container 添加和更新完成

Co-authored-by: quehh <scienceol@outlook.com>

.github/workflows/multi-platform-build.yml

@@ -0,0 +1,132 @@
+name: Multi-Platform Conda Build
+
+on:
+  push:
+    branches: [ main, dev ]
+    tags: [ 'v*' ]
+  pull_request:
+    branches: [ main, dev ]
+  workflow_dispatch:
+    inputs:
+      platforms:
+        description: '选择构建平台 (逗号分隔): linux-64, osx-64, osx-arm64, win-64'
+        required: false
+        default: 'osx-arm64'
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - os: ubuntu-latest
+          platform: linux-64
+          env_file: unilabos-linux-64.yaml
+        - os: macos-13 # Intel
+          platform: osx-64
+          env_file: unilabos-osx-64.yaml
+        - os: macos-latest # ARM64
+          platform: osx-arm64
+          env_file: unilabos-osx-arm64.yaml
+        - os: windows-latest
+          platform: win-64
+          env_file: unilabos-win64.yaml
+
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Check if platform should be built
+      id: should_build
+      run: |
+        if [[ "${{ github.event_name }}" != "workflow_dispatch" ]]; then
+          echo "should_build=true" >> $GITHUB_OUTPUT
+        elif [[ -z "${{ github.event.inputs.platforms }}" ]]; then
+          echo "should_build=true" >> $GITHUB_OUTPUT
+        elif [[ "${{ github.event.inputs.platforms }}" == *"${{ matrix.platform }}"* ]]; then
+          echo "should_build=true" >> $GITHUB_OUTPUT
+        else
+          echo "should_build=false" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Setup Miniconda
+      if: steps.should_build.outputs.should_build == 'true'
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniconda-version: "latest"
+        channels: conda-forge,robostack-staging,defaults
+        channel-priority: strict
+        activate-environment: build-env
+        auto-activate-base: false
+        auto-update-conda: false
+        show-channel-urls: true
+
+    - name: Install boa and build tools
+      if: steps.should_build.outputs.should_build == 'true'
+      run: |
+        conda install -c conda-forge boa conda-build
+
+    - name: Show environment info
+      if: steps.should_build.outputs.should_build == 'true'
+      run: |
+        conda info
+        conda list | grep -E "(boa|conda-build)"
+        echo "Platform: ${{ matrix.platform }}"
+        echo "OS: ${{ matrix.os }}"
+
+    - name: Build conda package
+      if: steps.should_build.outputs.should_build == 'true'
+      run: |
+        if [[ "${{ matrix.platform }}" == "osx-arm64" ]]; then
+          boa build -m ./recipes/conda_build_config.yaml -m ./recipes/macos_sdk_config.yaml ./recipes/ros-humble-unilabos-msgs
+        else
+          boa build -m ./recipes/conda_build_config.yaml ./recipes/ros-humble-unilabos-msgs
+        fi
+
+    - name: List built packages
+      if: steps.should_build.outputs.should_build == 'true'
+      run: |
+        echo "Built packages in conda-bld:"
+        find $CONDA_PREFIX/conda-bld -name "*.tar.bz2" | head -10
+        ls -la $CONDA_PREFIX/conda-bld/${{ matrix.platform }}/ || echo "${{ matrix.platform }} directory not found"
+        ls -la $CONDA_PREFIX/conda-bld/noarch/ || echo "noarch directory not found"
+        echo "CONDA_PREFIX: $CONDA_PREFIX"
+        echo "Full path would be: $CONDA_PREFIX/conda-bld/**/*.tar.bz2"
+
+    - name: Prepare artifacts for upload
+      if: steps.should_build.outputs.should_build == 'true'
+      run: |
+        mkdir -p ${{ runner.temp }}/conda-packages
+        find $CONDA_PREFIX/conda-bld -name "*.tar.bz2" -exec cp {} ${{ runner.temp }}/conda-packages/ \;
+        echo "Copied files to temp directory:"
+        ls -la ${{ runner.temp }}/conda-packages/
+
+    - name: Upload conda package artifacts
+      if: steps.should_build.outputs.should_build == 'true'
+      uses: actions/upload-artifact@v4
+      with:
+        name: conda-package-${{ matrix.platform }}
+        path: ${{ runner.temp }}/conda-packages
+        if-no-files-found: warn
+        retention-days: 30
+
+    - name: Create release assets (on tags)
+      if: steps.should_build.outputs.should_build == 'true' && startsWith(github.ref, 'refs/tags/')
+      run: |
+        mkdir -p release-assets
+        find $CONDA_PREFIX/conda-bld -name "*.tar.bz2" -exec cp {} release-assets/ \;
+
+    - name: Upload to release
+      if: steps.should_build.outputs.should_build == 'true' && startsWith(github.ref, 'refs/tags/')
+      uses: softprops/action-gh-release@v1
+      with:
+        files: release-assets/*
+        draft: false
+        prerelease: false

