs": { - "vessel": vessel, - "filtrate_vessel": filtrate_vessel, + "vessel": filter_vessel_id, + "filtrate_vessel": actual_filtrate_vessel, "stir": stir, "stir_speed": stir_speed, "temp": temp, "continue_heatchill": continue_heatchill, - "volume": volume + "volume": transfer_volume } + } + action_sequence.append(filter_action) + + # 过滤后等待 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 10} }) - return action_sequence \ No newline at end of file + # === 第四步：如果不继续加热搅拌，停止加热器 === + if heatchill_id and not continue_heatchill and (temp != 25.0 or stir): + print(f"FILTER: 停止加热搅拌器") + + stop_action = { + "device_id": heatchill_id, + "action_name": "heat_chill_stop", + "action_kwargs": { + "vessel": filter_vessel_id + } + } + action_sequence.append(stop_action) + + print(f"FILTER: 生成了 {len(action_sequence)} 个动作") + print(f"FILTER: 过滤协议生成完成") + + return action_sequence + + +# 便捷函数：常用过滤方案 +def generate_gravity_filter_protocol( + G: nx.DiGraph, + vessel: str, + filtrate_vessel: str = "" +) -> List[Dict[str, Any]]: + """重力过滤：室温，无搅拌""" + return generate_filter_protocol(G, vessel, filtrate_vessel, False, 0.0, 25.0, False, 0.0) + + +def generate_hot_filter_protocol( + G: nx.DiGraph, + vessel: str, + filtrate_vessel: str = "", + temp: float = 60.0 +) -> List[Dict[str, Any]]: + """热过滤：高温过滤，防止结晶析出""" + return generate_filter_protocol(G, vessel, filtrate_vessel, False, 0.0, temp, False, 0.0) + + +def generate_stirred_filter_protocol( + G: nx.DiGraph, + vessel: str, + filtrate_vessel: str = "", + stir_speed: float = 200.0 +) -> List[Dict[str, Any]]: + """搅拌过滤：低速搅拌，防止滤饼堵塞""" + return generate_filter_protocol(G, vessel, filtrate_vessel, True, stir_speed, 25.0, False, 0.0) + + +def generate_hot_stirred_filter_protocol( + G: nx.DiGraph, + vessel: str, + filtrate_vessel: str = "", + temp: float = 60.0, + stir_speed: float = 300.0 +) -> List[Dict[str, Any]]: + """热搅拌过滤：高温搅拌过滤""" + return generate_filter_protocol(G, vessel, filtrate_vessel, True, stir_speed, temp, False, 0.0) \ No newline at end of file diff --git a/unilabos/compile/filter_through_protocol.py b/unilabos/compile/filter_through_protocol.py index 009756b1..314dbc74 100644 --- a/unilabos/compile/filter_through_protocol.py +++ b/unilabos/compile/filter_through_protocol.py @@ -1,5 +1,72 @@ from typing import List, Dict, Any import networkx as nx +from .pump_protocol import generate_pump_protocol + + +def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float: + """获取容器中的液体体积""" + if vessel not in G.nodes(): + return 0.0 + + vessel_data = G.nodes[vessel].get('data', {}) + liquids = vessel_data.get('liquid', []) + + total_volume = 0.0 + for liquid in liquids: + if isinstance(liquid, dict) and 'liquid_volume' in liquid: + total_volume += liquid['liquid_volume'] + + return total_volume + + +def find_filter_through_vessel(G: nx.DiGraph, filter_through: str) -> str: + """查找过滤介质容器""" + # 直接使用 filter_through 参数作为容器名称 + if filter_through in G.nodes(): + return filter_through + + # 尝试常见的过滤介质容器命名 + possible_names = [ + f"filter_{filter_through}", + f"{filter_through}_filter", + f"column_{filter_through}", + f"{filter_through}_column", + "filter_through_vessel", + "column_vessel", + "chromatography_column", + "filter_column" + ] + + for vessel_name in possible_names: + if vessel_name in G.nodes(): + return vessel_name + + raise ValueError(f"未找到过滤介质容器 '{filter_through}'。尝试了以下名称: {[filter_through] + possible_names}") + + +def find_eluting_solvent_vessel(G: nx.DiGraph, eluting_solvent: str) -> str: + """查找洗脱溶剂容器""" + if not eluting_solvent: + return "" + + # 按照命名规则查找溶剂瓶 + solvent_vessel_id = f"flask_{eluting_solvent}" + + if solvent_vessel_id in G.nodes(): + return solvent_vessel_id + + # 如果直接匹配失败，尝试模糊匹配 + for node in G.nodes(): + if node.startswith('flask_') and eluting_solvent.lower() in node.lower(): + return node + + # 如果还是找不到，列出所有可用的溶剂瓶 + available_flasks = [node for node in G.nodes() + if node.startswith('flask_') + and G.nodes[node].get('type') == 'container'] + + raise ValueError(f"找不到洗脱溶剂 '{eluting_solvent}' 对应的溶剂瓶。可用溶剂瓶: {available_flasks}") + def generate_filter_through_protocol( G: nx.DiGraph, @@ -12,10 +79,15 @@ def generate_filter_through_protocol( residence_time: float = 0.0 ) -> List[Dict[str, Any]]: """ - 生成通过过滤介质过滤的协议序列 + 生成通过过滤介质过滤的协议序列，复用 pump_protocol 的成熟算法 + + 过滤流程： + 1. 液体转移：将样品从源容器转移到过滤介质 + 2. 重力过滤：液体通过过滤介质自动流到目标容器 + 3. 洗脱操作：将洗脱溶剂通过过滤介质洗脱目标物质 Args: - G: 有向图，节点为设备和容器 + G: 有向图，节点为设备和容器，边为流体管道 from_vessel: 源容器的名称，即物质起始所在的容器 to_vessel: 目标容器的名称，物质过滤后要到达的容器 filter_through: 过滤时所通过的介质，如滤纸、柱子等 @@ -28,123 +100,288 @@ def generate_filter_through_protocol( List[Dict[str, Any]]: 过滤操作的动作序列 Raises: - ValueError: 当找不到必要的设备时抛出异常 + ValueError: 当找不到必要的设备或容器时 Examples: - filter_through_protocol = generate_filter_through_protocol( - G, "reactor", "collection_flask", "celite", "ethanol", 50.0, 2, 60.0 + filter_through_actions = generate_filter_through_protocol( + G, "reaction_mixture", "collection_bottle_1", "celite", "ethanol", 20.0, 2, 30.0 ) """ action_sequence = [] - # 验证容器是否存在 + print(f"FILTER_THROUGH: 开始生成通过过滤协议") + print(f" - 源容器: {from_vessel}") + print(f" - 目标容器: {to_vessel}") + print(f" - 过滤介质: {filter_through}") + print(f" - 洗脱溶剂: {eluting_solvent}") + print(f" - 洗脱体积: {eluting_volume} mL" if eluting_volume > 0 else " - 洗脱体积: 无") + print(f" - 洗脱重复次数: {eluting_repeats}") + print(f" - 停留时间: {residence_time}s" if residence_time > 0 else " - 停留时间: 无") + + # 验证源容器和目标容器存在 if from_vessel not in G.nodes(): - raise ValueError(f"源容器 {from_vessel} 不存在于图中") + raise ValueError(f"源容器 '{from_vessel}' 不存在于系统中") if to_vessel not in G.nodes(): - raise ValueError(f"目标容器 {to_vessel} 不存在于图中") - - # 查找转移泵设备（用于液体转移） - pump_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_transfer_pump'] - - if not pump_nodes: - raise ValueError("没有找到可用的转移泵设备") - - pump_id = pump_nodes[0] + raise ValueError(f"目标容器 '{to_vessel}' 不存在于系统中") - # 查找过滤设备（可选，如果有专门的过滤设备） - filter_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_filter'] + # 获取源容器中的液体体积 + source_volume = get_vessel_liquid_volume(G, from_vessel) + print(f"FILTER_THROUGH: 源容器 {from_vessel} 中有 {source_volume} mL 液体") - filter_id = filter_nodes[0] if filter_nodes else None + # 查找过滤介质容器 + try: + filter_through_vessel = find_filter_through_vessel(G, filter_through) + print(f"FILTER_THROUGH: 找到过滤介质容器: {filter_through_vessel}") + except ValueError as e: + raise ValueError(f"无法找到过滤介质容器: {str(e)}") - # 查找洗脱溶剂容器（如果需要洗脱） - eluting_vessel = None - if eluting_solvent and eluting_volume > 0: - eluting_vessel = f"flask_{eluting_solvent}" - if eluting_vessel not in G.nodes(): - # 查找可用的溶剂容器 - available_vessels = [node for node in G.nodes() - if node.startswith('flask_') and - G.nodes[node].get('type') == 'container'] - if available_vessels: - eluting_vessel = available_vessels[0] - else: - raise ValueError(f"没有找到洗脱溶剂容器 {eluting_solvent}") + # 查找洗脱溶剂容器（如果需要） + eluting_vessel = "" + if eluting_solvent and eluting_volume > 0 and eluting_repeats > 0: + try: + eluting_vessel = find_eluting_solvent_vessel(G, eluting_solvent) + print(f"FILTER_THROUGH: 找到洗脱溶剂容器: {eluting_vessel}") + except ValueError as e: + raise ValueError(f"无法找到洗脱溶剂容器: {str(e)}") - # 步骤1：将样品从源容器转移到过滤装置（模拟通过过滤介质） - # 这里我们将过滤过程分解为多个转移步骤来模拟通过介质的过程 + # === 第一步：将样品从源容器转移到过滤介质 === + transfer_volume = source_volume if source_volume > 0 else 100.0 # 默认100mL + print(f"FILTER_THROUGH: 将 {transfer_volume} mL 样品从 {from_vessel} 转移到 {filter_through_vessel}") - # 首先转移样品（模拟样品通过过滤介质） - action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", - "action_kwargs": { - "from_vessel": from_vessel, - "to_vessel": to_vessel, - "volume": 0.0, # 转移所有液体，体积由系统确定 - "amount": f"通过 {filter_through} 过滤", - "time": residence_time if residence_time > 0 else 0.0, - "viscous": False, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": True # 通过过滤介质可能涉及固体分离 - } - }) + try: + # 使用成熟的 pump_protocol 算法进行液体转移 + sample_transfer_actions = generate_pump_protocol( + G=G, + from_vessel=from_vessel, + to_vessel=filter_through_vessel, + volume=transfer_volume, + flowrate=0.8, # 较慢的流速，避免冲击过滤介质 + transfer_flowrate=1.2 + ) + action_sequence.extend(sample_transfer_actions) + except Exception as e: + raise ValueError(f"无法将样品转移到过滤介质: {str(e)}") - # 步骤2：如果有专门的过滤设备，使用过滤设备处理 - if filter_id: + # === 第二步：等待样品通过过滤介质（停留时间） === + if residence_time > 0: + print(f"FILTER_THROUGH: 等待样品在过滤介质中停留 {residence_time}s") action_sequence.append({ - "device_id": filter_id, - "action_name": "filter_sample", - "action_kwargs": { - "vessel": to_vessel, - "filtrate_vessel": to_vessel, - "stir": False, - "stir_speed": 0.0, - "temp": 25.0, - "continue_heatchill": False, - "volume": 0.0 - } + "action_name": "wait", + "action_kwargs": {"time": residence_time} + }) + else: + # 即使没有指定停留时间，也等待一段时间让液体通过 + default_wait_time = max(10, transfer_volume / 10) # 根据体积估算等待时间 + print(f"FILTER_THROUGH: 等待样品通过过滤介质 {default_wait_time}s") + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": default_wait_time} }) - # 步骤3：洗脱操作（如果指定了洗脱溶剂和重复次数） + # === 第三步：洗脱操作（如果指定了洗脱参数） === if eluting_solvent and eluting_volume > 0 and eluting_repeats > 0 and eluting_vessel: - for repeat in range(eluting_repeats): - # 添加洗脱溶剂 + print(f"FILTER_THROUGH: 开始洗脱操作 - {eluting_repeats} 次，每次 {eluting_volume} mL {eluting_solvent}") + + for repeat_idx in range(eluting_repeats): + print(f"FILTER_THROUGH: 第 {repeat_idx + 1}/{eluting_repeats} 次洗脱") + + try: + # 将洗脱溶剂转移到过滤介质 + eluting_transfer_actions = generate_pump_protocol( + G=G, + from_vessel=eluting_vessel, + to_vessel=filter_through_vessel, + volume=eluting_volume, + flowrate=0.6, # 洗脱用更慢的流速 + transfer_flowrate=1.0 + ) + action_sequence.extend(eluting_transfer_actions) + except Exception as e: + raise ValueError(f"第 {repeat_idx + 1} 次洗脱转移失败: {str(e)}") + + # 等待洗脱溶剂通过过滤介质 + eluting_wait_time = max(30, eluting_volume / 5) # 根据洗脱体积估算等待时间 + print(f"FILTER_THROUGH: 等待第 {repeat_idx + 1} 次洗脱液通过 {eluting_wait_time}s") action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", - "action_kwargs": { - "from_vessel": eluting_vessel, - "to_vessel": to_vessel, - "volume": eluting_volume, - "amount": f"洗脱溶剂 {eluting_solvent} - 第 {repeat + 1} 次", - "time": 0.0, - "viscous": False, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": False - } + "action_name": "wait", + "action_kwargs": {"time": eluting_wait_time} }) - # 如果有过滤设备，再次过滤洗脱液 - if filter_id: + # 洗脱间隔等待 + if repeat_idx < eluting_repeats - 1: # 不是最后一次洗脱 action_sequence.append({ - "device_id": filter_id, - "action_name": "filter_sample", - "action_kwargs": { - "vessel": to_vessel, - "filtrate_vessel": to_vessel, - "stir": False, - "stir_speed": 0.0, - "temp": 25.0, - "continue_heatchill": False, - "volume": eluting_volume - } + "action_name": "wait", + "action_kwargs": {"time": 10} }) - return action_sequence \ No newline at end of file + # === 第四步：最终等待，确保所有液体完全通过 === + print(f"FILTER_THROUGH: 最终等待，确保所有液体完全通过过滤介质") + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 20} + }) + + print(f"FILTER_THROUGH: 生成了 {len(action_sequence)} 个动作") + print(f"FILTER_THROUGH: 通过过滤协议生成完成") + print(f"FILTER_THROUGH: 样品从 {from_vessel} 通过 {filter_through} 到达 {to_vessel}") + if eluting_repeats > 0: + total_eluting_volume = eluting_volume * eluting_repeats + print(f"FILTER_THROUGH: 总洗脱体积: {total_eluting_volume} mL {eluting_solvent}") + + return action_sequence + + +# 便捷函数：常用过滤方案 +def generate_gravity_column_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + column_material: str = "silica_gel" +) -> List[Dict[str, Any]]: + """重力柱层析：简单重力过滤，无洗脱""" + return generate_filter_through_protocol(G, from_vessel, to_vessel, column_material, "", 0.0, 0, 0.0) + + +def generate_celite_filter_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + wash_solvent: str = "ethanol", + wash_volume: float = 20.0 +) -> List[Dict[str, Any]]: + """硅藻土过滤：用于去除固体杂质""" + return generate_filter_through_protocol(G, from_vessel, to_vessel, "celite", wash_solvent, wash_volume, 1, 30.0) + + +def generate_column_chromatography_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + column_material: str = "silica_gel", + eluting_solvent: str = "ethyl_acetate", + eluting_volume: float = 30.0, + eluting_repeats: int = 3 +) -> List[Dict[str, Any]]: + """柱层析：多次洗脱分离""" + return generate_filter_through_protocol( + G, from_vessel, to_vessel, column_material, eluting_solvent, eluting_volume, eluting_repeats, 60.0 + ) + + +def generate_solid_phase_extraction_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + spe_cartridge: str = "C18", + eluting_solvent: str = "methanol", + eluting_volume: float = 15.0, + eluting_repeats: int = 2 +) -> List[Dict[str, Any]]: + """固相萃取：C18柱或其他SPE柱""" + return generate_filter_through_protocol( + G, from_vessel, to_vessel, spe_cartridge, eluting_solvent, eluting_volume, eluting_repeats, 120.0 + ) + + +def generate_resin_filter_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + resin_type: str = "ion_exchange", + regeneration_solvent: str = "NaCl_solution", + regeneration_volume: float = 25.0 +) -> List[Dict[str, Any]]: + """树脂过滤：离子交换树脂或其他功能树脂""" + return generate_filter_through_protocol( + G, from_vessel, to_vessel, resin_type, regeneration_solvent, regeneration_volume, 1, 180.0 + ) + + +def generate_multi_step_purification_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + filter_steps: List[Dict[str, Any]] +) -> List[Dict[str, Any]]: + """ + 多步骤纯化：连续多个过滤介质 + + Args: + G: 网络图 + from_vessel: 源容器 + to_vessel: 最终目标容器 + filter_steps: 过滤步骤列表，每个元素包含过滤参数 + + Returns: + List[Dict[str, Any]]: 完整的动作序列 + + Example: + filter_steps = [ + { + "to_vessel": "intermediate_vessel_1", + "filter_through": "celite", + "eluting_solvent": "", + "eluting_volume": 0.0, + "eluting_repeats": 0, + "residence_time": 30.0 + }, + { + "from_vessel": "intermediate_vessel_1", + "to_vessel": "final_vessel", + "filter_through": "silica_gel", + "eluting_solvent": "ethyl_acetate", + "eluting_volume": 20.0, + "eluting_repeats": 2, + "residence_time": 60.0 + } + ] + """ + action_sequence = [] + + current_from_vessel = from_vessel + + for i, step in enumerate(filter_steps): + print(f"FILTER_THROUGH: 处理第 {i+1}/{len(filter_steps)} 个过滤步骤") + + # 使用步骤中指定的参数，或使用默认值 + step_from_vessel = step.get('from_vessel', current_from_vessel) + step_to_vessel = step.get('to_vessel', to_vessel if i == len(filter_steps) - 1 else f"intermediate_vessel_{i+1}") + + # 生成单个过滤步骤的协议 + step_actions = generate_filter_through_protocol( + G=G, + from_vessel=step_from_vessel, + to_vessel=step_to_vessel, + filter_through=step.get('filter_through', 'silica_gel'), + eluting_solvent=step.get('eluting_solvent', ''), + eluting_volume=step.get('eluting_volume', 0.0), + eluting_repeats=step.get('eluting_repeats', 0), + residence_time=step.get('residence_time', 0.0) + ) + + action_sequence.extend(step_actions) + + # 更新下一步的源容器 + current_from_vessel = step_to_vessel + + # 在步骤之间加入等待时间 + if i < len(filter_steps) - 1: # 不是最后一个步骤 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 15} + }) + + print(f"FILTER_THROUGH: 多步骤纯化协议生成完成，共 {len(action_sequence)} 个动作") + return action_sequence + + +# 测试函数 +def test_filter_through_protocol(): + """测试通过过滤协议的示例""" + print("=== FILTER THROUGH PROTOCOL 测试 ===") + print("测试完成") + + +if __name__ == "__main__": + test_filter_through_protocol() \ No newline at end of file diff --git a/unilabos/compile/heatchill_protocol.py b/unilabos/compile/heatchill_protocol.py index ac8ca172..5ce09928 100644 --- a/unilabos/compile/heatchill_protocol.py +++ b/unilabos/compile/heatchill_protocol.py @@ -1,33 +1,61 @@ -from typing import List, Dict, Any +from typing import List, Dict, Any, Optional import networkx as nx + +def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str: + """ + 查找与指定容器相连的加热/冷却设备 + """ + # 查找所有加热/冷却设备节点 + heatchill_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_heatchill'] + + # 检查哪个加热/冷却设备与目标容器相连（机械连接） + for heatchill in heatchill_nodes: + if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill): + return heatchill + + # 如果没有直接连接，返回第一个可用的加热/冷却设备 + if heatchill_nodes: + return heatchill_nodes[0] + + raise ValueError("系统中未找到可用的加热/冷却设备") + + def generate_heat_chill_protocol( G: nx.DiGraph, vessel: str, temp: float, time: float, - stir: bool, - stir_speed: float, - purpose: str + stir: bool = False, + stir_speed: float = 300.0, + purpose: str = "加热/冷却操作" ) -> List[Dict[str, Any]]: """ - 生成加热/冷却操作的协议序列 - 严格按照 HeatChill.action + 生成加热/冷却操作的协议序列 - 带时间限制的完整操作 """ action_sequence = [] - # 查找加热/冷却设备 - heatchill_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_heatchill'] - - if not heatchill_nodes: - raise ValueError("没有找到可用的加热/冷却设备") - - heatchill_id = heatchill_nodes[0] + print(f"HEATCHILL: 开始生成加热/冷却协议") + print(f" - 容器: {vessel}") + print(f" - 目标温度: {temp}°C") + print(f" - 持续时间: {time}秒") + print(f" - 使用内置搅拌: {stir}, 速度: {stir_speed} RPM") + print(f" - 目的: {purpose}") + # 1. 验证容器存在 if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") + raise ValueError(f"容器 '{vessel}' 不存在于系统中") + + # 2. 查找加热/冷却设备 + try: + heatchill_id = find_connected_heatchill(G, vessel) + print(f"HEATCHILL: 找到加热/冷却设备: {heatchill_id}") + except ValueError as e: + raise ValueError(f"无法找到加热/冷却设备: {str(e)}") - action_sequence.append({ + # 3. 执行加热/冷却操作 + heatchill_action = { "device_id": heatchill_id, "action_name": "heat_chill", "action_kwargs": { @@ -36,10 +64,13 @@ def generate_heat_chill_protocol( "time": time, "stir": stir, "stir_speed": stir_speed, - "purpose": purpose + "status": "start" } - }) + } + + action_sequence.append(heatchill_action) + print(f"HEATCHILL: 生成了 {len(action_sequence)} 个动作") return action_sequence @@ -47,25 +78,31 @@ def generate_heat_chill_start_protocol( G: nx.DiGraph, vessel: str, temp: float, - purpose: str + purpose: str = "开始加热/冷却" ) -> List[Dict[str, Any]]: """ - 生成开始加热/冷却操作的协议序列 - 严格按照 HeatChillStart.action + 生成开始加热/冷却操作的协议序列 """ action_sequence = [] - heatchill_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_heatchill'] - - if not heatchill_nodes: - raise ValueError("没有找到可用的加热/冷却设备") - - heatchill_id = heatchill_nodes[0] + print(f"HEATCHILL_START: 开始生成加热/冷却启动协议") + print(f" - 容器: {vessel}") + print(f" - 目标温度: {temp}°C") + print(f" - 目的: {purpose}") + # 1. 验证容器存在 if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") + raise ValueError(f"容器 '{vessel}' 不存在于系统中") - action_sequence.append({ + # 2. 查找加热/冷却设备 + try: + heatchill_id = find_connected_heatchill(G, vessel) + print(f"HEATCHILL_START: 找到加热/冷却设备: {heatchill_id}") + except ValueError as e: + raise ValueError(f"无法找到加热/冷却设备: {str(e)}") + + # 3. 执行开始加热/冷却操作 + heatchill_start_action = { "device_id": heatchill_id, "action_name": "heat_chill_start", "action_kwargs": { @@ -73,8 +110,11 @@ def generate_heat_chill_start_protocol( "temp": temp, "purpose": purpose } - }) + } + + action_sequence.append(heatchill_start_action) + print(f"HEATCHILL_START: 生成了 {len(action_sequence)} 个动作") return action_sequence @@ -84,34 +124,250 @@ def generate_heat_chill_stop_protocol( ) -> List[Dict[str, Any]]: """ 生成停止加热/冷却操作的协议序列 - - Args: - G: 有向图，节点为设备和容器 - vessel: 容器名称 - - Returns: - List[Dict[str, Any]]: 停止加热/冷却操作的动作序列 """ action_sequence = [] - # 查找加热/冷却设备 - heatchill_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_heatchill'] - - if not heatchill_nodes: - raise ValueError("没有找到可用的加热/冷却设备") - - heatchill_id = heatchill_nodes[0] + print(f"HEATCHILL_STOP: 开始生成加热/冷却停止协议") + print(f" - 容器: {vessel}") + # 1. 验证容器存在 if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") + raise ValueError(f"容器 '{vessel}' 不存在于系统中") - action_sequence.append({ + # 2. 查找加热/冷却设备 + try: + heatchill_id = find_connected_heatchill(G, vessel) + print(f"HEATCHILL_STOP: 找到加热/冷却设备: {heatchill_id}") + except ValueError as e: + raise ValueError(f"无法找到加热/冷却设备: {str(e)}") + + # 3. 执行停止加热/冷却操作 + heatchill_stop_action = { "device_id": heatchill_id, "action_name": "heat_chill_stop", "action_kwargs": { "vessel": vessel } - }) + } + + action_sequence.append(heatchill_stop_action) + + print(f"HEATCHILL_STOP: 生成了 {len(action_sequence)} 个动作") + return action_sequence + + +def generate_heat_chill_to_temp_protocol( + G: nx.DiGraph, + vessel: str, + temp: float, + active: bool = True, + continue_heatchill: bool = False, + stir: bool = False, + stir_speed: Optional[float] = None, + purpose: Optional[str] = None +) -> List[Dict[str, Any]]: + """ + 生成加热/冷却到指定温度的协议序列 - 智能温控协议 + + **关键修复**: 学习 pump_protocol 的模式，直接使用设备基础动作，不依赖特定的 Action 文件 + """ + action_sequence = [] - return action_sequence \ No newline at end of file + # 设置默认值 + if stir_speed is None: + stir_speed = 300.0 + if purpose is None: + purpose = f"智能温控到 {temp}°C" + + print(f"HEATCHILL_TO_TEMP: 开始生成智能温控协议") + print(f" - 容器: {vessel}") + print(f" - 目标温度: {temp}°C") + print(f" - 主动控温: {active}") + print(f" - 达到温度后继续: {continue_heatchill}") + print(f" - 搅拌: {stir}, 速度: {stir_speed} RPM") + print(f" - 目的: {purpose}") + + # 1. 验证容器存在 + if vessel not in G.nodes(): + raise ValueError(f"容器 '{vessel}' 不存在于系统中") + + # 2. 查找加热/冷却设备 + try: + heatchill_id = find_connected_heatchill(G, vessel) + print(f"HEATCHILL_TO_TEMP: 找到加热/冷却设备: {heatchill_id}") + except ValueError as e: + raise ValueError(f"无法找到加热/冷却设备: {str(e)}") + + # 3. 根据参数选择合适的基础动作组合 (学习 pump_protocol 的模式) + if not active: + print(f"HEATCHILL_TO_TEMP: 非主动模式，仅等待") + action_sequence.append({ + "action_name": "wait", + "action_kwargs": { + "time": 10.0, + "purpose": f"等待容器 {vessel} 自然达到 {temp}°C" + } + }) + else: + if continue_heatchill: + # 持续模式：使用 heat_chill_start 基础动作 + print(f"HEATCHILL_TO_TEMP: 使用持续温控模式") + action_sequence.append({ + "device_id": heatchill_id, + "action_name": "heat_chill_start", # ← 直接使用设备基础动作 + "action_kwargs": { + "vessel": vessel, + "temp": temp, + "purpose": f"{purpose} (持续保温)" + } + }) + else: + # 一次性模式：使用 heat_chill 基础动作 + print(f"HEATCHILL_TO_TEMP: 使用一次性温控模式") + estimated_time = max(60.0, min(900.0, abs(temp - 25.0) * 30.0)) + print(f"HEATCHILL_TO_TEMP: 估算所需时间: {estimated_time}秒") + + action_sequence.append({ + "device_id": heatchill_id, + "action_name": "heat_chill", # ← 直接使用设备基础动作 + "action_kwargs": { + "vessel": vessel, + "temp": temp, + "time": estimated_time, + "stir": stir, + "stir_speed": stir_speed, + "status": "start" + } + }) + + print(f"HEATCHILL_TO_TEMP: 生成了 {len(action_sequence)} 个动作") + return action_sequence + + +# 扩展版本的加热/冷却协议，集成智能温控功能 +def generate_smart_heat_chill_protocol( + G: nx.DiGraph, + vessel: str, + temp: float, + time: float = 0.0, # 0表示自动估算 + active: bool = True, + continue_heatchill: bool = False, + stir: bool = False, + stir_speed: float = 300.0, + purpose: str = "智能加热/冷却" +) -> List[Dict[str, Any]]: + """ + 这个函数集成了 generate_heat_chill_to_temp_protocol 的智能逻辑， + 但使用现有的 Action 类型 + """ + # 如果时间为0，自动估算 + if time == 0.0: + estimated_time = max(60.0, min(900.0, abs(temp - 25.0) * 30.0)) + time = estimated_time + + if continue_heatchill: + # 使用持续模式 + return generate_heat_chill_start_protocol(G, vessel, temp, purpose) + else: + # 使用定时模式 + return generate_heat_chill_protocol(G, vessel, temp, time, stir, stir_speed, purpose) + + +# 便捷函数 +def generate_heating_protocol( + G: nx.DiGraph, + vessel: str, + temp: float, + time: float = 300.0, + stir: bool = True, + stir_speed: float = 300.0 +) -> List[Dict[str, Any]]: + """生成加热协议的便捷函数""" + return generate_heat_chill_protocol( + G=G, vessel=vessel, temp=temp, time=time, + stir=stir, stir_speed=stir_speed, purpose=f"加热到 {temp}°C" + ) + + +def generate_cooling_protocol( + G: nx.DiGraph, + vessel: str, + temp: float, + time: float = 600.0, + stir: bool = True, + stir_speed: float = 200.0 +) -> List[Dict[str, Any]]: + """生成冷却协议的便捷函数""" + return generate_heat_chill_protocol( + G=G, vessel=vessel, temp=temp, time=time, + stir=stir, stir_speed=stir_speed, purpose=f"冷却到 {temp}°C" + ) + + +# # 温度预设快捷函数 +# def generate_room_temp_protocol( +# G: nx.DiGraph, +# vessel: str, +# stir: bool = False +# ) -> List[Dict[str, Any]]: +# """返回室温的快捷函数""" +# return generate_heat_chill_to_temp_protocol( +# G=G, +# vessel=vessel, +# temp=25.0, +# active=True, +# continue_heatchill=False, +# stir=stir, +# purpose="冷却到室温" +# ) + + +# def generate_reflux_heating_protocol( +# G: nx.DiGraph, +# vessel: str, +# temp: float, +# time: float = 3600.0 # 1小时回流 +# ) -> List[Dict[str, Any]]: +# """回流加热的快捷函数""" +# return generate_heat_chill_protocol( +# G=G, +# vessel=vessel, +# temp=temp, +# time=time, +# stir=True, +# stir_speed=400.0, # 回流时较快搅拌 +# purpose=f"回流加热到 {temp}°C" +# ) + + +# def generate_ice_bath_protocol( +# G: nx.DiGraph, +# vessel: str, +# time: float = 600.0 # 10分钟冰浴 +# ) -> List[Dict[str, Any]]: +# """冰浴冷却的快捷函数""" +# return generate_heat_chill_protocol( +# G=G, +# vessel=vessel, +# temp=0.0, +# time=time, +# stir=True, +# stir_speed=150.0, # 冰浴时缓慢搅拌 +# purpose="冰浴冷却到 0°C" +# ) + + +# 测试函数 +def test_heatchill_protocol(): + """测试加热/冷却协议的示例""" + print("=== HEAT CHILL PROTOCOL 测试 ===") + print("完整的四个协议函数：") + print("1. generate_heat_chill_protocol - 带时间限制的完整操作") + print("2. generate_heat_chill_start_protocol - 持续加热/冷却") + print("3. generate_heat_chill_stop_protocol - 停止加热/冷却") + print("4. generate_heat_chill_to_temp_protocol - 智能温控 (您的 HeatChillToTemp)") + print("测试完成") + + +if __name__ == "__main__": + test_heatchill_protocol() \ No newline at end of file diff --git a/unilabos/compile/pump_protocol.py b/unilabos/compile/pump_protocol.py index 8dab4d47..cddb8632 100644 --- a/unilabos/compile/pump_protocol.py +++ b/unilabos/compile/pump_protocol.py @@ -8,7 +8,8 @@ def is_integrated_pump(node_name): def find_connected_pump(G, valve_node): for neighbor in G.neighbors(valve_node): - if "pump" in G.nodes[neighbor]["class"]: + node_class = G.nodes[neighbor].get("class") or "" # 防止 None + if "pump" in node_class: return neighbor raise ValueError(f"未找到与阀 {valve_node} 唯一相连的泵节点") diff --git a/unilabos/compile/run_column_protocol.py b/unilabos/compile/run_column_protocol.py index 5aebc2b6..f6b9214f 100644 --- a/unilabos/compile/run_column_protocol.py +++ b/unilabos/compile/run_column_protocol.py @@ -1,5 +1,87 @@ from typing import List, Dict, Any import networkx as nx +from .pump_protocol import generate_pump_protocol + + +def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float: + """获取容器中的液体体积""" + if vessel not in G.nodes(): + return 0.0 + + vessel_data = G.nodes[vessel].get('data', {}) + liquids = vessel_data.get('liquid', []) + + total_volume = 0.0 + for liquid in liquids: + if isinstance(liquid, dict): + # 支持两种格式：新格式 (name, volume) 和旧格式 (liquid_type, liquid_volume) + volume = liquid.get('volume') or liquid.get('liquid_volume', 0.0) + total_volume += volume + + return total_volume + + +def find_column_device(G: nx.DiGraph, column: str) -> str: + """查找柱层析设备""" + # 首先检查是否有虚拟柱设备 + column_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_column'] + + if column_nodes: + return column_nodes[0] + + # 如果没有虚拟柱设备，抛出异常 + raise ValueError(f"系统中未找到柱层析设备。请确保配置了 virtual_column 设备") + + +def find_column_vessel(G: nx.DiGraph, column: str) -> str: + """查找柱容器""" + # 直接使用 column 参数作为容器名称 + if column in G.nodes(): + return column + + # 尝试常见的柱容器命名规则 + possible_names = [ + f"column_{column}", + f"{column}_column", + f"vessel_{column}", + f"{column}_vessel", + "column_vessel", + "chromatography_column", + "silica_column", + "preparative_column" + ] + + for vessel_name in possible_names: + if vessel_name in G.nodes(): + return vessel_name + + raise ValueError(f"未找到柱容器 '{column}'。尝试了以下名称: {[column] + possible_names}") + + +def find_eluting_solvent_vessel(G: nx.DiGraph, eluting_solvent: str) -> str: + """查找洗脱溶剂容器""" + if not eluting_solvent: + return "" + + # 按照命名规则查找溶剂瓶 + solvent_vessel_id = f"flask_{eluting_solvent}" + + if solvent_vessel_id in G.nodes(): + return solvent_vessel_id + + # 如果直接匹配失败，尝试模糊匹配 + for node in G.nodes(): + if node.startswith('flask_') and eluting_solvent.lower() in node.lower(): + return node + + # 如果还是找不到，列出所有可用的溶剂瓶 + available_flasks = [node for node in G.nodes() + if node.startswith('flask_') + and G.nodes[node].get('type') == 'container'] + + raise ValueError(f"找不到洗脱溶剂 '{eluting_solvent}' 对应的溶剂瓶。可用溶剂瓶: {available_flasks}") + def generate_run_column_protocol( G: nx.DiGraph, @@ -11,92 +93,220 @@ def generate_run_column_protocol( 生成柱层析分离的协议序列 Args: - G: 有向图，节点为设备和容器 + G: 有向图，节点为设备和容器，边为流体管道 from_vessel: 源容器的名称，即样品起始所在的容器 to_vessel: 目标容器的名称，分离后的样品要到达的容器 column: 所使用的柱子的名称 Returns: List[Dict[str, Any]]: 柱层析分离操作的动作序列 - - Raises: - ValueError: 当找不到必要的设备时抛出异常 - - Examples: - run_column_protocol = generate_run_column_protocol(G, "reactor", "collection_flask", "silica_column") """ action_sequence = [] - # 验证容器是否存在 + print(f"RUN_COLUMN: 开始生成柱层析协议") + print(f" - 源容器: {from_vessel}") + print(f" - 目标容器: {to_vessel}") + print(f" - 柱子: {column}") + + # 验证源容器和目标容器存在 if from_vessel not in G.nodes(): - raise ValueError(f"源容器 {from_vessel} 不存在于图中") + raise ValueError(f"源容器 '{from_vessel}' 不存在于系统中") if to_vessel not in G.nodes(): - raise ValueError(f"目标容器 {to_vessel} 不存在于图中") + raise ValueError(f"目标容器 '{to_vessel}' 不存在于系统中") + + # 查找柱层析设备 + column_device_id = None + column_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_column'] - # 查找转移泵设备（用于样品转移） - pump_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_transfer_pump'] + if column_nodes: + column_device_id = column_nodes[0] + print(f"RUN_COLUMN: 找到柱层析设备: {column_device_id}") + else: + print(f"RUN_COLUMN: 警告 - 未找到柱层析设备") - if not pump_nodes: - raise ValueError("没有找到可用的转移泵设备") + # 获取源容器中的液体体积 + source_volume = get_vessel_liquid_volume(G, from_vessel) + print(f"RUN_COLUMN: 源容器 {from_vessel} 中有 {source_volume} mL 液体") - pump_id = pump_nodes[0] + # === 第一步：样品转移到柱子（如果柱子是容器） === + if column in G.nodes() and G.nodes[column].get('type') == 'container': + print(f"RUN_COLUMN: 样品转移 - {source_volume} mL 从 {from_vessel} 到 {column}") + + try: + sample_transfer_actions = generate_pump_protocol( + G=G, + from_vessel=from_vessel, + to_vessel=column, + volume=source_volume if source_volume > 0 else 100.0, + flowrate=2.0 + ) + action_sequence.extend(sample_transfer_actions) + except Exception as e: + print(f"RUN_COLUMN: 样品转移失败: {str(e)}") - # 查找柱层析设备 - column_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_column'] - - if not column_nodes: - raise ValueError("没有找到可用的柱层析设备") - - column_id = column_nodes[0] - - # 步骤1：将样品从源容器转移到柱子上 - action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", - "action_kwargs": { - "from_vessel": from_vessel, - "to_vessel": column_id, # 将样品转移到柱子设备 - "volume": 0.0, # 转移所有液体，体积由系统确定 - "amount": f"样品上柱 - 使用 {column}", - "time": 0.0, - "viscous": False, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": False - } - }) - - # 步骤2：运行柱层析分离 - action_sequence.append({ - "device_id": column_id, - "action_name": "run_column", - "action_kwargs": { - "from_vessel": from_vessel, - "to_vessel": to_vessel, - "column": column - } - }) - - # 步骤3：将分离后的产物从柱子转移到目标容器 - action_sequence.append({ - "device_id": pump_id, - "action_name": "transfer", - "action_kwargs": { - "from_vessel": column_id, # 从柱子设备转移 - "to_vessel": to_vessel, - "volume": 0.0, # 转移所有液体，体积由系统确定 - "amount": f"收集分离产物 - 来自 {column}", - "time": 0.0, - "viscous": False, - "rinsing_solvent": "", - "rinsing_volume": 0.0, - "rinsing_repeats": 0, - "solid": False + # === 第二步：使用柱层析设备执行分离 === + if column_device_id: + print(f"RUN_COLUMN: 使用柱层析设备执行分离") + + column_separation_action = { + "device_id": column_device_id, + "action_name": "run_column", + "action_kwargs": { + "from_vessel": from_vessel, + "to_vessel": to_vessel, + "column": column + } } - }) + action_sequence.append(column_separation_action) + + # 等待柱层析设备完成分离 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 60} + }) - return action_sequence \ No newline at end of file + # === 第三步：从柱子转移到目标容器（如果需要） === + if column in G.nodes() and column != to_vessel: + print(f"RUN_COLUMN: 产物转移 - 从 {column} 到 {to_vessel}") + + try: + product_transfer_actions = generate_pump_protocol( + G=G, + from_vessel=column, + to_vessel=to_vessel, + volume=source_volume * 0.8 if source_volume > 0 else 80.0, # 假设有一些损失 + flowrate=1.5 + ) + action_sequence.extend(product_transfer_actions) + except Exception as e: + print(f"RUN_COLUMN: 产物转移失败: {str(e)}") + + print(f"RUN_COLUMN: 生成了 {len(action_sequence)} 个动作") + return action_sequence + + +# 便捷函数：常用柱层析方案 +def generate_flash_column_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + column_material: str = "silica_gel", + mobile_phase: str = "ethyl_acetate", + mobile_phase_volume: float = 100.0 +) -> List[Dict[str, Any]]: + """快速柱层析：高流速分离""" + return generate_run_column_protocol( + G, from_vessel, to_vessel, column_material, + mobile_phase, mobile_phase_volume, 1, "", 0.0, 3.0 + ) + + +def generate_preparative_column_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + column_material: str = "silica_gel", + equilibration_solvent: str = "hexane", + eluting_solvent: str = "ethyl_acetate", + eluting_volume: float = 50.0, + eluting_repeats: int = 3 +) -> List[Dict[str, Any]]: + """制备柱层析：带平衡和多次洗脱""" + return generate_run_column_protocol( + G, from_vessel, to_vessel, column_material, + eluting_solvent, eluting_volume, eluting_repeats, + equilibration_solvent, 30.0, 1.5 + ) + + +def generate_gradient_column_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + column_material: str = "silica_gel", + gradient_solvents: List[str] = None, + gradient_volumes: List[float] = None +) -> List[Dict[str, Any]]: + """梯度洗脱柱层析：多种溶剂系统""" + if gradient_solvents is None: + gradient_solvents = ["hexane", "ethyl_acetate", "methanol"] + if gradient_volumes is None: + gradient_volumes = [50.0, 50.0, 30.0] + + action_sequence = [] + + # 每种溶剂单独执行一次柱层析 + for i, (solvent, volume) in enumerate(zip(gradient_solvents, gradient_volumes)): + print(f"RUN_COLUMN: 梯度洗脱第 {i+1}/{len(gradient_solvents)} 步: {volume} mL {solvent}") + + # 第一步使用源容器，后续步骤使用柱子作为源 + step_from_vessel = from_vessel if i == 0 else column_material + # 最后一步使用目标容器，其他步骤使用柱子作为目标 + step_to_vessel = to_vessel if i == len(gradient_solvents) - 1 else column_material + + step_actions = generate_run_column_protocol( + G, step_from_vessel, step_to_vessel, column_material, + solvent, volume, 1, "", 0.0, 1.0 + ) + action_sequence.extend(step_actions) + + # 在梯度步骤之间加入等待时间 + if i < len(gradient_solvents) - 1: + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 20} + }) + + return action_sequence + + +def generate_reverse_phase_column_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + column_material: str = "C18", + aqueous_phase: str = "water", + organic_phase: str = "methanol", + gradient_ratio: float = 0.5 +) -> List[Dict[str, Any]]: + """反相柱层析：C18柱，水-有机相梯度""" + # 先用水相平衡 + equilibration_volume = 20.0 + # 然后用有机相洗脱 + eluting_volume = 30.0 * gradient_ratio + + return generate_run_column_protocol( + G, from_vessel, to_vessel, column_material, + organic_phase, eluting_volume, 2, + aqueous_phase, equilibration_volume, 0.8 + ) + + +def generate_ion_exchange_column_protocol( + G: nx.DiGraph, + from_vessel: str, + to_vessel: str, + column_material: str = "ion_exchange", + buffer_solution: str = "buffer", + salt_solution: str = "NaCl_solution", + salt_volume: float = 40.0 +) -> List[Dict[str, Any]]: + """离子交换柱层析：缓冲液平衡，盐溶液洗脱""" + return generate_run_column_protocol( + G, from_vessel, to_vessel, column_material, + salt_solution, salt_volume, 1, + buffer_solution, 25.0, 0.5 + ) + + +# 测试函数 +def test_run_column_protocol(): + """测试柱层析协议的示例""" + print("=== RUN COLUMN PROTOCOL 测试 ===") + print("测试完成") + + +if __name__ == "__main__": + test_run_column_protocol() \ No newline at end of file diff --git a/unilabos/compile/stir_protocol.py b/unilabos/compile/stir_protocol.py index 90a207cd..6fc865cd 100644 --- a/unilabos/compile/stir_protocol.py +++ b/unilabos/compile/stir_protocol.py @@ -1,6 +1,28 @@ from typing import List, Dict, Any import networkx as nx + +def find_connected_stirrer(G: nx.DiGraph, vessel: str = None) -> str: + """ + 查找与指定容器相连的搅拌设备，或查找可用的搅拌设备 + """ + # 查找所有搅拌设备节点 + stirrer_nodes = [node for node in G.nodes() + if (G.nodes[node].get('class') or '') == 'virtual_stirrer'] + + if vessel: + # 检查哪个搅拌设备与目标容器相连（机械连接） + for stirrer in stirrer_nodes: + if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer): + return stirrer + + # 如果没有指定容器或没有直接连接，返回第一个可用的搅拌设备 + if stirrer_nodes: + return stirrer_nodes[0] + + raise ValueError("系统中未找到可用的搅拌设备") + + def generate_stir_protocol( G: nx.DiGraph, stir_time: float, @@ -8,37 +30,24 @@ def generate_stir_protocol( settling_time: float ) -> List[Dict[str, Any]]: """ - 生成搅拌操作的协议序列 - - Args: - G: 有向图，节点为设备和容器 - stir_time: 搅拌时间 (秒) - stir_speed: 搅拌速度 (rpm) - settling_time: 沉降时间 (秒) - - Returns: - List[Dict[str, Any]]: 搅拌操作的动作序列 - - Raises: - ValueError: 当找不到搅拌设备时抛出异常 - - Examples: - stir_protocol = generate_stir_protocol(G, 300.0, 500.0, 60.0) + 生成搅拌操作的协议序列 - 定时搅拌 + 沉降 """ action_sequence = [] - # 查找搅拌设备 - stirrer_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_stirrer'] - - if not stirrer_nodes: - raise ValueError("没有找到可用的搅拌设备") + print(f"STIR: 开始生成搅拌协议") + print(f" - 搅拌时间: {stir_time}秒") + print(f" - 搅拌速度: {stir_speed} RPM") + print(f" - 沉降时间: {settling_time}秒") - # 使用第一个可用的搅拌器 - stirrer_id = stirrer_nodes[0] + # 查找搅拌设备 + try: + stirrer_id = find_connected_stirrer(G) + print(f"STIR: 找到搅拌设备: {stirrer_id}") + except ValueError as e: + raise ValueError(f"无法找到搅拌设备: {str(e)}") # 执行搅拌操作 - action_sequence.append({ + stir_action = { "device_id": stirrer_id, "action_name": "stir", "action_kwargs": { @@ -46,8 +55,11 @@ def generate_stir_protocol( "stir_speed": stir_speed, "settling_time": settling_time } - }) + } + action_sequence.append(stir_action) + + print(f"STIR: 生成了 {len(action_sequence)} 个动作") return action_sequence @@ -58,33 +70,28 @@ def generate_start_stir_protocol( purpose: str ) -> List[Dict[str, Any]]: """ - 生成开始搅拌操作的协议序列 - - Args: - G: 有向图，节点为设备和容器 - vessel: 搅拌容器 - stir_speed: 搅拌速度 (rpm) - purpose: 搅拌目的 - - Returns: - List[Dict[str, Any]]: 开始搅拌操作的动作序列 + 生成开始搅拌操作的协议序列 - 持续搅拌 """ action_sequence = [] - # 查找搅拌设备 - stirrer_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_stirrer'] + print(f"START_STIR: 开始生成启动搅拌协议") + print(f" - 容器: {vessel}") + print(f" - 搅拌速度: {stir_speed} RPM") + print(f" - 目的: {purpose}") - if not stirrer_nodes: - raise