.gitignore

@@ -234,3 +234,7 @@ CATKIN_IGNORE
 
 *.graphml
 unilabos/device_mesh/view_robot.rviz
+
+
+# Certs
+**/.certs

test/commands/resource_add.md

@@ -2,4 +2,10 @@
 
 ```bash
 ros2 action send_goal /devices/host_node/create_resource_detailed unilabos_msgs/action/_resource_create_from_outer/ResourceCreateFromOuter "{ resources: [ { 'category': '', 'children': [], 'config': { 'type': 'Well', 'size_x': 6.86, 'size_y': 6.86, 'size_z': 10.67, 'rotation': { 'x': 0, 'y': 0, 'z': 0, 'type': 'Rotation' }, 'category': 'well', 'model': null, 'max_volume': 360, 'material_z_thickness': 0.5, 'compute_volume_from_height': null, 'compute_height_from_volume': null, 'bottom_type': 'flat', 'cross_section_type': 'circle' }, 'data': { 'liquids': [], 'pending_liquids': [], 'liquid_history': [] }, 'id': 'plate_well_11_7', 'name': 'plate_well_11_7', 'pose': { 'orientation': { 'w': 1.0, 'x': 0.0, 'y': 0.0, 'z': 0.0 }, 'position': { 'x': 0.0, 'y': 0.0, 'z': 0.0 } }, 'sample_id': '', 'parent': 'plate', 'type': 'device' } ], device_ids: [ 'PLR_STATION' ], bind_parent_ids: [ 'plate' ], bind_locations: [ { 'x': 0.0, 'y': 0.0, 'z': 0.0 } ], other_calling_params: [ '{}' ] }"
+```
+
+使用mock_all.json启动，重新捕获MockContainerForChiller1
+
+```bash
+ros2 action send_goal /devices/host_node/create_resource unilabos_msgs/action/_resource_create_from_outer_easy/ResourceCreateFromOuterEasy "{ 'res_id': 'MockContainerForChiller1', 'device_id': 'MockChiller1', 'class_name': 'container', 'parent': 'MockChiller1', 'bind_locations': { 'x': 0.0, 'y': 0.0, 'z': 0.0 }, 'liquid_input_slot': [ -1 ], 'liquid_type': [ 'CuCl2' ], 'liquid_volume': [ 100.0 ], 'slot_on_deck': '' }"
 ```

test/experiments/mock_devices/mock_all.json

@@ -3,7 +3,9 @@
         {  
             "id": "MockChiller1",  
             "name": "模拟冷却器",  
-            "children": [],  
+            "children": [
+                "MockContainerForChiller1"
+            ],
             "parent": null,  
             "type": "device",  
             "class": "mock_chiller",  
@@ -25,6 +27,22 @@
                 "purpose": ""
             }  
         },
+        {
+            "id": "MockContainerForChiller1",
+            "name": "模拟容器",
+            "type": "container",
+            "parent": "MockChiller1",
+            "position": {
+                "x": 5,
+                "y": 0,
+                "z": 0
+            },
+            "data": {
+                "liquid_type": "CuCl2",
+                "liquid_volume": "100"
+            },
+            "children": []
+        },
         {  
             "id": "MockFilter1",  
             "name": "模拟过滤器",  