ValueError("没有找到可用的搅拌设备") - - stirrer_id = stirrer_nodes[0] - - # 验证容器是否存在 + # 验证容器存在 if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") + raise ValueError(f"容器 '{vessel}' 不存在于系统中") - action_sequence.append({ + # 查找搅拌设备 + try: + stirrer_id = find_connected_stirrer(G, vessel) + print(f"START_STIR: 找到搅拌设备: {stirrer_id}") + except ValueError as e: + raise ValueError(f"无法找到搅拌设备: {str(e)}") + + # 执行开始搅拌操作 + start_stir_action = { "device_id": stirrer_id, "action_name": "start_stir", "action_kwargs": { @@ -92,8 +99,11 @@ def generate_start_stir_protocol( "stir_speed": stir_speed, "purpose": purpose } - }) + } + action_sequence.append(start_stir_action) + + print(f"START_STIR: 生成了 {len(action_sequence)} 个动作") return action_sequence @@ -103,35 +113,54 @@ def generate_stop_stir_protocol( ) -> List[Dict[str, Any]]: """ 生成停止搅拌操作的协议序列 - - Args: - G: 有向图，节点为设备和容器 - vessel: 搅拌容器 - - Returns: - List[Dict[str, Any]]: 停止搅拌操作的动作序列 """ action_sequence = [] - # 查找搅拌设备 - stirrer_nodes = [node for node in G.nodes() - if G.nodes[node].get('class') == 'virtual_stirrer'] - - if not stirrer_nodes: - raise ValueError("没有找到可用的搅拌设备") + print(f"STOP_STIR: 开始生成停止搅拌协议") + print(f" - 容器: {vessel}") - stirrer_id = stirrer_nodes[0] - - # 验证容器是否存在 + # 验证容器存在 if vessel not in G.nodes(): - raise ValueError(f"容器 {vessel} 不存在于图中") + raise ValueError(f"容器 '{vessel}' 不存在于系统中") - action_sequence.append({ + # 查找搅拌设备 + try: + stirrer_id = find_connected_stirrer(G, vessel) + print(f"STOP_STIR: 找到搅拌设备: {stirrer_id}") + except ValueError as e: + raise ValueError(f"无法找到搅拌设备: {str(e)}") + + # 执行停止搅拌操作 + stop_stir_action = { "device_id": stirrer_id, "action_name": "stop_stir", "action_kwargs": { "vessel": vessel } - }) + } - return action_sequence \ No newline at end of file + action_sequence.append(stop_stir_action) + + print(f"STOP_STIR: 生成了 {len(action_sequence)} 个动作") + return action_sequence + + +# 便捷函数 +def generate_fast_stir_protocol( + G: nx.DiGraph, + time: float = 300.0, + speed: float = 800.0, + settling: float = 60.0 +) -> List[Dict[str, Any]]: + """快速搅拌的便捷函数""" + return generate_stir_protocol(G, time, speed, settling) + + +def generate_gentle_stir_protocol( + G: nx.DiGraph, + time: float = 600.0, + speed: float = 200.0, + settling: float = 120.0 +) -> List[Dict[str, Any]]: + """温和搅拌的便捷函数""" + return generate_stir_protocol(G, time, speed, settling) \ No newline at end of file diff --git a/unilabos/config/config.py b/unilabos/config/config.py index 0cf999e6..32ebf682 100644 --- a/unilabos/config/config.py +++ b/unilabos/config/config.py @@ -10,8 +10,9 @@ class BasicConfig: ENV = "pro" # 'test' config_path = "" - is_host_mode = True # 从registry.py移动过来 + is_host_mode = True slave_no_host = False # 是否跳过rclient.wait_for_service() + upload_registry = False machine_name = "undefined" vis_2d_enable = False diff --git a/unilabos/devices/virtual/virtual_centrifuge.py b/unilabos/devices/virtual/virtual_centrifuge.py index 20366ab1..79f9dce0 100644 --- a/unilabos/devices/virtual/virtual_centrifuge.py +++ b/unilabos/devices/virtual/virtual_centrifuge.py @@ -1,158 +1,213 @@ import asyncio import logging -from typing import Dict, Any +import time as time_module +from typing import Dict, Any, Optional + class VirtualCentrifuge: - """Virtual centrifuge device for CentrifugeProtocol testing""" - - def __init__(self, device_id: str = None, config: Dict[str, Any] = None, **kwargs): + """Virtual centrifuge device - 简化版，只保留核心功能""" + + def __init__(self, device_id: Optional[str] = None, config: Optional[Dict[str, Any]] = None, **kwargs): # 处理可能的不同调用方式 - if device_id is None and 'id' in kwargs: - device_id = kwargs.pop('id') - if config is None and 'config' in kwargs: - config = kwargs.pop('config') - + if device_id is None and "id" in kwargs: + device_id = kwargs.pop("id") + if config is None and "config" in kwargs: + config = kwargs.pop("config") + # 设置默认值 self.device_id = device_id or "unknown_centrifuge" self.config = config or {} - + self.logger = logging.getLogger(f"VirtualCentrifuge.{self.device_id}") self.data = {} - - # 添加调试信息 - print(f"=== VirtualCentrifuge {self.device_id} is being created! ===") - print(f"=== Config: {self.config} ===") - print(f"=== Kwargs: {kwargs} ===") - + # 从config或kwargs中获取配置参数 - self.port = self.config.get('port') or kwargs.get('port', 'VIRTUAL') - self._max_speed = self.config.get('max_speed') or kwargs.get('max_speed', 15000.0) - self._max_temp = self.config.get('max_temp') or kwargs.get('max_temp', 40.0) - self._min_temp = self.config.get('min_temp') or kwargs.get('min_temp', 4.0) - - # 处理其他kwargs参数，但跳过已知的配置参数 - skip_keys = {'port', 'max_speed', 'max_temp', 'min_temp'} + self.port = self.config.get("port") or kwargs.get("port", "VIRTUAL") + self._max_speed = self.config.get("max_speed") or kwargs.get("max_speed", 15000.0) + self._max_temp = self.config.get("max_temp") or kwargs.get("max_temp", 40.0) + self._min_temp = self.config.get("min_temp") or kwargs.get("min_temp", 4.0) + + # 处理其他kwargs参数 + skip_keys = {"port", "max_speed", "max_temp", "min_temp"} for key, value in kwargs.items(): if key not in skip_keys and not hasattr(self, key): setattr(self, key, value) - + async def initialize(self) -> bool: """Initialize virtual centrifuge""" - print(f"=== VirtualCentrifuge {self.device_id} initialize() called! ===") self.logger.info(f"Initializing virtual centrifuge {self.device_id}") + + # 只保留核心状态 self.data.update({ "status": "Idle", + "centrifuge_state": "Stopped", # Stopped, Running, Completed, Error "current_speed": 0.0, "target_speed": 0.0, "current_temp": 25.0, "target_temp": 25.0, - "max_speed": self._max_speed, - "max_temp": self._max_temp, - "min_temp": self._min_temp, - "centrifuge_state": "Stopped", "time_remaining": 0.0, "progress": 0.0, - "message": "" + "message": "Ready for centrifugation" }) return True - + async def cleanup(self) -> bool: """Cleanup virtual centrifuge""" self.logger.info(f"Cleaning up virtual centrifuge {self.device_id}") - return True - - async def centrifuge(self, vessel: str, speed: float, time: float, temp: float = 25.0) -> bool: - """Execute centrifuge action - matches Centrifuge action""" - self.logger.info(f"Centrifuge: vessel={vessel}, speed={speed} RPM, time={time}s, temp={temp}°C") + self.data.update({ + "status": "Offline", + "centrifuge_state": "Offline", + "current_speed": 0.0, + "current_temp": 25.0, + "message": "System offline" + }) + return True + + async def centrifuge( + self, + vessel: str, + speed: float, + time: float, + temp: float = 25.0 + ) -> bool: + """Execute centrifuge action - 简化的离心流程""" + self.logger.info(f"Centrifuge: vessel={vessel}, speed={speed} rpm, time={time}s, temp={temp}°C") + # 验证参数 - if speed > self._max_speed: - self.logger.error(f"Speed {speed} exceeds maximum {self._max_speed}") - self.data["message"] = f"速度 {speed} 超过最大值 {self._max_speed}" + if speed > self._max_speed or speed < 100.0: + error_msg = f"离心速度 {speed} rpm 超出范围 (100-{self._max_speed} rpm)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "centrifuge_state": "Error", + "message": error_msg + }) return False - + if temp > self._max_temp or temp < self._min_temp: - self.logger.error(f"Temperature {temp} outside range {self._min_temp}-{self._max_temp}") - self.data["message"] = f"温度 {temp} 超出范围 {self._min_temp}-{self._max_temp}" + error_msg = f"温度 {temp}°C 超出范围 ({self._min_temp}-{self._max_temp}°C)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "centrifuge_state": "Error", + "message": error_msg + }) return False - + # 开始离心 self.data.update({ - "status": "Running", - "centrifuge_state": "Centrifuging", - "target_speed": speed, + "status": f"离心中: {vessel}", + "centrifuge_state": "Running", "current_speed": speed, - "target_temp": temp, + "target_speed": speed, "current_temp": temp, + "target_temp": temp, "time_remaining": time, - "vessel": vessel, "progress": 0.0, - "message": f"离心中: {vessel} at {speed} RPM" - }) - - # 模拟离心过程 - simulation_time = min(time, 5.0) # 最多等待5秒用于测试 - await asyncio.sleep(simulation_time) - - # 离心完成 - self.data.update({ - "status": "Idle", - "centrifuge_state": "Stopped", - "current_speed": 0.0, - "target_speed": 0.0, - "time_remaining": 0.0, - "progress": 100.0, - "message": f"离心完成: {vessel}" + "message": f"Centrifuging {vessel} at {speed} rpm, {temp}°C" }) - - self.logger.info(f"Centrifuge completed for vessel {vessel}") - return True - - # 状态属性 + + try: + # 离心过程 - 实时更新进度 + start_time = time_module.time() + total_time = time + + while True: + current_time = time_module.time() + elapsed = current_time - start_time + remaining = max(0, total_time - elapsed) + progress = min(100.0, (elapsed / total_time) * 100) + + # 更新状态 + self.data.update({ + "time_remaining": remaining, + "progress": progress, + "status": f"离心中: {vessel} | {speed} rpm | {temp}°C | {progress:.1f}% | 剩余: {remaining:.0f}s", + "message": f"Centrifuging: {progress:.1f}% complete, {remaining:.0f}s remaining" + }) + + # 时间到了，退出循环 + if remaining <= 0: + break + + # 每秒更新一次 + await asyncio.sleep(1.0) + + # 离心完成 + self.data.update({ + "status": f"离心完成: {vessel} | {speed} rpm | {time}s", + "centrifuge_state": "Completed", + "progress": 100.0, + "time_remaining": 0.0, + "current_speed": 0.0, # 停止旋转 + "current_temp": 25.0, # 恢复室温 + "message": f"Centrifugation completed: {vessel} at {speed} rpm for {time}s" + }) + + self.logger.info(f"Centrifugation completed: {vessel} at {speed} rpm for {time}s") + return True + + except Exception as e: + # 出错处理 + self.logger.error(f"Error during centrifugation: {str(e)}") + + self.data.update({ + "status": f"离心错误: {str(e)}", + "centrifuge_state": "Error", + "current_speed": 0.0, + "current_temp": 25.0, + "progress": 0.0, + "time_remaining": 0.0, + "message": f"Centrifugation failed: {str(e)}" + }) + return False + + # === 核心状态属性 === @property def status(self) -> str: return self.data.get("status", "Unknown") - + + @property + def centrifuge_state(self) -> str: + return self.data.get("centrifuge_state", "Unknown") + @property def current_speed(self) -> float: return self.data.get("current_speed", 0.0) - + @property def target_speed(self) -> float: return self.data.get("target_speed", 0.0) - + @property def current_temp(self) -> float: return self.data.get("current_temp", 25.0) - + @property def target_temp(self) -> float: return self.data.get("target_temp", 25.0) - + @property def max_speed(self) -> float: - return self.data.get("max_speed", self._max_speed) - + return self._max_speed + @property def max_temp(self) -> float: - return self.data.get("max_temp", self._max_temp) - + return self._max_temp + @property def min_temp(self) -> float: - return self.data.get("min_temp", self._min_temp) - - @property - def centrifuge_state(self) -> str: - return self.data.get("centrifuge_state", "Unknown") - + return self._min_temp + @property def time_remaining(self) -> float: return self.data.get("time_remaining", 0.0) - + @property def progress(self) -> float: return self.data.get("progress", 0.0) - + @property def message(self) -> str: return self.data.get("message", "") \ No newline at end of file diff --git a/unilabos/devices/virtual/virtual_filter.py b/unilabos/devices/virtual/virtual_filter.py index 71a984aa..ca2e8b2c 100644 --- a/unilabos/devices/virtual/virtual_filter.py +++ b/unilabos/devices/virtual/virtual_filter.py @@ -1,151 +1,221 @@ import asyncio import logging -from typing import Dict, Any +import time as time_module +from typing import Dict, Any, Optional + class VirtualFilter: - """Virtual filter device for FilterProtocol testing""" + """Virtual filter device - 完全按照 Filter.action 规范""" - def __init__(self, device_id: str = None, config: Dict[str, Any] = None, **kwargs): - # 处理可能的不同调用方式 + def __init__(self, device_id: Optional[str] = None, config: Optional[Dict[str, Any]] = None, **kwargs): if device_id is None and 'id' in kwargs: device_id = kwargs.pop('id') if config is None and 'config' in kwargs: config = kwargs.pop('config') - # 设置默认值 self.device_id = device_id or "unknown_filter" self.config = config or {} - self.logger = logging.getLogger(f"VirtualFilter.{self.device_id}") self.data = {} - # 添加调试信息 - print(f"=== VirtualFilter {self.device_id} is being created! ===") - print(f"=== Config: {self.config} ===") - print(f"=== Kwargs: {kwargs} ===") - # 从config或kwargs中获取配置参数 self.port = self.config.get('port') or kwargs.get('port', 'VIRTUAL') self._max_temp = self.config.get('max_temp') or kwargs.get('max_temp', 100.0) self._max_stir_speed = self.config.get('max_stir_speed') or kwargs.get('max_stir_speed', 1000.0) + self._max_volume = self.config.get('max_volume') or kwargs.get('max_volume', 500.0) - # 处理其他kwargs参数，但跳过已知的配置参数 - skip_keys = {'port', 'max_temp', 'max_stir_speed'} + # 处理其他kwargs参数 + skip_keys = {'port', 'max_temp', 'max_stir_speed', 'max_volume'} for key, value in kwargs.items(): if key not in skip_keys and not hasattr(self, key): setattr(self, key, value) async def initialize(self) -> bool: """Initialize virtual filter""" - print(f"=== VirtualFilter {self.device_id} initialize() called! ===") self.logger.info(f"Initializing virtual filter {self.device_id}") + + # 按照 Filter.action 的 feedback 字段初始化 self.data.update({ "status": "Idle", - "filter_state": "Ready", - "current_temp": 25.0, - "target_temp": 25.0, - "max_temp": self._max_temp, - "stir_speed": 0.0, - "max_stir_speed": self._max_stir_speed, - "filtered_volume": 0.0, - "progress": 0.0, - "message": "" + "progress": 0.0, # Filter.action feedback + "current_temp": 25.0, # Filter.action feedback + "filtered_volume": 0.0, # Filter.action feedback + "current_status": "Ready for filtration", # Filter.action feedback + "message": "Ready for filtration" }) return True async def cleanup(self) -> bool: """Cleanup virtual filter""" self.logger.info(f"Cleaning up virtual filter {self.device_id}") + + self.data.update({ + "status": "Offline", + "current_status": "System offline", + "message": "System offline" + }) return True - async def filter_sample(self, vessel: str, filtrate_vessel: str = "", stir: bool = False, - stir_speed: float = 300.0, temp: float = 25.0, - continue_heatchill: bool = False, volume: float = 0.0) -> bool: - """Execute filter action - matches Filter action""" - self.logger.info(f"Filter: vessel={vessel}, filtrate_vessel={filtrate_vessel}, stir={stir}, volume={volume}") + async def filter( + self, + vessel: str, + filtrate_vessel: str = "", + stir: bool = False, + stir_speed: float = 300.0, + temp: float = 25.0, + continue_heatchill: bool = False, + volume: float = 0.0 + ) -> bool: + """Execute filter action - 完全按照 Filter.action 参数""" + self.logger.info(f"Filter: vessel={vessel}, filtrate_vessel={filtrate_vessel}") + self.logger.info(f" stir={stir}, stir_speed={stir_speed}, temp={temp}") + self.logger.info(f" continue_heatchill={continue_heatchill}, volume={volume}") # 验证参数 - if temp > self._max_temp: - self.logger.error(f"Temperature {temp} exceeds maximum {self._max_temp}") - self.data["message"] = f"温度 {temp} 超过最大值 {self._max_temp}" + if temp > self._max_temp or temp < 4.0: + error_msg = f"温度 {temp}°C 超出范围 (4-{self._max_temp}°C)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "current_status": f"Error: {error_msg}", + "message": error_msg + }) return False if stir and stir_speed > self._max_stir_speed: - self.logger.error(f"Stir speed {stir_speed} exceeds maximum {self._max_stir_speed}") - self.data["message"] = f"搅拌速度 {stir_speed} 超过最大值 {self._max_stir_speed}" + error_msg = f"搅拌速度 {stir_speed} RPM 超出范围 (0-{self._max_stir_speed} RPM)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "current_status": f"Error: {error_msg}", + "message": error_msg + }) + return False + + if volume > self._max_volume: + error_msg = f"过滤体积 {volume} mL 超出范围 (0-{self._max_volume} mL)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "current_status": f"Error: {error_msg}", + "message": error_msg + }) return False # 开始过滤 + filter_volume = volume if volume > 0 else 50.0 + self.data.update({ - "status": "Running", - "filter_state": "Filtering", - "target_temp": temp, + "status": f"过滤中: {vessel}", "current_temp": temp, - "stir_speed": stir_speed if stir else 0.0, - "vessel": vessel, - "filtrate_vessel": filtrate_vessel, - "target_volume": volume, + "filtered_volume": 0.0, "progress": 0.0, - "message": f"过滤中: {vessel}" - }) - - # 模拟过滤过程 - simulation_time = min(volume / 10.0 if volume > 0 else 5.0, 10.0) - await asyncio.sleep(simulation_time) - - # 过滤完成 - filtered_vol = volume if volume > 0 else 50.0 # 默认过滤量 - self.data.update({ - "status": "Idle", - "filter_state": "Ready", - "current_temp": 25.0 if not continue_heatchill else temp, - "target_temp": 25.0 if not continue_heatchill else temp, - "stir_speed": 0.0 if not stir else stir_speed, - "filtered_volume": filtered_vol, - "progress": 100.0, - "message": f"过滤完成: {filtered_vol}mL" + "current_status": f"Filtering {vessel} → {filtrate_vessel}", + "message": f"Starting filtration: {vessel} → {filtrate_vessel}" }) - self.logger.info(f"Filter completed: {filtered_vol}mL from {vessel}") - return True + try: + # 过滤过程 - 实时更新进度 + start_time = time_module.time() + # 根据体积和搅拌估算过滤时间 + base_time = filter_volume / 5.0 # 5mL/s 基础速度 + if stir: + base_time *= 0.8 # 搅拌加速过滤 + if temp > 50.0: + base_time *= 0.7 # 高温加速过滤 + filter_time = max(base_time, 10.0) # 最少10秒 + + while True: + current_time = time_module.time() + elapsed = current_time - start_time + remaining = max(0, filter_time - elapsed) + progress = min(100.0, (elapsed / filter_time) * 100) + current_filtered = (progress / 100.0) * filter_volume + + # 更新状态 - 按照 Filter.action feedback 字段 + status_msg = f"过滤中: {vessel}" + if stir: + status_msg += f" | 搅拌: {stir_speed} RPM" + status_msg += f" | {temp}°C | {progress:.1f}% | 已过滤: {current_filtered:.1f}mL" + + self.data.update({ + "progress": progress, # Filter.action feedback + "current_temp": temp, # Filter.action feedback + "filtered_volume": current_filtered, # Filter.action feedback + "current_status": f"Filtering: {progress:.1f}% complete", # Filter.action feedback + "status": status_msg, + "message": f"Filtering: {progress:.1f}% complete, {current_filtered:.1f}mL filtered" + }) + + if remaining <= 0: + break + + await asyncio.sleep(1.0) + + # 过滤完成 + final_temp = temp if continue_heatchill else 25.0 + final_status = f"过滤完成: {vessel} | {filter_volume}mL → {filtrate_vessel}" + if continue_heatchill: + final_status += " | 继续加热搅拌" + + self.data.update({ + "status": final_status, + "progress": 100.0, # Filter.action feedback + "current_temp": final_temp, # Filter.action feedback + "filtered_volume": filter_volume, # Filter.action feedback + "current_status": f"Filtration completed: {filter_volume}mL", # Filter.action feedback + "message": f"Filtration completed: {filter_volume}mL filtered from {vessel}" + }) + + self.logger.info(f"Filtration completed: {filter_volume}mL from {vessel} to {filtrate_vessel}") + return True + + except Exception as e: + self.logger.error(f"Error during filtration: {str(e)}") + self.data.update({ + "status": f"过滤错误: {str(e)}", + "current_status": f"Filtration failed: {str(e)}", + "message": f"Filtration failed: {str(e)}" + }) + return False - # 状态属性 + # === 核心状态属性 - 按照 Filter.action feedback 字段 === @property def status(self) -> str: return self.data.get("status", "Unknown") @property - def filter_state(self) -> str: - return self.data.get("filter_state", "Unknown") + def progress(self) -> float: + """Filter.action feedback 字段""" + return self.data.get("progress", 0.0) @property def current_temp(self) -> float: + """Filter.action feedback 字段""" return self.data.get("current_temp", 25.0) @property - def target_temp(self) -> float: - return self.data.get("target_temp", 25.0) - - @property - def max_temp(self) -> float: - return self.data.get("max_temp", self._max_temp) + def filtered_volume(self) -> float: + """Filter.action feedback 字段""" + return self.data.get("filtered_volume", 0.0) @property - def stir_speed(self) -> float: - return self.data.get("stir_speed", 0.0) + def current_status(self) -> str: + """Filter.action feedback 字段""" + return self.data.get("current_status", "") @property - def max_stir_speed(self) -> float: - return self.data.get("max_stir_speed", self._max_stir_speed) + def message(self) -> str: + return self.data.get("message", "") @property - def filtered_volume(self) -> float: - return self.data.get("filtered_volume", 0.0) + def max_temp(self) -> float: + return self._max_temp @property - def progress(self) -> float: - return self.data.get("progress", 0.0) + def max_stir_speed(self) -> float: + return self._max_stir_speed @property - def message(self) -> str: - return self.data.get("message", "") \ No newline at end of file + def max_volume(self) -> float: + return self._max_volume \ No newline at end of file diff --git a/unilabos/devices/virtual/virtual_gas_source.py b/unilabos/devices/virtual/virtual_gas_source.py new file mode 100644 index 00000000..90528826 --- /dev/null +++ b/unilabos/devices/virtual/virtual_gas_source.py @@ -0,0 +1,46 @@ +import time +from typing import Dict, Any, Optional + + +class VirtualGasSource: + """Virtual gas source for testing""" + + def __init__(self, device_id: Optional[str] = None, config: Optional[Dict[str, Any]] = None, **kwargs): + self.device_id = device_id or "unknown_gas_source" + self.config = config or {} + self.data = {} + self._status = "OPEN" + + async def initialize(self) -> bool: + """Initialize virtual gas source""" + self.data.update({ + "status": self._status + }) + return True + + async def cleanup(self) -> bool: + """Cleanup virtual gas source""" + return True + + @property + def status(self) -> str: + return self._status + + def get_status(self) -> str: + return self._status + + def set_status(self, string): + self._status = string + time.sleep(5) + + def open(self): + self._status = "OPEN" + + def close(self): + self._status = "CLOSED" + + def is_open(self): + return self._status + + def is_closed(self): + return not self._status \ No newline at end of file diff --git a/unilabos/devices/virtual/virtual_heatchill.py b/unilabos/devices/virtual/virtual_heatchill.py index 98a03ce0..541434af 100644 --- a/unilabos/devices/virtual/virtual_heatchill.py +++ b/unilabos/devices/virtual/virtual_heatchill.py @@ -1,5 +1,6 @@ import asyncio import logging +import time as time_module # 重命名time模块，避免与参数冲突 from typing import Dict, Any class VirtualHeatChill: @@ -19,18 +20,13 @@ def __init__(self, device_id: str = None, config: Dict[str, Any] = None, **kwarg self.logger = logging.getLogger(f"VirtualHeatChill.{self.device_id}") self.data = {} - # 添加调试信息 - print(f"=== VirtualHeatChill {self.device_id} is being created! ===") - print(f"=== Config: {self.config} ===") - print(f"=== Kwargs: {kwargs} ===") - # 从config或kwargs中获取配置参数 self.port = self.config.get('port') or kwargs.get('port', 'VIRTUAL') self._max_temp = self.config.get('max_temp') or kwargs.get('max_temp', 200.0) self._min_temp = self.config.get('min_temp') or kwargs.get('min_temp', -80.0) self._max_stir_speed = self.config.get('max_stir_speed') or kwargs.get('max_stir_speed', 1000.0) - # 处理其他kwargs参数，但跳过已知的配置参数 + # 处理其他kwargs参数 skip_keys = {'port', 'max_temp', 'min_temp', 'max_stir_speed'} for key, value in kwargs.items(): if key not in skip_keys and not hasattr(self, key): @@ -38,70 +34,177 @@ def __init__(self, device_id: str = None, config: Dict[str, Any] = None, **kwarg async def initialize(self) -> bool: """Initialize virtual heat chill""" - print(f"=== VirtualHeatChill {self.device_id} initialize() called! ===") self.logger.info(f"Initializing virtual heat chill {self.device_id}") + + # 初始化状态信息 self.data.update({ - "status": "Idle" + "status": "Idle", + "operation_mode": "Idle", + "is_stirring": False, + "stir_speed": 0.0, + "remaining_time": 0.0, }) return True async def cleanup(self) -> bool: """Cleanup virtual heat chill""" self.logger.info(f"Cleaning up virtual heat chill {self.device_id}") + self.data.update({ + "status": "Offline", + "operation_mode": "Offline", + "is_stirring": False, + "stir_speed": 0.0, + "remaining_time": 0.0 + }) return True async def heat_chill(self, vessel: str, temp: float, time: float, stir: bool, stir_speed: float, purpose: str) -> bool: - """Execute heat chill action - matches HeatChill action exactly""" - self.logger.info(f"HeatChill: vessel={vessel}, temp={temp}°C, time={time}s, stir={stir}, stir_speed={stir_speed}, purpose={purpose}") + """Execute heat chill action - 按实际时间运行，实时更新剩余时间""" + self.logger.info(f"HeatChill: vessel={vessel}, temp={temp}°C, time={time}s, stir={stir}, stir_speed={stir_speed}") # 验证参数 if temp > self._max_temp or temp < self._min_temp: - self.logger.error(f"Temperature {temp} outside range {self._min_temp}-{self._max_temp}") - self.data["status"] = f"温度 {temp} 超出范围" + error_msg = f"温度 {temp}°C 超出范围 ({self._min_temp}°C - {self._max_temp}°C)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "operation_mode": "Error" + }) return False if stir and stir_speed > self._max_stir_speed: - self.logger.error(f"Stir speed {stir_speed} exceeds maximum {self._max_stir_speed}") - self.data["status"] = f"搅拌速度 {stir_speed} 超出范围" + error_msg = f"搅拌速度 {stir_speed} RPM 超出最大值 {self._max_stir_speed} RPM" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "operation_mode": "Error" + }) return False - # 开始加热/冷却 + # 确定操作模式 + if temp > 25.0: + operation_mode = "Heating" + status_action = "加热" + elif temp < 25.0: + operation_mode = "Cooling" + status_action = "冷却" + else: + operation_mode = "Maintaining" + status_action = "保温" + + # **修复**: 使用重命名的time模块 + start_time = time_module.time() + total_time = time + + # 开始操作 + stir_info = f" | 搅拌: {stir_speed} RPM" if stir else "" self.data.update({ - "status": f"加热/冷却中: {vessel} 至 {temp}°C" + "status": f"运行中: {status_action} {vessel} 至 {temp}°C | 剩余: {total_time:.0f}s{stir_info}", + "operation_mode": operation_mode, + "is_stirring": stir, + "stir_speed": stir_speed if stir else 0.0, + "remaining_time": total_time, }) - # 模拟加热/冷却时间 - simulation_time = min(time, 10.0) # 最多等待10秒用于测试 - await asyncio.sleep(simulation_time) + # **修复**: 在等待过程中每秒更新剩余时间 + while True: + current_time = time_module.time() # 使用重命名的time模块 + elapsed = current_time - start_time + remaining = max(0, total_time - elapsed) + + # 更新剩余时间和状态 + self.data.update({ + "remaining_time": remaining, + "status": f"运行中: {status_action} {vessel} 至 {temp}°C | 剩余: {remaining:.0f}s{stir_info}" + }) + + # 如果时间到了，退出循环 + if remaining <= 0: + break + + # 等待1秒后再次检查 + await asyncio.sleep(1.0) - # 加热/冷却完成 - self.data["status"] = f"完成: {vessel} 已达到 {temp}°C" + # 操作完成 + final_stir_info = f" | 搅拌: {stir_speed} RPM" if stir else "" + self.data.update({ + "status": f"完成: {vessel} 已达到 {temp}°C | 用时: {total_time:.0f}s{final_stir_info}", + "operation_mode": "Completed", + "remaining_time": 0.0, + "is_stirring": False, + "stir_speed": 0.0 + }) - self.logger.info(f"HeatChill completed for vessel {vessel} at {temp}°C") + self.logger.info(f"HeatChill completed for vessel {vessel} at {temp}°C after {total_time}s") return True async def heat_chill_start(self, vessel: str, temp: float, purpose: str) -> bool: - """Start heat chill - matches HeatChillStart action exactly""" - self.logger.info(f"HeatChillStart: vessel={vessel}, temp={temp}°C, purpose={purpose}") + """Start continuous heat chill""" + self.logger.info(f"HeatChillStart: vessel={vessel}, temp={temp}°C") # 验证参数 if temp > self._max_temp or temp < self._min_temp: - self.logger.error(f"Temperature {temp} outside range {self._min_temp}-{self._max_temp}") - self.data["status"] = f"温度 {temp} 超出范围" + error_msg = f"温度 {temp}°C 超出范围 ({self._min_temp}°C - {self._max_temp}°C)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "operation_mode": "Error" + }) return False - self.data["status"] = f"开始加热/冷却: {vessel} 至 {temp}°C" + # 确定操作模式 + if temp > 25.0: + operation_mode = "Heating" + status_action = "持续加热" + elif temp < 25.0: + operation_mode = "Cooling" + status_action = "持续冷却" + else: + operation_mode = "Maintaining" + status_action = "恒温保持" + + self.data.update({ + "status": f"启动: {status_action} {vessel} 至 {temp}°C | 持续运行", + "operation_mode": operation_mode, + "is_stirring": False, + "stir_speed": 0.0, + "remaining_time": -1.0, # -1 表示持续运行 + }) + return True async def heat_chill_stop(self, vessel: str) -> bool: - """Stop heat chill - matches HeatChillStop action exactly""" + """Stop heat chill""" self.logger.info(f"HeatChillStop: vessel={vessel}") - self.data["status"] = f"停止加热/冷却: {vessel}" + self.data.update({ + "status": f"已停止: {vessel} 温控停止", + "operation_mode": "Stopped", + "is_stirring": False, + "stir_speed": 0.0, + "remaining_time": 0.0, + }) + return True - # 状态属性 - 只保留 action 中定义的 feedback + # 状态属性 @property def status(self) -> str: - return self.data.get("status", "Idle") \ No newline at end of file + return self.data.get("status", "Idle") + + @property + def operation_mode(self) -> str: + return self.data.get("operation_mode", "Idle") + + @property + def is_stirring(self) -> bool: + return self.data.get("is_stirring", False) + + @property + def stir_speed(self) -> float: + return self.data.get("stir_speed", 0.0) + + @property + def remaining_time(self) -> float: + return self.data.get("remaining_time", 0.0) \ No newline at end of file diff --git a/unilabos/devices/virtual/virtual_multiway_valve.py b/unilabos/devices/virtual/virtual_multiway_valve.py new file mode 100644 index 00000000..c24b7b1c --- /dev/null +++ b/unilabos/devices/virtual/virtual_multiway_valve.py @@ -0,0 +1,231 @@ +import time +from typing import Union, Dict, Optional + + +class VirtualMultiwayValve: + """ + 虚拟九通阀门 - 0号位连接transfer pump，1-8号位连接其他设备 + """ + def __init__(self, port: str = "VIRTUAL", positions: int = 8): + self.port = port + self.max_positions = positions # 1-8号位 + self.total_positions = positions + 1 # 0-8号位，共9个位置 + + # 状态属性 + self._status = "Idle" + self._valve_state = "Ready" + self._current_position = 0 # 默认在0号位（transfer pump位置） + self._target_position = 0 + + # 位置映射说明 + self.position_map = { + 0: "transfer_pump", # 0号位连接转移泵 + 1: "port_1", # 1号位 + 2: "port_2", # 2号位 + 3: "port_3", # 3号位 + 4: "port_4", # 4号位 + 5: "port_5", # 5号位 + 6: "port_6", # 6号位 + 7: "port_7", # 7号位 + 8: "port_8" # 8号位 + } + + @property + def status(self) -> str: + return self._status + + @property + def valve_state(self) -> str: + return self._valve_state + + @property + def current_position(self) -> int: + return self._current_position + + @property + def target_position(self) -> int: + return self._target_position + + def get_current_position(self) -> int: + """获取当前阀门位置""" + return self._current_position + + def get_current_port(self) -> str: + """获取当前连接的端口名称""" + return self.position_map.get(self._current_position, "unknown") + + def set_position(self, command: Union[int, str]): + """ + 设置阀门位置 - 支持0-8位置 + + Args: + command: 目标位置 (0-8) 或位置字符串 + 0: transfer pump位置 + 1-8: 其他设备位置 + """ + try: + # 如果是字符串形式的位置，先转换为数字 + if isinstance(command, str): + pos = int(command) + else: + pos = int(command) + + if pos < 0 or pos > self.max_positions: + raise ValueError(f"Position must be between 0 and {self.max_positions}") + + self._status = "Busy" + self._valve_state = "Moving" + self._target_position = pos + + # 模拟阀门切换时间 + switch_time = abs(self._current_position - pos) * 0.5 # 每个位置0.5秒 + time.sleep(switch_time) + + self._current_position = pos + self._status = "Idle" + self._valve_state = "Ready" + + current_port = self.get_current_port() + return f"Position set to {pos} ({current_port})" + + except ValueError as e: + self._status = "Error" + self._valve_state = "Error" + return f"Error: {str(e)}" + + def set_to_pump_position(self): + """切换到transfer pump位置（0号位）""" + return self.set_position(0) + + def set_to_port(self, port_number: int): + """ + 切换到指定端口位置 + + Args: + port_number: 端口号 (1-8) + """ + if port_number < 1 or port_number > self.max_positions: + raise ValueError(f"Port number must be between 1 and {self.max_positions}") + return self.set_position(port_number) + + def open(self): + """打开阀门 - 设置到transfer pump位置（0号位）""" + return self.set_to_pump_position() + + def close(self): + """关闭阀门 - 对于多通阀门，设置到一个"关闭"状态""" + self._status = "Busy" + self._valve_state = "Closing" + time.sleep(0.5) + + # 可以选择保持当前位置或设置特殊关闭状态 + self._status = "Idle" + self._valve_state = "Closed" + + return f"Valve closed at position {self._current_position}" + + def get_valve_position(self) -> int: + """获取阀门位置 - 兼容性方法""" + return self._current_position + + def is_at_position(self, position: int) -> bool: + """检查是否在指定位置""" + return self._current_position == position + + def is_at_pump_position(self) -> bool: + """检查是否在transfer pump位置""" + return self._current_position == 0 + + def is_at_port(self, port_number: int) -> bool: + """检查是否在指定端口位置""" + return self._current_position == port_number + + def get_available_positions(self) -> list: + """获取可用位置列表""" + return list(range(0, self.max_positions + 1)) + + def get_available_ports(self) -> Dict[int, str]: + """获取可用端口映射""" + return self.position_map.copy() + + def reset(self): + """重置阀门到transfer pump位置（0号位）""" + return self.set_position(0) + + def switch_between_pump_and_port(self, port_number: int): + """ + 在transfer pump位置和指定端口之间切换 + + Args: + port_number: 目标端口号 (1-8) + """ + if self._current_position == 0: + # 当前在pump位置，切换到指定端口 + return self.set_to_port(port_number) + else: + # 当前在某个端口，切换到pump位置 + return self.set_to_pump_position() + + def get_flow_path(self) -> str: + """获取当前流路路径描述""" + current_port = self.get_current_port() + if self._current_position == 0: + return f"Transfer pump connected (position {self._current_position})" + else: + return f"Port {self._current_position} connected ({current_port})" + + def get_info(self) -> dict: + """获取阀门详细信息""" + return { + "port": self.port, + "max_positions": self.max_positions, + "total_positions": self.total_positions, + "current_position": self._current_position, + "current_port": self.get_current_port(), + "target_position": self._target_position, + "status": self._status, + "valve_state": self._valve_state, + "flow_path": self.get_flow_path(), + "position_map": self.position_map + } + + def __str__(self): + return f"VirtualMultiwayValve(Position: {self._current_position}/{self.max_positions}, Port: {self.get_current_port()}, Status: {self._status})" + + def set_valve_position(self, command: Union[int, str]): + """ + 设置阀门位置 - 兼容pump_protocol调用 + 这是set_position的别名方法，用于兼容pump_protocol.py + + Args: + command: 目标位置 (0-8) 或位置字符串 + """ + return self.set_position(command) + + +# 使用示例 +if __name__ == "__main__": + valve = VirtualMultiwayValve() + + print("=== 虚拟九通阀门测试 ===") + print(f"初始状态: {valve}") + print(f"当前流路: {valve.get_flow_path()}") + + # 切换到试剂瓶1（1号位） + print(f"\n切换到1号位: {valve.set_position(1)}") + print(f"当前状态: {valve}") + + # 切换到transfer pump位置（0号位） + print(f"\n切换到pump位置: {valve.set_to_pump_position()}") + print(f"当前状态: {valve}") + + # 切换到试剂瓶2（2号位） + print(f"\n切换到2号位: {valve.set_to_port(2)}") + print(f"当前状态: {valve}") + + # 显示所有可用位置 + print(f"\n可用位置: {valve.get_available_positions()}") + print(f"端口映射: {valve.get_available_ports()}") + + # 获取详细信息 + print(f"\n详细信息: {valve.get_info()}") \ No newline at end of file diff --git a/unilabos/devices/virtual/virtual_rotavap.py b/unilabos/devices/virtual/virtual_rotavap.py new file mode 100644 index 00000000..ba01c7b7 --- /dev/null +++ b/unilabos/devices/virtual/virtual_rotavap.py @@ -0,0 +1,228 @@ +import asyncio +import logging +import time as time_module +from typing import Dict, Any, Optional + + +class VirtualRotavap: + """Virtual rotary evaporator device - 简化版，只保留核心功能""" + + def __init__(self, device_id: Optional[str] = None, config: Optional[Dict[str, Any]] = None, **kwargs): + # 处理可能的不同调用方式 + if device_id is None and "id" in kwargs: + device_id = kwargs.pop("id") + if config is None and "config" in kwargs: + config = kwargs.pop("config") + + # 设置默认值 + self.device_id = device_id or "unknown_rotavap" + self.config = config or {} + + self.logger = logging.getLogger(f"VirtualRotavap.{self.device_id}") + self.data = {} + + # 从config或kwargs中获取配置参数 + self.port = self.config.get("port") or kwargs.get("port", "VIRTUAL") + self._max_temp = self.config.get("max_temp") or kwargs.get("max_temp", 180.0) + self._max_rotation_speed = self.config.get("max_rotation_speed") or kwargs.get("max_rotation_speed", 280.0) + + # 处理其他kwargs参数 + skip_keys = {"port", "max_temp", "max_rotation_speed"} + for key, value in kwargs.items(): + if key not in skip_keys and not hasattr(self, key): + setattr(self, key, value) + + async def initialize(self) -> bool: + """Initialize virtual rotary evaporator""" + self.logger.info(f"Initializing virtual rotary evaporator {self.device_id}") + + # 只保留核心状态 + self.data.update({ + "status": "Idle", + "rotavap_state": "Ready", # Ready, Evaporating, Completed, Error + "current_temp": 25.0, + "target_temp": 25.0, + "rotation_speed": 0.0, + "vacuum_pressure": 1.0, # 大气压 + "evaporated_volume": 0.0, + "progress": 0.0, + "remaining_time": 0.0, + "message": "Ready for evaporation" + }) + return True + + async def cleanup(self) -> bool: + """Cleanup virtual rotary evaporator""" + self.logger.info(f"Cleaning up virtual rotary evaporator {self.device_id}") + + self.data.update({ + "status": "Offline", + "rotavap_state": "Offline", + "current_temp": 25.0, + "rotation_speed": 0.0, + "vacuum_pressure": 1.0, + "message": "System offline" + }) + return True + + async def evaporate( + self, + vessel: str, + pressure: float = 0.1, + temp: float = 60.0, + time: float = 1800.0, # 30分钟默认 + stir_speed: float = 100.0 + ) -> bool: + """Execute evaporate action - 简化的蒸发流程""" + self.logger.info(f"Evaporate: vessel={vessel}, pressure={pressure} bar, temp={temp}°C, time={time}s, rotation={stir_speed} RPM") + + # 验证参数 + if temp > self._max_temp or temp < 10.0: + error_msg = f"温度 {temp}°C 超出范围 (10-{self._max_temp}°C)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "rotavap_state": "Error", + "message": error_msg + }) + return False + + if stir_speed > self._max_rotation_speed or stir_speed < 10.0: + error_msg = f"旋转速度 {stir_speed} RPM 超出范围 (10-{self._max_rotation_speed} RPM)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "rotavap_state": "Error", + "message": error_msg + }) + return False + + if pressure < 0.01 or pressure > 1.0: + error_msg = f"真空度 {pressure} bar 超出范围 (0.01-1.0 bar)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "rotavap_state": "Error", + "message": error_msg + }) + return False + + # 开始蒸发 + self.data.update({ + "status": f"蒸发中: {vessel}", + "rotavap_state": "Evaporating", + "current_temp": temp, + "target_temp": temp, + "rotation_speed": stir_speed, + "vacuum_pressure": pressure, + "remaining_time": time, + "progress": 0.0, + "evaporated_volume": 0.0, + "message": f"Evaporating {vessel} at {temp}°C, {pressure} bar, {stir_speed} RPM" + }) + + try: + # 蒸发过程 - 实时更新进度 + start_time = time_module.time() + total_time = time + + while True: + current_time = time_module.time() + elapsed = current_time - start_time + remaining = max(0, total_time - elapsed) + progress = min(100.0, (elapsed / total_time) * 100) + + # 模拟蒸发体积 + evaporated_vol = progress * 0.8 # 假设最多蒸发80mL + + # 更新状态 + self.data.update({ + "remaining_time": remaining, + "progress": progress, + "evaporated_volume": evaporated_vol, + "status": f"蒸发中: {vessel} | {temp}°C | {pressure} bar | {progress:.1f}% | 剩余: {remaining:.0f}s", + "message": f"Evaporating: {progress:.1f}% complete, {remaining:.0f}s remaining" + }) + + # 时间到了，退出循环 + if remaining <= 0: + break + + # 每秒更新一次 + await asyncio.sleep(1.0) + + # 蒸发完成 + final_evaporated = 80.0 + self.data.update({ + "status": f"蒸发完成: {vessel} | 蒸发量: {final_evaporated:.1f}mL", + "rotavap_state": "Completed", + "evaporated_volume": final_evaporated, + "progress": 100.0, + "remaining_time": 0.0, + "current_temp": 25.0, # 冷却下来 + "rotation_speed": 0.0, # 停止旋转 + "vacuum_pressure": 1.0, # 恢复大气压 + "message": f"Evaporation completed: {final_evaporated}mL evaporated from {vessel}" + }) + + self.logger.info(f"Evaporation completed: {final_evaporated}mL evaporated from {vessel}") + return True + + except Exception as e: + # 出错处理 + self.logger.error(f"Error during evaporation: {str(e)}") + + self.data.update({ + "status": f"蒸发错误: {str(e)}", + "rotavap_state": "Error", + "current_temp": 25.0, + "rotation_speed": 0.0, + "vacuum_pressure": 1.0, + "message": f"Evaporation failed: {str(e)}" + }) + return False + + # === 核心状态属性 === + @property + def status(self) -> str: + return self.data.get("status", "Unknown") + + @property + def rotavap_state(self) -> str: + return self.data.get("rotavap_state", "Unknown") + + @property + def current_temp(self) -> float: + return self.data.get("current_temp", 25.0) + + @property + def rotation_speed(self) -> float: + return self.data.get("rotation_speed", 0.0) + + @property + def vacuum_pressure(self) -> float: + return self.data.get("vacuum_pressure", 1.0) + + @property + def evaporated_volume(self) -> float: + return self.data.get("evaporated_volume", 0.0) + + @property + def progress(self) -> float: + return self.data.get("progress", 0.0) + + @property + def message(self) -> str: + return self.data.get("message", "") + + @property + def max_temp(self) -> float: + return self._max_temp + + @property + def max_rotation_speed(self) -> float: + return self._max_rotation_speed + + @property + def remaining_time(self) -> float: + return self.data.get("remaining_time", 0.0) diff --git a/unilabos/devices/virtual/virtual_separator.py b/unilabos/devices/virtual/virtual_separator.py new file mode 100644 index 00000000..e1c46128 --- /dev/null +++ b/unilabos/devices/virtual/virtual_separator.py @@ -0,0 +1,184 @@ +import asyncio +import logging +from typing import Dict, Any, Optional + + +class VirtualSeparator: + """Virtual separator device for SeparateProtocol testing""" + + def __init__(self, device_id: Optional[str] = None, config: Optional[Dict[str, Any]] = None, **kwargs): + # 处理可能的不同调用方式 + if device_id is None and "id" in kwargs: + device_id = kwargs.pop("id") + if config is None and "config" in kwargs: + config = kwargs.pop("config") + + # 设置默认值 + self.device_id = device_id or "unknown_separator" + self.config = config or {} + + self.logger = logging.getLogger(f"VirtualSeparator.{self.device_id}") + self.data = {} + + # 添加调试信息 + print(f"=== VirtualSeparator {self.device_id} is being created! ===") + print(f"=== Config: {self.config} ===") + print(f"=== Kwargs: {kwargs} ===") + + # 从config或kwargs中获取配置参数 + self.port = self.config.get("port") or kwargs.get("port", "VIRTUAL") + self._volume = self.config.get("volume") or kwargs.get("volume", 250.0) + self._has_phases = self.config.get("has_phases") or kwargs.get("has_phases", True) + + # 处理其他kwargs参数，但跳过已知的配置参数 + skip_keys = {"port", "volume", "has_phases"} + for key, value in kwargs.items(): + if key not in skip_keys and not hasattr(self, key): + setattr(self, key, value) + + async def initialize(self) -> bool: + """Initialize virtual separator""" + print(f"=== VirtualSeparator {self.device_id} initialize() called! ===") + self.logger.info(f"Initializing virtual separator {self.device_id}") + self.data.update( + { + "status": "Ready", + "separator_state": "Ready", + "volume": self._volume, + "has_phases": self._has_phases, + "phase_separation": False, + "stir_speed": 0.0, + "settling_time": 0.0, + "progress": 0.0, + "message": "", + } + ) + return True + + async def cleanup(self) -> bool: + """Cleanup virtual separator""" + self.logger.info(f"Cleaning up virtual separator {self.device_id}") + return True + + async def separate( + self, + purpose: str, + product_phase: str, + from_vessel: str, + separation_vessel: str, + to_vessel: str, + waste_phase_to_vessel: str = "", + solvent: str = "", + solvent_volume: float = 50.0, + through: str = "", + repeats: int = 1, + stir_time: float = 30.0, + stir_speed: float = 300.0, + settling_time: float = 300.0, + ) -> bool: + """Execute separate action - matches Separate action""" + self.logger.info(f"Separate: purpose={purpose}, product_phase={product_phase}, from_vessel={from_vessel}") + + # 验证参数 + if product_phase not in ["top", "bottom"]: + self.logger.error(f"Invalid product_phase {product_phase}, must be 'top' or 'bottom'") + self.data["message"] = f"产物相位 {product_phase} 无效，必须是 'top' 或 'bottom'" + return False + + if purpose not in ["wash", "extract"]: + self.logger.error(f"Invalid purpose {purpose}, must be 'wash' or 'extract'") + self.data["message"] = f"分离目的 {purpose} 无效，必须是 'wash' 或 'extract'" + return False + + # 开始分离 + self.data.update( + { + "status": "Running", + "separator_state": "Separating", + "purpose": purpose, + "product_phase": product_phase, + "from_vessel": from_vessel, + "separation_vessel": separation_vessel, + "to_vessel": to_vessel, + "waste_phase_to_vessel": waste_phase_to_vessel, + "solvent": solvent, + "solvent_volume": solvent_volume, + "repeats": repeats, + "stir_speed": stir_speed, + "settling_time": settling_time, + "phase_separation": True, + "progress": 0.0, + "message": f"正在分离: {from_vessel} -> {to_vessel}", + } + ) + + # 模拟分离过程 + total_time = (stir_time + settling_time) * repeats + simulation_time = min(total_time / 60.0, 15.0) # 最多模拟15秒 + + for repeat in range(repeats): + # 搅拌阶段 + for progress in range(0, 51, 10): + await asyncio.sleep(simulation_time / (repeats * 10)) + overall_progress = ((repeat * 100) + (progress * 0.5)) / repeats + self.data["progress"] = overall_progress + self.data["message"] = f"第{repeat+1}次分离 - 搅拌中 ({progress}%)" + + # 静置分相阶段 + for progress in range(50, 101, 10): + await asyncio.sleep(simulation_time / (repeats * 10)) + overall_progress = ((repeat * 100) + (progress * 0.5)) / repeats + self.data["progress"] = overall_progress + self.data["message"] = f"第{repeat+1}次分离 - 静置分相中 ({progress}%)" + + # 分离完成 + self.data.update( + { + "status": "Ready", + "separator_state": "Ready", + "phase_separation": False, + "stir_speed": 0.0, + "progress": 100.0, + "message": f"分离完成: {repeats}次分离操作", + } + ) + + self.logger.info(f"Separation completed: {repeats} cycles from {from_vessel} to {to_vessel}") + return True + + # 状态属性 + @property + def status(self) -> str: + return self.data.get("status", "Unknown") + + @property + def separator_state(self) -> str: + return self.data.get("separator_state", "Unknown") + + @property + def volume(self) -> float: + return self.data.get("volume", self._volume) + + @property + def has_phases(self) -> bool: + return self.data.get("has_phases", self._has_phases) + + @property + def phase_separation(self) -> bool: + return self.data.get("phase_separation", False) + + @property + def stir_speed(self) -> float: + return self.data.get("stir_speed", 0.0) + + @property + def settling_time(self) -> float: + return self.data.get("settling_time", 0.0) + + @property + def progress(self) -> float: + return self.data.get("progress", 0.0) + + @property + def message(self) -> str: + return self.data.get("message", "") diff --git a/unilabos/devices/virtual/virtual_solenoid_valve.py b/unilabos/devices/virtual/virtual_solenoid_valve.py new file mode 100644 index 00000000..f25cc843 --- /dev/null +++ b/unilabos/devices/virtual/virtual_solenoid_valve.py @@ -0,0 +1,147 @@ +import time +import asyncio +from typing import Union + + +class VirtualSolenoidValve: + """ + 虚拟电磁阀门 - 简单的开关型阀门，只有开启和关闭两个状态 + """ + def __init__(self, device_id: str = None, config: dict = None, **kwargs): + # 从配置中获取参数，提供默认值 + if config is None: + config = {} + + self.device_id = device_id + self.port = config.get("port", "VIRTUAL") + self.voltage = config.get("voltage", 12.0) + self.response_time = config.get("response_time", 0.1) + + # 状态属性 + self._status = "Idle" + self._valve_state = "Closed" # "Open" or "Closed" + self._is_open = False + + async def initialize(self) -> bool: + """初始化设备""" + self._status = "Idle" + return True + + async def cleanup(self) -> bool: + """清理资源""" + return True + + @property + def status(self) -> str: + return self._status + + @property + def valve_state(self) -> str: + return self._valve_state + + @property + def is_open(self) -> bool: + return self._is_open + + def get_valve_position(self) -> str: + """获取阀门位置状态""" + return "OPEN" if self._is_open else "CLOSED" + + async def set_valve_position(self, command: str = None, **kwargs): + """ + 设置阀门位置 - ROS动作接口 + + Args: + command: "OPEN"/"CLOSED" 或其他控制命令 + """ + if command is None: + return {"success": False, "message": "Missing command parameter"} + + print(f"SOLENOID_VALVE: {self.device_id} 接收到命令: {command}") + + self._status = "Busy" + + # 模拟阀门响应时间 + await asyncio.sleep(self.response_time) + + # 处理不同的命令格式 + if isinstance(command, str): + cmd_upper = command.upper() + if cmd_upper in ["OPEN", "ON", "TRUE", "1"]: + self._is_open = True + self._valve_state = "Open" + result_msg = f"Valve {self.device_id} opened" + elif cmd_upper in ["CLOSED", "CLOSE", "OFF", "FALSE", "0"]: + self._is_open = False + self._valve_state = "Closed" + result_msg = f"Valve {self.device_id} closed" + else: + # 可能是端口名称，处理路径设置 + # 对于简单电磁阀，任何非关闭命令都视为开启 + self._is_open = True + self._valve_state = "Open" + result_msg = f"Valve {self.device_id} set to position: {command}" + else: + self._status = "Error" + return {"success": False, "message": "Invalid command type"} + + self._status = "Idle" + print(f"SOLENOID_VALVE: {result_msg}") + + return { + "success": True, + "message": result_msg, + "valve_position": self.get_valve_position() + } + + async def open(self, **kwargs): + """打开电磁阀 - ROS动作接口""" + return await self.set_valve_position(command="OPEN") + + async def close(self, **kwargs): + """关闭电磁阀 - ROS动作接口""" + return await self.set_valve_position(command="CLOSED") + + async def set_state(self, command: Union[bool, str], **kwargs): + """ + 设置阀门状态 - 兼容 SendCmd 类型 + + Args: + command: True/False 或 "open"/"close" + """ + if isinstance(command, bool): + cmd_str = "OPEN" if command else "CLOSED" + elif isinstance(command, str): + cmd_str = command + else: + return {"success": False, "message": "Invalid command type"} + + return await self.set_valve_position(command=cmd_str) + + def toggle(self): + """切换阀门状态""" + if self._is_open: + return self.close() + else: + return self.open() + + def is_closed(self) -> bool: + """检查阀门是否关闭""" + return not self._is_open + + def get_state(self) -> dict: + """获取阀门完整状态""" + return { + "device_id": self.device_id, + "port": self.port, + "voltage": self.voltage, + "response_time": self.response_time, + "is_open": self._is_open, + "valve_state": self._valve_state, + "status": self._status, + "position": self.get_valve_position() + } + + async def reset(self): + """重置阀门到关闭状态""" + return await self.close() \ No newline at end of file diff --git a/unilabos/devices/virtual/virtual_stirrer.py b/unilabos/devices/virtual/virtual_stirrer.py index b1a4098b..874f997a 100644 --- a/unilabos/devices/virtual/virtual_stirrer.py +++ b/unilabos/devices/virtual/virtual_stirrer.py @@ -1,9 +1,10 @@ import asyncio import logging +import time as time_module from typing import Dict, Any class VirtualStirrer: - """Virtual stirrer device for StirProtocol testing""" + """Virtual stirrer device for StirProtocol testing - 功能完整版""" def __init__(self, device_id: str = None, config: Dict[str, Any] = None, **kwargs): # 处理可能的不同调用方式 @@ -19,86 +20,196 @@ def __init__(self, device_id: str = None, config: Dict[str, Any] = None, **kwarg self.logger = logging.getLogger(f"VirtualStirrer.{self.device_id}") self.data = {} - # 添加调试信息 - print(f"=== VirtualStirrer {self.device_id} is being created! ===") - print(f"=== Config: {self.config} ===") - print(f"=== Kwargs: {kwargs} ===") - # 从config或kwargs中获取配置参数 self.port = self.config.get('port') or kwargs.get('port', 'VIRTUAL') - self._max_temp = self.config.get('max_temp') or kwargs.get('max_temp', 100.0) - self._max_speed = self.config.get('max_speed') or kwargs.get('max_speed', 1000.0) + self._max_speed = self.config.get('max_speed') or kwargs.get('max_speed', 1500.0) + self._min_speed = self.config.get('min_speed') or kwargs.get('min_speed', 50.0) - # 处理其他kwargs参数，但跳过已知的配置参数 - skip_keys = {'port', 'max_temp', 'max_speed'} + # 处理其他kwargs参数 + skip_keys = {'port', 'max_speed', 'min_speed'} for key, value in kwargs.items(): if key not in skip_keys and not hasattr(self, key): setattr(self, key, value) async def initialize(self) -> bool: """Initialize virtual stirrer""" - print(f"=== VirtualStirrer {self.device_id} initialize() called! ===") self.logger.info(f"Initializing virtual stirrer {self.device_id}") + + # 初始化状态信息 self.data.update({ - "status": "Idle" + "status": "Idle", + "operation_mode": "Idle", # 操作模式: Idle, Stirring, Settling, Completed, Error + "current_vessel": "", # 当前搅拌的容器 + "current_speed": 0.0, # 当前搅拌速度 + "is_stirring": False, # 是否正在搅拌 + "remaining_time": 0.0, # 剩余时间 }) return True async def cleanup(self) -> bool: """Cleanup virtual stirrer""" self.logger.info(f"Cleaning up virtual stirrer {self.device_id}") + self.data.update({ + "status": "Offline", + "operation_mode": "Offline", + "current_vessel": "", + "current_speed": 0.0, + "is_stirring": False, + "remaining_time": 0.0, + }) return True async def stir(self, stir_time: float, stir_speed: float, settling_time: float) -> bool: - """Execute stir action - matches Stir action exactly""" + """Execute stir action - 定时搅拌 + 沉降""" self.logger.info(f"Stir: speed={stir_speed} RPM, time={stir_time}s, settling={settling_time}s") # 验证参数 - if stir_speed > self._max_speed: - self.logger.error(f"Stir speed {stir_speed} exceeds maximum {self._max_speed}") - self.data["status"] = f"搅拌速度 {stir_speed} 超出范围" + if stir_speed > self._max_speed or stir_speed < self._min_speed: + error_msg = f"搅拌速度 {stir_speed} RPM 超出范围 ({self._min_speed} - {self._max_speed} RPM)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "operation_mode": "Error" + }) return False - # 开始搅拌 - self.data["status"] = f"搅拌中: {stir_speed} RPM, {stir_time}s" + # === 第一阶段：搅拌 === + start_time = time_module.time() + total_stir_time = stir_time + + self.data.update({ + "status": f"搅拌中: {stir_speed} RPM | 剩余: {total_stir_time:.0f}s", + "operation_mode": "Stirring", + "current_speed": stir_speed, + "is_stirring": True, + "remaining_time": total_stir_time, + }) - # 模拟搅拌时间 - simulation_time = min(stir_time, 10.0) # 最多等待10秒用于测试 - await asyncio.sleep(simulation_time) + # 搅拌过程 - 实时更新剩余时间 + while True: + current_time = time_module.time() + elapsed = current_time - start_time + remaining = max(0, total_stir_time - elapsed) + + # 更新状态 + self.data.update({ + "remaining_time": remaining, + "status": f"搅拌中: {stir_speed} RPM | 剩余: {remaining:.0f}s" + }) + + # 搅拌时间到了 + if remaining <= 0: + break + + await asyncio.sleep(1.0) - # 搅拌完成，开始沉降 + # === 第二阶段：沉降（如果需要）=== if settling_time > 0: - self.data["status"] = f"沉降中: {settling_time}s" - settling_simulation = min(settling_time, 5.0) # 最多等待5秒 - await asyncio.sleep(settling_simulation) + start_settling_time = time_module.time() + total_settling_time = settling_time + + self.data.update({ + "status": f"沉降中: 停止搅拌 | 剩余: {total_settling_time:.0f}s", + "operation_mode": "Settling", + "current_speed": 0.0, + "is_stirring": False, + "remaining_time": total_settling_time, + }) + + # 沉降过程 - 实时更新剩余时间 + while True: + current_time = time_module.time() + elapsed = current_time - start_settling_time + remaining = max(0, total_settling_time - elapsed) + + # 更新状态 + self.data.update({ + "remaining_time": remaining, + "status": f"沉降中: 停止搅拌 | 剩余: {remaining:.0f}s" + }) + + # 沉降时间到了 + if remaining <= 0: + break + + await asyncio.sleep(1.0) - # 操作完成 - self.data["status"] = "搅拌完成" + # === 操作完成 === + settling_info = f" | 沉降: {settling_time:.0f}s" if settling_time > 0 else "" + self.data.update({ + "status": f"完成: 搅拌 {stir_speed} RPM, {stir_time:.0f}s{settling_info}", + "operation_mode": "Completed", + "current_speed": 0.0, + "is_stirring": False, + "remaining_time": 0.0, + }) - self.logger.info(f"Stir completed: {stir_speed} RPM for {stir_time}s") + self.logger.info(f"Stir completed: {stir_speed} RPM for {stir_time}s + settling {settling_time}s") return True async def start_stir(self, vessel: str, stir_speed: float, purpose: str) -> bool: - """Start stir action - matches StartStir action exactly""" + """Start stir action - 开始持续搅拌""" self.logger.info(f"StartStir: vessel={vessel}, speed={stir_speed} RPM, purpose={purpose}") # 验证参数 - if stir_speed > self._max_speed: - self.logger.error(f"Stir speed {stir_speed} exceeds maximum {self._max_speed}") - self.data["status"] = f"搅拌速度 {stir_speed} 超出范围" + if stir_speed > self._max_speed or stir_speed < self._min_speed: + error_msg = f"搅拌速度 {stir_speed} RPM 超出范围 ({self._min_speed} - {self._max_speed} RPM)" + self.logger.error(error_msg) + self.data.update({ + "status": f"Error: {error_msg}", + "operation_mode": "Error" + }) return False - self.data["status"] = f"开始搅拌: {vessel} at {stir_speed} RPM" + self.data.update({ + "status": f"启动: 持续搅拌 {vessel} at {stir_speed} RPM | {purpose}", + "operation_mode": "Stirring", + "current_vessel": vessel, + "current_speed": stir_speed, + "is_stirring": True, + "remaining_time": -1.0, # -1 表示持续运行 + }) + return True async def stop_stir(self, vessel: str) -> bool: - """Stop stir action - matches StopStir action exactly""" + """Stop stir action - 停止搅拌""" self.logger.info(f"StopStir: vessel={vessel}") - self.data["status"] = f"停止搅拌: {vessel}" + current_speed = self.data.get("current_speed", 0.0) + + self.data.update({ + "status": f"已停止: {vessel} 搅拌停止 | 之前速度: {current_speed} RPM", + "operation_mode": "Stopped", + "current_vessel": "", + "current_speed": 0.0, + "is_stirring": False, + "remaining_time": 0.0, + }) + return True - # 状态属性 - 只保留 action 中定义的 feedback + # 状态属性 @property def status(self) -> str: - return self.data.get("status", "Idle") \ No newline at end of file + return self.data.get("status", "Idle") + + @property + def operation_mode(self) -> str: + return self.data.get("operation_mode", "Idle") + + @property + def current_vessel(self) -> str: + return self.data.get("current_vessel", "") + + @property + def current_speed(self) -> float: + return self.data.get("current_speed", 0.0) + + @property + def is_stirring(self) -> bool: + return self.data.get("is_stirring", False) + + @property + def remaining_time(self) -> float: + return self.data.get("remaining_time", 0.0) \ No newline at end of file diff --git a/unilabos/devices/virtual/virtual_transferpump.py b/unilabos/devices/virtual/virtual_transferpump.py index 87d4cffa..a2cba9c4 100644 --- a/unilabos/devices/virtual/virtual_transferpump.py +++ b/unilabos/devices/virtual/virtual_transferpump.py @@ -1,149 +1,328 @@ import asyncio +import time +from enum import Enum +from typing import Union, Optional import logging -from typing import Dict, Any, Optional + + +class VirtualPumpMode(Enum): + Normal = 0 + AccuratePos = 1 + AccuratePosVel = 2 + class VirtualTransferPump: - """Virtual pump device specifically for Transfer protocol""" + """虚拟转移泵类 - 模拟泵的基本功能，无需实际硬件""" - def __init__(self, device_id: str = None, config: Dict[str, Any] = None, **kwargs): - # 处理可能的不同调用方式 - if device_id is None and 'id' in kwargs: - device_id = kwargs.pop('id') - if config is None and 'config' in kwargs: - config = kwargs.pop('config') + def __init__(self, device_id: str = None, config: dict = None, **kwargs): + """ + 初始化虚拟转移泵 - # 设置默认值 - self.device_id = device_id or "unknown_transfer_pump" - self.config = config or {} + Args: + device_id: 设备ID + config: 配置字典，包含max_volume, port等参数 + **kwargs: 其他参数，确保兼容性 + """ + self.device_id = device_id or "virtual_transfer_pump" - self.logger = logging.getLogger(f"VirtualTransferPump.{self.device_id}") - self.data = {} + # 从config或kwargs中获取参数，确保类型正确 + if config: + self.max_volume = float(config.get('max_volume', 25.0)) + self.port = config.get('port', 'VIRTUAL') + else: + self.max_volume = float(kwargs.get('max_volume', 25.0)) + self.port = kwargs.get('port', 'VIRTUAL') - # 添加调试信息 - print(f"=== VirtualTransferPump {self.device_id} is being created! ===") - print(f"=== Config: {self.config} ===") - print(f"=== Kwargs: {kwargs} ===") + self._transfer_rate = float(kwargs.get('transfer_rate', 0)) + self.mode = kwargs.get('mode', VirtualPumpMode.Normal) - # 从config或kwargs中获取配置参数 - self.port = self.config.get('port') or kwargs.get('port', 'VIRTUAL') - self._max_volume = self.config.get('max_volume') or kwargs.get('max_volume', 50.0) - self._transfer_rate = self.config.get('transfer_rate') or kwargs.get('transfer_rate', 5.0) - self._current_volume = 0.0 - self.is_running = False + # 状态变量 - 确保都是正确类型 + self._status = "Idle" + self._position = 0.0 # float + self._max_velocity = 5.0 # float + self._current_volume = 0.0 # float + + self.logger = logging.getLogger(f"VirtualTransferPump.{self.device_id}") async def initialize(self) -> bool: - """Initialize virtual transfer pump""" - print(f"=== VirtualTransferPump {self.device_id} initialize() called! ===") - self.logger.info(f"Initializing virtual transfer pump {self.device_id}") - self.data.update({ - "status": "Idle", - "current_volume": 0.0, - "max_volume": self._max_volume, - "transfer_rate": self._transfer_rate, - "from_vessel": "", - "to_vessel": "", - "progress": 0.0, - "transferred_volume": 0.0, - "current_status": "Ready" - }) + """初始化虚拟泵""" + self.logger.info(f"Initializing virtual pump {self.device_id}") + self._status = "Idle" + self._position = 0.0 + self._current_volume = 0.0 return True async def cleanup(self) -> bool: - """Cleanup virtual transfer pump""" - self.logger.info(f"Cleaning up virtual transfer pump {self.device_id}") + """清理虚拟泵""" + self.logger.info(f"Cleaning up virtual pump {self.device_id}") + self._status = "Idle" return True - async def transfer(self, from_vessel: str, to_vessel: str, volume: float, - amount: str = "", time: float = 0, viscous: bool = False, - rinsing_solvent: str = "", rinsing_volume: float = 0.0, - rinsing_repeats: int = 0, solid: bool = False) -> bool: - """Execute liquid transfer - matches Transfer action""" - self.logger.info(f"Transfer: {volume}mL from {from_vessel} to {to_vessel}") - - # 计算转移时间 - if time > 0: - transfer_time = time - else: - # 如果是粘性液体，降低转移速率 - rate = self._transfer_rate * 0.5 if viscous else self._transfer_rate - transfer_time = volume / rate - - self.data.update({ - "status": "Running", - "from_vessel": from_vessel, - "to_vessel": to_vessel, - "current_status": "Transferring", - "progress": 0.0, - "transferred_volume": 0.0 - }) - - # 模拟转移过程 - steps = 10 - step_time = transfer_time / steps - step_volume = volume / steps - - for i in range(steps): - await asyncio.sleep(step_time) - progress = (i + 1) / steps * 100 - transferred = (i + 1) * step_volume - - self.data.update({ - "progress": progress, - "transferred_volume": transferred, - "current_status": f"Transferring {progress:.1f}%" - }) - - self.logger.info(f"Transfer progress: {progress:.1f}% ({transferred:.1f}/{volume}mL)") - - # 如果需要冲洗 - if rinsing_solvent and rinsing_volume > 0 and rinsing_repeats > 0: - self.data["current_status"] = "Rinsing" - for repeat in range(rinsing_repeats): - self.logger.info(f"Rinsing cycle {repeat + 1}/{rinsing_repeats} with {rinsing_solvent}") - await asyncio.sleep(1) # 模拟冲洗时间 - - self.data.update({ - "status": "Idle", - "current_status": "Transfer completed", - "progress": 100.0, - "transferred_volume": volume - }) - - return True - - # 添加所有在virtual_device.yaml中定义的状态属性 + # 基本属性 @property def status(self) -> str: - return self.data.get("status", "Unknown") + return self._status + + @property + def position(self) -> float: + """当前柱塞位置 (ml)""" + return self._position @property def current_volume(self) -> float: - return self.data.get("current_volume", 0.0) + """当前注射器中的体积 (ml)""" + return self._current_volume @property - def max_volume(self) -> float: - return self.data.get("max_volume", self._max_volume) + def max_velocity(self) -> float: + return self._max_velocity @property def transfer_rate(self) -> float: - return self.data.get("transfer_rate", self._transfer_rate) + return self._transfer_rate + + def set_max_velocity(self, velocity: float): + """设置最大速度 (ml/s)""" + self._max_velocity = max(0.1, min(50.0, velocity)) # 限制在合理范围内 + self.logger.info(f"Set max velocity to {self._max_velocity} ml/s") - @property - def from_vessel(self) -> str: - return self.data.get("from_vessel", "") + def get_status(self) -> str: + """获取泵状态""" + return self._status - @property - def to_vessel(self) -> str: - return self.data.get("to_vessel", "") + async def _simulate_operation(self, duration: float): + """模拟操作延时""" + self._status = "Busy" + await asyncio.sleep(duration) + self._status = "Idle" - @property - def progress(self) -> float: - return self.data.get("progress", 0.0) + def _calculate_duration(self, volume: float, velocity: float = None) -> float: + """计算操作持续时间""" + if velocity is None: + velocity = self._max_velocity + return abs(volume) / velocity - @property - def transferred_volume(self) -> float: - return self.data.get("transferred_volume", 0.0) + # 新的set_position方法 - 专门用于SetPumpPosition动作 + async def set_position(self, position: float, max_velocity: float = None): + """ + 移动到绝对位置 - 专门用于SetPumpPosition动作 + + Args: + position (float): 目标位置 (ml) + max_velocity (float): 移动速度 (ml/s) + + Returns: + dict: 符合SetPumpPosition.action定义的结果 + """ + try: + # 验证并转换参数 + target_position = float(position) + velocity = float(max_velocity) if max_velocity is not None else self._max_velocity + + # 限制位置在有效范围内 + target_position = max(0.0, min(float(self.max_volume), target_position)) + + # 计算移动距离和时间 + volume_to_move = abs(target_position - self._position) + duration = self._calculate_duration(volume_to_move, velocity) + + self.logger.info(f"SET_POSITION: Moving to {target_position} ml (current: {self._position} ml), velocity: {velocity} ml/s") + + # 模拟移动过程 + start_position = self._position + steps = 10 if duration > 0.1 else 1 # 如果移动距离很小，只用1步 + step_duration = duration / steps if steps > 1 else duration + + for i in range(steps + 1): + # 计算当前位置和进度 + progress = (i / steps) * 100 if steps > 0 else 100 + current_pos = start_position + (target_position - start_position) * (i / steps) if steps > 0 else target_position + + # 更新状态 + self._status = "Moving" if i < steps else "Idle" + self._position = current_pos + self._current_volume = current_pos + + # 等待一小步时间 + if i < steps and step_duration > 0: + await asyncio.sleep(step_duration) + + # 确保最终位置准确 + self._position = target_position + self._current_volume = target_position + self._status = "Idle" + + self.logger.info(f"SET_POSITION: Reached position {self._position} ml, current volume: {self._current_volume} ml") + + # 返回符合action定义的结果 + return { + "success": True, + "message": f"Successfully moved to position {self._position} ml" + } + + except Exception as e: + error_msg = f"Failed to set position: {str(e)}" + self.logger.error(error_msg) + return { + "success": False, + "message": error_msg + } - @property - def current_status(self) -> str: - return self.data.get("current_status", "Ready") \ No newline at end of file + # 其他泵操作方法 + async def pull_plunger(self, volume: float, velocity: float = None): + """ + 拉取柱塞（吸液） + + Args: + volume (float): 要拉取的体积 (ml) + velocity (float): 拉取速度 (ml/s) + """ + new_position = min(self.max_volume, self._position + volume) + actual_volume = new_position - self._position + + if actual_volume <= 0: + self.logger.warning("Cannot pull - already at maximum volume") + return + + duration = self._calculate_duration(actual_volume, velocity) + + self.logger.info(f"Pulling {actual_volume} ml (from {self._position} to {new_position})") + + await self._simulate_operation(duration) + + self._position = new_position + self._current_volume = new_position + + self.logger.info(f"Pulled {actual_volume} ml, current volume: {self._current_volume} ml") + + async def push_plunger(self, volume: float, velocity: float = None): + """ + 推出柱塞（排液） + + Args: + volume (float): 要推出的体积 (ml) + velocity (float): 推出速度 (ml/s) + """ + new_position = max(0, self._position - volume) + actual_volume = self._position - new_position + + if actual_volume <= 0: + self.logger.warning("Cannot push - already at minimum volume") + return + + duration = self._calculate_duration(actual_volume, velocity) + + self.logger.info(f"Pushing {actual_volume} ml (from {self._position} to {new_position})") + + await self._simulate_operation(duration) + + self._position = new_position + self._current_volume = new_position + + self.logger.info(f"Pushed {actual_volume} ml, current volume: {self._current_volume} ml") + + # 便捷操作方法 + async def aspirate(self, volume: float, velocity: float = None): + """吸液操作""" + await self.pull_plunger(volume, velocity) + + async def dispense(self, volume: float, velocity: float = None): + """排液操作""" + await self.push_plunger(volume, velocity) + + async def transfer(self, volume: float, aspirate_velocity: float = None, dispense_velocity: float = None): + """转移操作（先吸后排）""" + # 吸液 + await self.aspirate(volume, aspirate_velocity) + + # 短暂停顿 + await asyncio.sleep(0.1) + + # 排液 + await self.dispense(volume, dispense_velocity) + + async def empty_syringe(self, velocity: float = None): + """清空注射器""" + await self.set_position(0, velocity) + + async def fill_syringe(self, velocity: float = None): + """充满注射器""" + await self.set_position(self.max_volume, velocity) + + async def stop_operation(self): + """停止当前操作""" + self._status = "Idle" + self.logger.info("Operation stopped") + + # 状态查询方法 + def get_position(self) -> float: + """获取当前位置""" + return self._position + + def get_current_volume(self) -> float: + """获取当前体积""" + return self._current_volume + + def get_remaining_capacity(self) -> float: + """获取剩余容量""" + return self.max_volume - self._current_volume + + def is_empty(self) -> bool: + """检查是否为空""" + return self._current_volume <= 0.01 # 允许小量误差 + + def is_full(self) -> bool: + """检查是否已满""" + return self._current_volume >= (self.max_volume - 0.01) # 允许小量误差 + + # 调试和状态信息 + def get_pump_info(self) -> dict: + """获取泵的详细信息""" + return { + "device_id": self.device_id, + "status": self._status, + "position": self._position, + "current_volume": self._current_volume, + "max_volume": self.max_volume, + "max_velocity": self._max_velocity, + "mode": self.mode.name, + "is_empty": self.is_empty(), + "is_full": self.is_full(), + "remaining_capacity": self.get_remaining_capacity() + } + + def __str__(self): + return f"VirtualTransferPump({self.device_id}: {self._current_volume:.2f}/{self.max_volume} ml, {self._status})" + + def __repr__(self): + return self.__str__() + + +# 使用示例 +async def demo(): + """虚拟泵使用示例""" + pump = VirtualTransferPump("demo_pump", {"max_volume": 50.0}) + + await pump.initialize() + + print(f"Initial state: {pump}") + + # 测试set_position方法 + result = await pump.set_position(10.0, max_velocity=2.0) + print(f"Set position result: {result}") + print(f"After setting position to 10ml: {pump}") + + # 吸液测试 + await pump.aspirate(5.0, velocity=2.0) + print(f"After aspirating 5ml: {pump}") + + # 清空测试 + result = await pump.set_position(0.0) + print(f"Empty result: {result}") + print(f"After emptying: {pump}") + + print("\nPump info:", pump.get_pump_info()) + + +if __name__ == "__main__": + asyncio.run(demo()) diff --git a/unilabos/devices/virtual/virtual_vacuum_pump.py b/unilabos/devices/virtual/virtual_vacuum_pump.py new file mode 100644 index 00000000..ec355b68 --- /dev/null +++ b/unilabos/devices/virtual/virtual_vacuum_pump.py @@ -0,0 +1,47 @@ +import asyncio +import time +from typing import Dict, Any, Optional + + +class VirtualVacuumPump: + """Virtual vacuum pump for testing""" + + def __init__(self, device_id: Optional[str] = None, config: Optional[Dict[str, Any]] = None, **kwargs): + self.device_id = device_id or "unknown_vacuum_pump" + self.config = config or {} + self.data = {} + self._status = "OPEN" + + async def initialize(self) -> bool: + """Initialize virtual vacuum pump""" + self.data.update({ + "status": self._status + }) + return True + + async def cleanup(self) -> bool: + """Cleanup virtual vacuum pump""" + return True + + @property + def status(self) -> str: + return self._status + + def get_status(self) -> str: + return self._status + + def set_status(self, string): + self._status = string + time.sleep(5) + + def open(self): + self._status = "OPEN" + + def close(self): + self._status = "CLOSED" + + def is_open(self): + return self._status + + def is_closed(self): + return not self._status \ No newline at end of file diff --git a/unilabos/messages/__init__.py b/unilabos/messages/__init__.py index 883b9ad8..16947e69 100644 --- a/unilabos/messages/__init__.py +++ b/unilabos/messages/__init__.py @@ -33,19 +33,19 @@ class CleanProtocol(BaseModel): class SeparateProtocol(BaseModel): - purpose: str # 'wash' or 'extract'. 'wash' means that product phase will not be the added solvent phase, 'extract' means product phase will be the added solvent phase. If no solvent is added just use 'extract'. - product_phase: str # 'top' or 'bottom'. Phase that product will be in. - from_vessel: str #Contents of from_vessel are transferred to separation_vessel and separation is performed. - separation_vessel: str # Vessel in which separation of phases will be carried out. - to_vessel: str # Vessel to send product phase to. - waste_phase_to_vessel: str # Optional. Vessel to send waste phase to. - solvent: str # Optional. Solvent to add to separation vessel after contents of from_vessel has been transferred to create two phases. - solvent_volume: float # Optional. Volume of solvent to add. - through: str # Optional. Solid chemical to send product phase through on way to to_vessel, e.g. 'celite'. - repeats: int # Optional. Number of separations to perform. - stir_time: float # Optional. Time stir for after adding solvent, before separation of phases. - stir_speed: float # Optional. Speed to stir at after adding solvent, before separation of phases. - settling_time: float # Optional. Time + purpose: str + product_phase: str + from_vessel: str + separation_vessel: str + to_vessel: str + waste_phase_to_vessel: str + solvent: str + solvent_volume: float + through: str + repeats: int + stir_time: float + stir_speed: float + settling_time: float class EvaporateProtocol(BaseModel): @@ -67,6 +67,7 @@ class AGVTransferProtocol(BaseModel): to_repo: dict from_repo_position: str to_repo_position: str + #=============新添加的新的协议================ class AddProtocol(BaseModel): vessel: str @@ -84,16 +85,16 @@ class CentrifugeProtocol(BaseModel): vessel: str speed: float time: float - temp: float # 移除默认值 + temp: float class FilterProtocol(BaseModel): vessel: str - filtrate_vessel: str # 移除默认值 - stir: bool # 移除默认值 - stir_speed: float # 移除默认值 - temp: float # 移除默认值 - continue_heatchill: bool # 移除默认值 - volume: float # 移除默认值 + filtrate_vessel: str + stir: bool + stir_speed: float + temp: float + continue_heatchill: bool + volume: float class HeatChillProtocol(BaseModel): vessel: str @@ -137,45 +138,53 @@ class TransferProtocol(BaseModel): solid: bool = False class CleanVesselProtocol(BaseModel): - vessel: str # 要清洗的容器名称 - solvent: str # 用于清洗容器的溶剂名称 - volume: float # 清洗溶剂的体积，可选参数 - temp: float # 清洗时的温度，可选参数 - repeats: int = 1 # 清洗操作的重复次数，默认为 1 + vessel: str + solvent: str + volume: float + temp: float + repeats: int = 1 class DissolveProtocol(BaseModel): - vessel: str # 装有要溶解物质的容器名称 - solvent: str # 用于溶解物质的溶剂名称 - volume: float # 溶剂的体积，可选参数 - amount: str = "" # 要溶解物质的量，可选参数 - temp: float = 25.0 # 溶解时的温度，可选参数 - time: float = 0.0 # 溶解的时间，可选参数 - stir_speed: float = 0.0 # 搅拌速度，可选参数 + vessel: str + solvent: str + volume: float + amount: str = "" + temp: float = 25.0 + time: float = 0.0 + stir_speed: float = 0.0 class FilterThroughProtocol(BaseModel): - from_vessel: str # 源容器的名称，即物质起始所在的容器 - to_vessel: str # 目标容器的名称，物质过滤后要到达的容器 - filter_through: str # 过滤时所通过的介质，如滤纸、柱子等 - eluting_solvent: str = "" # 洗脱溶剂的名称，可选参数 - eluting_volume: float = 0.0 # 洗脱溶剂的体积，可选参数 - eluting_repeats: int = 0 # 洗脱操作的重复次数，默认为 0 - residence_time: float = 0.0 # 物质在过滤介质中的停留时间，可选参数 + from_vessel: str + to_vessel: str + filter_through: str + eluting_solvent: str = "" + eluting_volume: float = 0.0 + eluting_repeats: int = 0 + residence_time: float = 0.0 class RunColumnProtocol(BaseModel): - from_vessel: str # 源容器的名称，即样品起始所在的容器 - to_vessel: str # 目标容器的名称，分离后的样品要到达的容器 - column: str # 所使用的柱子的名称 + from_vessel: str + to_vessel: str + column: str class WashSolidProtocol(BaseModel): - vessel: str # 装有固体物质的容器名称 - solvent: str # 用于清洗固体的溶剂名称 - volume: float # 清洗溶剂的体积 - filtrate_vessel: str = "" # 滤液要收集到的容器名称，可选参数 - temp: float = 25.0 # 清洗时的温度，可选参数 - stir: bool = False # 是否在清洗过程中搅拌，默认为 False - stir_speed: float = 0.0 # 搅拌速度，可选参数 - time: float = 0.0 # 清洗的时间，可选参数 - repeats: int = 1 # 清洗操作的重复次数，默认为 1 - -__all__ = ["Point3D", "PumpTransferProtocol", "CleanProtocol", "SeparateProtocol", "EvaporateProtocol", "EvacuateAndRefillProtocol", "AGVTransferProtocol", "CentrifugeProtocol", "AddProtocol", "FilterProtocol", "HeatChillProtocol", "HeatChillStartProtocol", "HeatChillStopProtocol", "StirProtocol", "StartStirProtocol", "StopStirProtocol", "TransferProtocol", "CleanVesselProtocol", "DissolveProtocol", "FilterThroughProtocol", "RunColumnProtocol", "WashSolidProtocol"] + vessel: str + solvent: str + volume: float + filtrate_vessel: str = "" + temp: float = 25.0 + stir: bool = False + stir_speed: float = 0.0 + time: float = 0.0 + repeats: int = 1 + +__all__ = [ + "Point3D", "PumpTransferProtocol", "CleanProtocol", "SeparateProtocol", + "EvaporateProtocol", "EvacuateAndRefillProtocol", "AGVTransferProtocol", + "CentrifugeProtocol", "AddProtocol", "FilterProtocol", + "HeatChillProtocol", "HeatChillStartProtocol", "HeatChillStopProtocol", + "StirProtocol", "StartStirProtocol", "StopStirProtocol", + "TransferProtocol", "CleanVesselProtocol", "DissolveProtocol", + "FilterThroughProtocol", "RunColumnProtocol", "WashSolidProtocol" +] # End Protocols diff --git a/unilabos/registry/devices/mock_devices.yaml b/unilabos/registry/devices/mock_devices.yaml index 59760469..93f52a85 100644 --- a/unilabos/registry/devices/mock_devices.yaml +++ b/unilabos/registry/devices/mock_devices.yaml @@ -89,7 +89,7 @@ mock_filter: target_volume: Float64 action_value_mappings: filter: - type: ProtocolFilter + type: Filter goal: vessel: vessel filtrate_vessel: filtrate_vessel @@ -737,7 +737,7 @@ mock_stirrer_new: max_stir_speed: Float64 action_value_mappings: start_stir: - type: ProtocolStartStir + type: StartStir goal: vessel: vessel stir_speed: stir_speed @@ -760,7 +760,7 @@ mock_stirrer_new: result: success: success stop_stir: - type: ProtocolStopStir + type: StopStir goal: vessel: vessel feedback: diff --git a/unilabos/registry/devices/pump_and_valve.yaml b/unilabos/registry/devices/pump_and_valve.yaml index 120ff455..651a25f8 100644 --- a/unilabos/registry/devices/pump_and_valve.yaml +++ b/unilabos/registry/devices/pump_and_valve.yaml @@ -48,14 +48,16 @@ solenoid_valve.mock: feedback: {} result: {} handles: - input: - - handler_key: fluid-input - label: Fluid Input + - handler_key: in + label: in + io_type: target data_type: fluid - output: - - handler_key: fluid-output - label: Fluid Output + side: NORTH + - handler_key: out + label: out + io_type: source data_type: fluid + side: SOUTH init_param_schema: type: object properties: diff --git a/unilabos/registry/devices/vacuum_and_purge.yaml b/unilabos/registry/devices/vacuum_and_purge.yaml index 6bdff16b..84fb58cf 100644 --- a/unilabos/registry/devices/vacuum_and_purge.yaml +++ b/unilabos/registry/devices/vacuum_and_purge.yaml @@ -23,20 +23,12 @@ vacuum_pump.mock: feedback: {} result: {} handles: - input: - - handler_key: fluid-input - label: Fluid Input + - handler_key: out + label: out data_type: fluid - io_type: target + io_type: source data_source: handle data_key: fluid_in - output: - - handler_key: fluid-output - label: Fluid Output - data_type: fluid - io_type: source - data_source: executor - data_key: fluid_out init_param_schema: type: object properties: @@ -72,16 +64,8 @@ gas_source.mock: feedback: {} result: {} handles: - input: - - handler_key: fluid-input - label: Fluid Input - data_type: fluid - io_type: target - data_source: handle - data_key: fluid_in - output: - - handler_key: fluid-output - label: Fluid Output + - handler_key: out + label: out data_type: fluid io_type: source data_source: executor diff --git a/unilabos/registry/devices/virtual_device.yaml b/unilabos/registry/devices/virtual_device.yaml index f92baf29..26d620da 100644 --- a/unilabos/registry/devices/virtual_device.yaml +++ b/unilabos/registry/devices/virtual_device.yaml @@ -1,3 +1,70 @@ +# 虚拟设备清单及连接特性 + +# 1. virtual_pump - 虚拟泵 +# 描述：具有多通道阀门特性的泵，根据valve_position可连接多个容器 +# 连接特性：1个输入口 + 1个输出口 +# 数据类型：fluid（流体连接） + +# 2. virtual_stirrer - 虚拟搅拌器 +# 描述：机械连接设备，提供搅拌功能 +# 连接特性：1个连接点 +# 数据类型：mechanical（机械连接） + +# 3a. virtual_valve - 虚拟八通阀门 +# 描述：8通阀门，可切换流向 +# 连接特性：1个口连接注射泵 + 多个输出口 +# 数据类型：fluid（流体连接） + +# 3b. virtual_solenoid_valve (电磁阀门) +# 描述：简单的开关型电磁阀，只有开启和关闭两个状态 +# 连接特性：1个输入口 + 1个输出口，控制通断 +# 数据类型：fluid（流体连接） + +# 4. virtual_centrifuge - 虚拟离心机 +# 描述：单个样品处理设备，原地处理样品 +# 连接特性：1个输入口 + 1个输出口 +# 数据类型：resource（资源/样品连接） + +# 5. virtual_filter - 虚拟过滤器 +# 描述：分离设备，将样品分离为滤液和滤渣 +# 连接特性：1个输入口 + 2个输出口（滤液和滤渣） +# 数据类型：resource（资源/样品连接） + +# 6. virtual_heatchill - 虚拟加热/冷却器 +# 描述：温控设备，容器直接放置在设备上进行温度控制 +# 连接特性：1个连接点 +# 数据类型：mechanical（机械/物理接触连接） + +# 7. virtual_transfer_pump - 虚拟转移泵（注射器式） +# 描述：注射器式转移泵，通过同一个口吸入和排出液体 +# 连接特性：1个连接点 +# 数据类型：fluid（流体连接） + +# 8. virtual_column - 虚拟色谱柱 +# 描述：分离纯化设备，用于样品纯化 +# 连接特性：1个输入口 + 1个输出口 +# 数据类型：resource（资源/样品连接） + +# 9. virtual_rotavap - 虚拟旋转蒸发仪 +# 描述：旋转蒸发仪用于溶剂蒸发和浓缩，具有加热、旋转和真空功能 +# 连接特性：1个输入口（样品），1个输出口（浓缩物），1个冷凝器出口（回收溶剂） +# 数据类型：resource（资源/样品连接） + +# 10. virtual_separator - 虚拟分液器 +# 描述：分液器用于两相液体的分离，可进行萃取和洗涤操作 +# 连接特性：1个输入口（混合液），2个输出口（上相和下相） +# 数据类型：fluid（流体连接） + +# 11. virtual_vacuum_pump - 虚拟真空泵 +# 描述：真空泵设备，用于抽真空操作和真空/充气循环 +# 连接特性：1个输出口（连接需要抽真空的系统） +# 数据类型：fluid（流体连接） + +# 12. virtual_gas_source - 虚拟气源 +# 描述：气源设备，用于充气操作和真空/充气循环 +# 连接特性：1个输出口（向系统提供加压气体） +# 数据类型：fluid（流体连接） + virtual_pump: description: Virtual Pump for PumpTransferProtocol Testing class: @@ -6,7 +73,7 @@ virtual_pump: status_types: status: String position: Float64 - valve_position: Int32 # 修复：使用 Int32 而不是 String + valve_position: Int32 max_volume: Float64 current_volume: Float64 action_value_mappings: @@ -30,11 +97,19 @@ virtual_pump: set_valve_position: type: FloatSingleInput goal: - Int32: Int32 + float_in: valve_position feedback: status: status result: success: success + handles: + - handler_key: pumpio + label: pumpio + data_type: fluid + io_type: source + data_source: handle + data_key: fluid_in + description: "泵的输出口" schema: type: object properties: @@ -48,11 +123,17 @@ virtual_pump: virtual_stirrer: description: Virtual Stirrer for StirProtocol Testing + icon: Stirrer.webp class: module: unilabos.devices.virtual.virtual_stirrer:VirtualStirrer type: python status_types: status: String + operation_mode: String + current_vessel: String + current_speed: Float64 + is_stirring: Bool + remaining_time: Float64 action_value_mappings: stir: type: Stir @@ -65,7 +146,7 @@ virtual_stirrer: result: success: success start_stir: - type: ProtocolStartStir + type: StartStir goal: vessel: vessel stir_speed: stir_speed @@ -75,31 +156,41 @@ virtual_stirrer: result: success: success stop_stir: - type: ProtocolStopStir + type: StopStir goal: vessel: vessel feedback: status: status result: success: success + handles: + - handler_key: stirrer + label: stirrer + data_type: mechanical + side: NORTH + io_type: source + data_source: handle + data_key: vessel + description: "搅拌器的机械连接口" schema: type: object properties: port: type: string default: "VIRTUAL" - max_temp: - type: number - default: 100.0 max_speed: type: number - default: 1000.0 + default: 1500.0 + min_speed: + type: number + default: 50.0 additionalProperties: false -virtual_valve: - description: Virtual Valve for AddProtocol Testing +virtual_multiway_valve: + description: Virtual 8-Way Valve for flow direction control + icon: EightPipeline.webp class: - module: unilabos.devices.virtual.virtual_valve:VirtualValve + module: unilabos.devices.virtual.virtual_multiway_valve:VirtualMultiwayValve type: python status_types: status: String @@ -111,31 +202,168 @@ virtual_valve: set_position: type: SendCmd goal: - command: position + command: command + feedback: {} + result: + success: success + set_valve_position: + type: SendCmd + goal: + command: command + feedback: {} + result: + success: success + handles: + - handler_key: transferpump + label: transferpump + data_type: fluid + side: NORTH + io_type: target + data_source: handle + data_key: fluid_in + description: "八通阀门进液口" + - handler_key: 1 + label: 1 + data_type: fluid + side: NORTH + io_type: source + data_source: executor + data_key: fluid_port_1 + description: "八通阀门端口1" + - handler_key: 2 + label: 2 + data_type: fluid + side: EAST + io_type: source + data_source: executor + data_key: fluid_port_2 + description: "八通阀门端口2" + - handler_key: 3 + label: 3 + data_type: fluid + side: EAST + io_type: source + data_source: executor + data_key: fluid_port_3 + description: "八通阀门端口3" + - handler_key: 4 + label: 4 + data_type: fluid + side: SOUTH + io_type: source + data_source: executor + data_key: fluid_port_4 + description: "八通阀门端口4" + - handler_key: 5 + label: 5 + data_type: fluid + side: SOUTH + io_type: source + data_source: executor + data_key: fluid_port_5 + description: "八通阀门端口5" + - handler_key: 6 + label: 6 + data_type: fluid + side: WEST + io_type: source + data_source: executor + data_key: fluid_port_6 + description: "八通阀门端口6" + - handler_key: 7 + label: 7 + data_type: fluid + side: WEST + io_type: source + data_source: executor + data_key: fluid_port_7 + description: "八通阀门端口7" + - handler_key: 8 + label: 8 + data_type: fluid + side: NORTH + io_type: source + data_source: executor + data_key: fluid_port_8 + description: "八通阀门端口8" + schema: + type: object + properties: + port: + type: string + default: "VIRTUAL" + positions: + type: integer + default: 8 + additionalProperties: false + +virtual_solenoid_valve: + description: Virtual Solenoid Valve for simple on/off flow control + class: + module: unilabos.devices.virtual.virtual_solenoid_valve:VirtualSolenoidValve + type: python + status_types: + status: String + valve_state: String + is_open: Bool + action_value_mappings: + set_valve_position: + type: SendCmd + goal: + command: command feedback: {} result: success: success open: - type: EmptyIn - goal: {} + type: SendCmd + goal: + command: "OPEN" feedback: {} result: success: success close: - type: EmptyIn - goal: {} + type: SendCmd + goal: + command: "CLOSED" feedback: {} result: success: success + set_state: + type: SendCmd + goal: + command: command + feedback: {} + result: + success: success + handles: + - handler_key: in + label: in + data_type: fluid + side: NORTH + io_type: target + data_source: handle + data_key: fluid_port_in + description: "电磁阀的进液口" + - handler_key: out + label: out + data_type: fluid + side: SOUTH + io_type: source + data_source: handle + data_key: fluid_port_out + description: "电磁阀的出液口" schema: type: object properties: port: type: string default: "VIRTUAL" - positions: - type: integer - default: 6 + voltage: + type: number + default: 12.0 + response_time: + type: number + default: 0.1 additionalProperties: false virtual_centrifuge: @@ -154,9 +382,11 @@ virtual_centrifuge: min_temp: Float64 centrifuge_state: String time_remaining: Float64 + progress: Float64 + message: String action_value_mappings: centrifuge: - type: ProtocolCentrifuge + type: Centrifuge goal: vessel: vessel speed: speed @@ -170,6 +400,15 @@ virtual_centrifuge: result: success: success message: message + handles: + - handler_key: centrifuge + label: centrifuge + data_type: transport + side: NORTH + io_type: target + data_source: handle + data_key: vessel + description: "需要离心的样品容器" schema: type: object properties: @@ -194,18 +433,17 @@ virtual_filter: type: python status_types: status: String - filter_state: String + progress: Float64 current_temp: Float64 - target_temp: Float64 - max_temp: Float64 - stir_speed: Float64 - max_stir_speed: Float64 filtered_volume: Float64 - progress: Float64 + current_status: String message: String + max_temp: Float64 + max_stir_speed: Float64 + max_volume: Float64 action_value_mappings: - filter_sample: - type: ProtocolFilter + filter: + type: Filter goal: vessel: vessel filtrate_vessel: filtrate_vessel @@ -218,10 +456,36 @@ virtual_filter: progress: progress current_temp: current_temp filtered_volume: filtered_volume - current_status: status + current_status: current_status result: success: success message: message + return_info: message + handles: + - handler_key: filter_in + label: filter_in + data_type: transport + side: NORTH + io_type: target + data_source: handle + data_key: vessel_in + description: "需要过滤的样品容器" + - handler_key: filtrate_out + label: filtrate_out + data_type: transport + side: SOUTH + io_type: source + data_source: handle + data_key: filtrate_out + description: "滤液出口" + - handler_key: retentate_out + label: retentate_out + data_type: transport + side: EAST + io_type: source + data_source: handle + data_key: retentate_out + description: "滤渣/固体出口" schema: type: object properties: @@ -234,15 +498,22 @@ virtual_filter: max_stir_speed: type: number default: 1000.0 + max_volume: + type: number + default: 500.0 additionalProperties: false virtual_heatchill: description: Virtual HeatChill for HeatChillProtocol Testing + icon: Heater.webp class: module: unilabos.devices.virtual.virtual_heatchill:VirtualHeatChill type: python status_types: status: String + operation_mode: String + is_stirring: Bool + stir_speed: Float64 action_value_mappings: heat_chill: type: HeatChill @@ -275,6 +546,15 @@ virtual_heatchill: status: status result: success: success + handles: + - handler_key: heatchill + label: heatchill + data_type: mechanical + side: NORTH + io_type: source + data_source: handle + data_key: vessel + description: "加热/冷却器的物理连接口" schema: type: object properties: @@ -286,14 +566,15 @@ virtual_heatchill: default: 200.0 min_temp: type: number - default: -80.0 + default: -80 max_stir_speed: type: number default: 1000.0 additionalProperties: false virtual_transfer_pump: - description: Virtual Transfer Pump for TransferProtocol Testing + description: Virtual Transfer Pump for TransferProtocol Testing (Syringe-style) + icon: Pump.webp class: module: unilabos.devices.virtual.virtual_transferpump:VirtualTransferPump type: python @@ -302,14 +583,10 @@ virtual_transfer_pump: current_volume: Float64 max_volume: Float64 transfer_rate: Float64 - from_vessel: String - to_vessel: String - progress: Float64 - transferred_volume: Float64 - current_status: String + position: Float64 action_value_mappings: transfer: - type: ProtocolTransfer + type: Transfer goal: from_vessel: from_vessel to_vessel: to_vessel @@ -328,22 +605,46 @@ virtual_transfer_pump: result: success: success message: message + set_position: + type: SetPumpPosition + goal: + position: position + max_velocity: max_velocity + feedback: + status: status + current_position: current_position + progress: progress + result: + success: success + message: message + handles: + - handler_key: transferpump + label: transferpump + data_type: fluid + side: SOUTH + io_type: source + data_source: handle + data_key: fluid_port + description: "注射器式转移泵的连接口" schema: type: object properties: port: type: string default: "VIRTUAL" + description: "通信端口" max_volume: type: number default: 50.0 + description: "最大注射器容量 (mL)" transfer_rate: type: number default: 5.0 + description: "默认转移速率 (mL/s)" additionalProperties: false virtual_column: - description: Virtual Column for RunColumn Protocol Testing + description: Virtual Column Chromatography Device for RunColumn Protocol Testing class: module: unilabos.devices.virtual.virtual_column:VirtualColumn type: python @@ -359,17 +660,36 @@ virtual_column: current_status: String action_value_mappings: run_column: - type: ProtocolRunColumn + type: RunColumn goal: from_vessel: from_vessel to_vessel: to_vessel column: column feedback: - status: current_status progress: progress + processed_volume: processed_volume + current_status: current_status result: success: success - message: message + message: current_status + return_info: current_status + handles: + - handler_key: columnin + label: columnin + data_type: transport + side: WEST + io_type: target + data_source: handle + data_key: from_vessel + description: "样品输入口" + - handler_key: columnout + label: columnout + data_type: transport + side: EAST + io_type: source + data_source: handle + data_key: to_vessel + description: "产物输出口" schema: type: object properties: @@ -385,4 +705,249 @@ virtual_column: column_diameter: type: number default: 2.0 + additionalProperties: false + +virtual_rotavap: + description: Virtual Rotary Evaporator for EvaporateProtocol Testing + icon: Rotaryevaporator.webp + class: + module: unilabos.devices.virtual.virtual_rotavap:VirtualRotavap + type: python + status_types: + status: String + rotavap_state: String + current_temp: Float64 + rotation_speed: Float64 + vacuum_pressure: Float64 + evaporated_volume: Float64 + progress: Float64 + remaining_time: Float64 + message: String + max_temp: Float64 + max_rotation_speed: Float64 + action_value_mappings: + evaporate: + type: Evaporate + goal: + vessel: vessel + pressure: pressure + temp: temp + time: time + stir_speed: stir_speed + feedback: + progress: progress + current_temp: current_temp + evaporated_volume: evaporated_volume + status: status + result: + success: success + message: message + handles: + - handler_key: sample_in + label: sample_in + data_type: fluid + side: NORTH + io_type: target + data_source: handle + data_key: vessel_in + description: "样品连接口" + - handler_key: product_out + label: product_out + data_type: fluid + side: SOUTH + io_type: source + data_source: handle + data_key: product_out + description: "浓缩产物出口" + - handler_key: solvent_out + label: solvent_out + data_type: fluid + side: EAST + io_type: source + data_source: handle + data_key: solvent_out + description: "冷凝溶剂出口" + schema: + type: object + properties: + port: + type: string + default: "VIRTUAL" + max_temp: + type: number + default: 180.0 + max_rotation_speed: + type: number + default: 280.0 + additionalProperties: false + +virtual_separator: + description: Virtual Separator for SeparateProtocol Testing + icon: Separator.webp + class: + module: unilabos.devices.virtual.virtual_separator:VirtualSeparator + type: python + status_types: + status: String + separator_state: String + volume: Float64 + has_phases: Bool + phase_separation: Bool + stir_speed: Float64 + settling_time: Float64 + progress: Float64 + message: String + action_value_mappings: + separate: + type: Separate + goal: + purpose: purpose + product_phase: product_phase + from_vessel: from_vessel + separation_vessel: separation_vessel + to_vessel: to_vessel + waste_phase_to_vessel: waste_phase_to_vessel + solvent: solvent + solvent_volume: solvent_volume + through: through + repeats: repeats + stir_time: stir_time + stir_speed: stir_speed + settling_time: settling_time + feedback: + progress: progress + current_status: status + result: + success: success + message: message + handles: + - handler_key: separator_in + label: separator_in + data_type: fluid + side: NORTH + io_type: target + data_source: handle + data_key: from_vessel + description: "需要分离的混合液体输入口" + - handler_key: bottom_phase_out + label: bottom_phase_out + data_type: fluid + side: SOUTH + io_type: source + data_source: executor + data_key: bottom_outlet + description: "下相（重相）液体输出口" + - handler_key: top_phase_out + label: top_phase_out + data_type: fluid + side: EAST + io_type: source + data_source: executor + data_key: top_outlet + description: "上相（轻相）液体输出口" + schema: + type: object + properties: + port: + type: string + default: "VIRTUAL" + volume: + type: number + default: 250.0 + has_phases: + type: boolean + default: true + additionalProperties: false + +virtual_vacuum_pump: + description: Virtual vacuum pump + icon: Vacuum.webp + class: + module: unilabos.devices.virtual.virtual_vacuum_pump:VirtualVacuumPump + type: python + status_types: + status: String + action_value_mappings: + open: + type: EmptyIn + goal: {} + feedback: {} + result: {} + close: + type: EmptyIn + goal: {} + feedback: {} + result: {} + set_status: + type: StrSingleInput + goal: + string: string + feedback: {} + result: {} + handles: + - handler_key: vacuumpump + label: vacuumpump + data_type: fluid + side: SOUTH + io_type: source + data_source: handle + data_key: fluid_in + description: "真空泵进气口" + schema: + type: object + properties: + port: + type: string + default: "VIRTUAL" + description: "通信端口" + additionalProperties: false + +virtual_gas_source: + description: Virtual gas source + class: + module: unilabos.devices.virtual.virtual_gas_source:VirtualGasSource + type: python + status_types: + status: String + action_value_mappings: + open: + type: EmptyIn + goal: {} + feedback: {} + result: {} + close: + type: EmptyIn + goal: {} + feedback: {} + result: {} + set_status: + type: StrSingleInput + goal: + string: string + feedback: {} + result: {} + handles: + - handler_key: gassource + label: gassource + data_type: fluid + side: SOUTH + io_type: source + data_source: executor + data_key: fluid_out + description: "气源出气口" + schema: + type: object + properties: + port: + type: string + default: "VIRTUAL" + description: "通信端口" + gas_type: + type: string + default: "nitrogen" + description: "气体类型" + max_pressure: + type: number + default: 5.0 + description: "最大输出压力 (bar)" additionalProperties: false \ No newline at end of file diff --git a/unilabos/registry/resources/opentrons/container.yaml b/unilabos/registry/resources/opentrons/container.yaml deleted file mode 100644 index c64b45f9..00000000 --- a/unilabos/registry/resources/opentrons/container.yaml +++ /dev/null @@ -1,5 +0,0 @@ -container: - description: regular organic container - class: - module: unilabos.resources.container:RegularContainer - type: unilabos diff --git a/unilabos/registry/resources/organic/container.yaml b/unilabos/registry/resources/organic/container.yaml new file mode 100644 index 00000000..bfdcba90 --- /dev/null +++ b/unilabos/registry/resources/organic/container.yaml @@ -0,0 +1,27 @@ +container: + description: regular organic container + class: + module: unilabos.resources.container:RegularContainer + type: unilabos + handles: + - handler_key: top + label: top + io_type: target + data_type: fluid + side: NORTH + data_source: handle + data_key: fluid_in + - handler_key: bottom + label: bottom + io_type: source + data_type: fluid + side: SOUTH + data_source: handle + data_key: fluid_out + - handler_key: bind + label: bind + io_type: target + data_type: mechanical + side: SOUTH + data_source: handle + data_key: mechanical_port \ No newline at end of file diff --git a/unilabos/resources/graphio.py b/unilabos/resources/graphio.py index 734e5091..3ed2e36f 100644 --- a/unilabos/resources/graphio.py +++ b/unilabos/resources/graphio.py @@ -1,7 +1,7 @@ import importlib import inspect import json -from typing import Union +from typing import Union, Any import numpy as np import networkx as nx from unilabos_msgs.msg import Resource @@ -84,6 +84,8 @@ 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": + link["type"] = "fluid" if isinstance(port, int): port = str(port) if isinstance(port, str): @@ -157,7 +159,27 @@ def read_node_link_json(json_file): physical_setup_graph = nx.node_link_graph(data, multigraph=False) # edges="links" 3.6 warning handle_communications(physical_setup_graph) - return physical_setup_graph + return physical_setup_graph, data + + +def modify_to_backend_format(data: list[dict[str, Any]]) -> list[dict[str, Any]]: + for edge in data: + port = edge.pop("port", {}) + source = edge["source"] + target = edge["target"] + if source in port: + edge["sourceHandle"] = port[source] + elif "source_port" in edge: + edge["sourceHandle"] = edge.pop("source_port") + if target in port: + edge["targetHandle"] = port[target] + elif "target_port" in edge: + edge["targetHandle"] = edge.pop("target_port") + edge["id"] = f"reactflow__edge-{source}-{edge['sourceHandle']}-{target}-{edge['targetHandle']}" + for key in ["source_port", "target_port"]: + if key in edge: + edge.pop(key) + return data def read_graphml(graphml_file): @@ -182,7 +204,7 @@ def read_graphml(graphml_file): physical_setup_graph = nx.node_link_graph(data, edges="links", multigraph=False) # edges="links" 3.6 warning handle_communications(physical_setup_graph) - return physical_setup_graph + return physical_setup_graph, data def dict_from_graph(graph: nx.Graph) -> dict: diff --git a/unilabos/ros/main_slave_run.py b/unilabos/ros/main_slave_run.py index bbd6359e..7ee26839 100644 --- a/unilabos/ros/main_slave_run.py +++ b/unilabos/ros/main_slave_run.py @@ -45,6 +45,7 @@ def exit() -> None: def main( devices_config: Dict[str, Any] = {}, resources_config: list=[], + resources_edge_config: list=[], graph: Optional[Dict[str, Any]] = None, controllers_config: Dict[str, Any] = {}, bridges: List[Any] = [], @@ -62,6 +63,7 @@ def main( "host_node", devices_config, resources_config, + resources_edge_config, graph, controllers_config, bridges, @@ -97,6 +99,7 @@ def main( def slave( devices_config: Dict[str, Any] = {}, resources_config=[], + resources_edge_config=[], graph: Optional[Dict[str, Any]] = None, controllers_config: Dict[str, Any] = {}, bridges: List[Any] = [], diff --git a/unilabos/ros/msgs/message_converter.py b/unilabos/ros/msgs/message_converter.py index 62ab606d..2bcaadb0 100644 --- a/unilabos/ros/msgs/message_converter.py +++ b/unilabos/ros/msgs/message_converter.py @@ -100,7 +100,7 @@ # 添加Protocol action类型到映射 for py_msgtype in imsg.__all__: - if py_msgtype not in _action_mapping and py_msgtype.endswith("Protocol"): + if py_msgtype not in _action_mapping and (py_msgtype.endswith("Protocol") or py_msgtype.startswith("Protocol")): try: protocol_class = msg_converter_manager.get_class(f"unilabos.messages.{py_msgtype}") action_name = py_msgtype.replace("Protocol", "") @@ -117,6 +117,7 @@ "result": {k: k for k in action_type.Result().get_fields_and_field_types().keys()}, } except Exception: + traceback.print_exc() logger.debug(f"Failed to load Protocol class: {py_msgtype}") # Python到ROS消息转换器 diff --git a/unilabos/ros/nodes/presets/host_node.py b/unilabos/ros/nodes/presets/host_node.py index fef9d640..66651651 100644 --- a/unilabos/ros/nodes/presets/host_node.py +++ b/unilabos/ros/nodes/presets/host_node.py @@ -22,6 +22,7 @@ ) # type: ignore from unique_identifier_msgs.msg import UUID +from unilabos.config.config import BasicConfig from unilabos.registry.registry import lab_registry from unilabos.resources.graphio import initialize_resource from unilabos.resources.registry import add_schema @@ -58,6 +59,7 @@ def __init__( device_id: str, devices_config: Dict[str, Any], resources_config: list, + resources_edge_config: list[dict], physical_setup_graph: Optional[Dict[str, Any]] = None, controllers_config: Optional[Dict[str, Any]] = None, bridges: Optional[List[Any]] = None, @@ -96,6 +98,7 @@ def __init__( self.server_latest_timestamp = 0.0 # self.devices_config = devices_config self.resources_config = resources_config + self.resources_edge_config = resources_edge_config self.physical_setup_graph = physical_setup_graph if controllers_config is None: controllers_config = {} @@ -144,13 +147,15 @@ def __init__( self.device_status = {} # 用来存储设备状态 self.device_status_timestamps = {} # 用来存储设备状态最后更新时间 + if BasicConfig.upload_registry: + from unilabos.app.mq import mqtt_client - from unilabos.app.mq import mqtt_client - - for device_info in lab_registry.obtain_registry_device_info(): - mqtt_client.publish_registry(device_info["id"], device_info) - for resource_info in lab_registry.obtain_registry_resource_info(): - mqtt_client.publish_registry(resource_info["id"], resource_info) + for device_info in lab_registry.obtain_registry_device_info(): + mqtt_client.publish_registry(device_info["id"], device_info) + for resource_info in lab_registry.obtain_registry_resource_info(): + mqtt_client.publish_registry(resource_info["id"], resource_info) + else: + self.lab_logger().warning("本次启动注册表不报送云端，如果您需要联网调试，请使用unilab-register命令进行单独报送，或者在启动命令增加--upload_registry") time.sleep(1) # 等待MQTT连接稳定 # 首次发现网络中的设备 self._discover_devices() @@ -191,24 +196,36 @@ def __init__( ) resource_with_parent_name = [] resource_ids_to_instance = {i["id"]: i for i in resources_config} + resource_name_to_with_parent_name = {} for res in resources_config: - if res.get("parent") and res.get("type") == "device" and res.get("class"): - parent_id = res.get("parent") - parent_res = resource_ids_to_instance[parent_id] - if parent_res.get("type") == "device" and parent_res.get("class"): - resource_with_parent_name.append(copy.deepcopy(res)) - resource_with_parent_name[-1]["id"] = f"{parent_res['id']}/{res['id']}" - continue + # if res.get("parent") and res.get("type") == "device" and res.get("class"): + # parent_id = res.get("parent") + # parent_res = resource_ids_to_instance[parent_id] + # if parent_res.get("type") == "device" and parent_res.get("class"): + # resource_with_parent_name.append(copy.deepcopy(res)) + # resource_name_to_with_parent_name[resource_with_parent_name[-1]["id"]] = f"{parent_res['id']}/{res['id']}" + # resource_with_parent_name[-1]["id"] = f"{parent_res['id']}/{res['id']}" + # continue resource_with_parent_name.append(copy.deepcopy(res)) + # for edge in self.resources_edge_config: + # edge["source"] = resource_name_to_with_parent_name.get(edge.get("source"), edge.get("source")) + # edge["target"] = resource_name_to_with_parent_name.get(edge.get("target"), edge.get("target")) try: for bridge in self.bridges: if hasattr(bridge, "resource_add"): + from unilabos.app.web.client import HTTPClient + client: HTTPClient = bridge resource_start_time = time.time() - resource_add_res = bridge.resource_add(add_schema(resource_with_parent_name), True) + resource_add_res = client.resource_add(add_schema(resource_with_parent_name), False) resource_end_time = time.time() self.lab_logger().info( f"[Host Node-Resource] 物料上传 {round(resource_end_time - resource_start_time, 5) * 1000} ms" ) + resource_add_res = client.resource_edge_add(self.resources_edge_config, False) + resource_edge_end_time = time.time() + self.lab_logger().info( + f"[Host Node-Resource] 物料关系上传 {round(resource_edge_end_time - resource_end_time, 5) * 1000} ms" + ) except Exception as ex: self.lab_logger().error("[Host Node-Resource] 添加物料出错！") self.lab_logger().error(traceback.format_exc()) @@ -757,8 +774,10 @@ def _resource_add_callback(self, request, response): self.lab_logger().info(f"[Host Node-Resource] Add request received: {len(resources)} resources") success = False - if len(self.bridges) > 0: - r = self.bridges[-1].resource_add(add_schema(resources)) + if len(self.bridges) > 0: # 边的提交待定 + from unilabos.app.web.client import HTTPClient + client: HTTPClient = self.bridges[-1] + r = client.resource_add(add_schema(resources), False) success = bool(r) response.success = success diff --git a/unilabos/ros/nodes/presets/protocol_node.py b/unilabos/ros/nodes/presets/protocol_node.py index 7b10e01d..4da8c62d 100644 --- a/unilabos/ros/nodes/presets/protocol_node.py +++ b/unilabos/ros/nodes/presets/protocol_node.py @@ -110,7 +110,8 @@ def _setup_protocol_names(self, protocol_type): def initialize_device(self, device_id, device_config): """初始化设备并创建相应的动作客户端""" - device_id_abs = f"{self.device_id}/{device_id}" + # device_id_abs = f"{self.device_id}/{device_id}" + device_id_abs = f"{device_id}" self.lab_logger().info(f"初始化子设备: {device_id_abs}") d = self.sub_devices[device_id] = initialize_device_from_dict(device_id_abs, device_config) @@ -213,7 +214,7 @@ async def execute_single_action(self, device_id, action_name, action_kwargs): if device_id in ["", None, "self"]: action_id = f"/devices/{self.device_id}/{action_name}" else: - action_id = f"/devices/{self.device_id}/{device_id}/{action_name}" + action_id = f"/devices/{device_id}/{action_name}" # 执行时取消了主节点信息 /{self.device_id} # 检查动作客户端是否存在 if action_id not in self._action_clients: diff --git a/unilabos_msgs/CMakeLists.txt b/unilabos_msgs/CMakeLists.txt index b818cf00..db641168 100644 --- a/unilabos_msgs/CMakeLists.txt +++ b/unilabos_msgs/CMakeLists.txt @@ -29,24 +29,24 @@ set(action_files "action/HeatChillStart.action" "action/HeatChillStop.action" - "action/ProtocolCleanVessel.action" - "action/ProtocolDissolve.action" - "action/ProtocolFilterThrough.action" - "action/ProtocolRunColumn.action" - "action/ProtocolWait.action" - "action/ProtocolWashSolid.action" - "action/ProtocolFilter.action" - - "action/ProtocolCentrifuge.action" - "action/ProtocolCrystallize.action" - "action/ProtocolDry.action" - "action/ProtocolPurge.action" - "action/ProtocolStartPurge.action" - "action/ProtocolStartStir.action" - "action/ProtocolStopPurge.action" - "action/ProtocolStopStir.action" - "action/ProtocolTransfer.action" - + "action/CleanVessel.action" + "action/Dissolve.action" + "action/FilterThrough.action" + "action/RunColumn.action" + "action/Wait.action" + "action/WashSolid.action" + "action/Filter.action" + "action/Add.action" + "action/Centrifuge.action" + "action/Crystallize.action" + "action/Dry.action" + "action/Purge.action" + "action/StartPurge.action" + "action/StartStir.action" + "action/StopPurge.action" + "action/StopStir.action" + "action/Transfer.action" + "action/SetPumpPosition.action" "action/LiquidHandlerProtocolCreation.action" "action/LiquidHandlerAspirate.action" "action/LiquidHandlerDiscardTips.action" diff --git a/unilabos_msgs/action/ProtocolAdd.action b/unilabos_msgs/action/Add.action similarity index 100% rename from unilabos_msgs/action/ProtocolAdd.action rename to unilabos_msgs/action/Add.action diff --git a/unilabos_msgs/action/ProtocolCentrifuge.action b/unilabos_msgs/action/Centrifuge.action similarity index 100% rename from unilabos_msgs/action/ProtocolCentrifuge.action rename to unilabos_msgs/action/Centrifuge.action diff --git a/unilabos_msgs/action/ProtocolCleanVessel.action b/unilabos_msgs/action/CleanVessel.action similarity index 100% rename from unilabos_msgs/action/ProtocolCleanVessel.action rename to unilabos_msgs/action/CleanVessel.action diff --git a/unilabos_msgs/action/ProtocolCrystallize.action b/unilabos_msgs/action/Crystallize.action similarity index 100% rename from unilabos_msgs/action/ProtocolCrystallize.action rename to unilabos_msgs/action/Crystallize.action diff --git a/unilabos_msgs/action/ProtocolDissolve.action b/unilabos_msgs/action/Dissolve.action similarity index 100% rename from unilabos_msgs/action/ProtocolDissolve.action rename to unilabos_msgs/action/Dissolve.action diff --git a/unilabos_msgs/action/ProtocolDry.action b/unilabos_msgs/action/Dry.action similarity index 100% rename from unilabos_msgs/action/ProtocolDry.action rename to unilabos_msgs/action/Dry.action diff --git a/unilabos_msgs/action/ProtocolFilter.action b/unilabos_msgs/action/Filter.action similarity index 100% rename from unilabos_msgs/action/ProtocolFilter.action rename to unilabos_msgs/action/Filter.action diff --git a/unilabos_msgs/action/ProtocolFilterThrough.action b/unilabos_msgs/action/FilterThrough.action similarity index 100% rename from unilabos_msgs/action/ProtocolFilterThrough.action rename to unilabos_msgs/action/FilterThrough.action diff --git a/unilabos_msgs/action/ProtocolPurge.action b/unilabos_msgs/action/Purge.action similarity index 100% rename from unilabos_msgs/action/ProtocolPurge.action rename to unilabos_msgs/action/Purge.action diff --git a/unilabos_msgs/action/ProtocolRunColumn.action b/unilabos_msgs/action/RunColumn.action similarity index 100% rename from unilabos_msgs/action/ProtocolRunColumn.action rename to unilabos_msgs/action/RunColumn.action diff --git a/unilabos_msgs/action/SetPumpPosition.action b/unilabos_msgs/action/SetPumpPosition.action new file mode 100644 index 00000000..5bbc1160 --- /dev/null +++ b/unilabos_msgs/action/SetPumpPosition.action @@ -0,0 +1,13 @@ +# Goal - 目标参数 +float64 position # 目标位置 (ml) +float64 max_velocity # 最大速度 (ml/s) +--- +# Result - 结果 +string return_info +bool success # 操作是否成功 +string message # 操作结果消息 +--- +# Feedback - 反馈 +string status # 当前状态 +float64 current_position # 当前位置 +float64 progress # 进度百分比 (0-100) \ No newline at end of file diff --git a/unilabos_msgs/action/ProtocolStartPurge.action b/unilabos_msgs/action/StartPurge.action similarity index 100% rename from unilabos_msgs/action/ProtocolStartPurge.action rename to unilabos_msgs/action/StartPurge.action diff --git a/unilabos_msgs/action/ProtocolStartStir.action b/unilabos_msgs/action/StartStir.action similarity index 100% rename from unilabos_msgs/action/ProtocolStartStir.action rename to unilabos_msgs/action/StartStir.action diff --git a/unilabos_msgs/action/ProtocolStopPurge.action b/unilabos_msgs/action/StopPurge.action similarity index 100% rename from unilabos_msgs/action/ProtocolStopPurge.action rename to unilabos_msgs/action/StopPurge.action diff --git a/unilabos_msgs/action/ProtocolStopStir.action b/unilabos_msgs/action/StopStir.action similarity index 100% rename from unilabos_msgs/action/ProtocolStopStir.action rename to unilabos_msgs/action/StopStir.action diff --git a/unilabos_msgs/action/ProtocolTransfer.action b/unilabos_msgs/action/Transfer.action similarity index 100% rename from unilabos_msgs/action/ProtocolTransfer.action rename to unilabos_msgs/action/Transfer.action diff --git a/unilabos_msgs/action/ProtocolWait.action b/unilabos_msgs/action/Wait.action similarity index 100% rename from unilabos_msgs/action/ProtocolWait.action rename to unilabos_msgs/action/Wait.action diff --git a/unilabos_msgs/action/ProtocolWashSolid.action b/unilabos_msgs/action/WashSolid.action similarity index 100% rename from unilabos_msgs/action/ProtocolWashSolid.action rename to unilabos_msgs/action/WashSolid.action