unilabos/registry/resources/opentrons/container.yaml

@@ -0,0 +1,5 @@
+container:
+  description: regular organic container
+  class: 
+    module: unilabos.resources.container:RegularContainer
+    type: unilabos

unilabos/resources/container.py

@@ -0,0 +1,67 @@
+import json
+
+from unilabos_msgs.msg import Resource
+
+from unilabos.ros.msgs.message_converter import convert_from_ros_msg
+
+
+class RegularContainer(object):
+    # 第一个参数必须是id传入
+    # noinspection PyShadowingBuiltins
+    def __init__(self, id: str):
+        self.id = id
+        self.ulr_resource = Resource()
+        self._data = None
+
+    @property
+    def ulr_resource_data(self):
+        if self._data is None:
+            self._data = json.loads(self.ulr_resource.data) if self.ulr_resource.data else {}
+        return self._data
+
+    @ulr_resource_data.setter
+    def ulr_resource_data(self, value: dict):
+        self._data = value
+        self.ulr_resource.data = json.dumps(self._data)
+
+    @property
+    def liquid_type(self):
+        return self.ulr_resource_data.get("liquid_type", None)
+
+    @liquid_type.setter
+    def liquid_type(self, value: str):
+        if value is not None:
+            self.ulr_resource_data["liquid_type"] = value
+        else:
+            self.ulr_resource_data.pop("liquid_type", None)
+
+    @property
+    def liquid_volume(self):
+        return self.ulr_resource_data.get("liquid_volume", None)
+
+    @liquid_volume.setter
+    def liquid_volume(self, value: float):
+        if value is not None:
+            self.ulr_resource_data["liquid_volume"] = value
+        else:
+            self.ulr_resource_data.pop("liquid_volume", None)
+
+    def get_ulr_resource(self) -> Resource:
+        """
+        获取UlrResource对象
+        :return: UlrResource对象
+        """
+        self.ulr_resource_data = self.ulr_resource_data  # 确保数据被更新
+        return self.ulr_resource
+
+    def get_ulr_resource_as_dict(self) -> Resource:
+        """
+        获取UlrResource对象
+        :return: UlrResource对象
+        """
+        to_dict = convert_from_ros_msg(self.get_ulr_resource())
+        to_dict["type"] = "container"
+        return to_dict
+
+    def __str__(self):
+        return f"{self.id}"

unilabos/resources/graphio.py

@@ -4,6 +4,10 @@ import json
 from typing import Union
 import numpy as np
 import networkx as nx
+from unilabos_msgs.msg import Resource
+
+from unilabos.resources.container import RegularContainer
+from unilabos.ros.msgs.message_converter import convert_from_ros_msg_with_mapping, convert_to_ros_msg
 
 try:
     from pylabrobot.resources.resource import Resource as ResourcePLR
@@ -466,6 +470,10 @@ def initialize_resource(resource_config: dict) -> list[dict]:
             if resource_config.get("position") is not None:
                 r["position"] = resource_config["position"]
             r = tree_to_list([r])
+        elif resource_class_config["type"] == "unilabos":
+            res_instance: RegularContainer = RESOURCE(id=resource_config["name"])
+            res_instance.ulr_resource = convert_to_ros_msg(Resource, {k:v for k,v in resource_config.items() if k != "class"})
+            r = [res_instance.get_ulr_resource_as_dict()]
         elif isinstance(RESOURCE, dict):
             r = [RESOURCE.copy()]
 

unilabos/ros/nodes/base_device_node.py

@@ -19,6 +19,7 @@ from rclpy.service import Service
 from unilabos_msgs.action import SendCmd
 from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response
 
+from unilabos.resources.container import RegularContainer
 from unilabos.resources.graphio import (
     convert_resources_to_type,
     convert_resources_from_type,
@@ -344,6 +345,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
             LIQUID_VOLUME = other_calling_param.pop("LIQUID_VOLUME", [])
             LIQUID_INPUT_SLOT = other_calling_param.pop("LIQUID_INPUT_SLOT", [])
             slot = other_calling_param.pop("slot", "-1")
+            resource = None
             if slot != "-1":  # slot为负数的时候采用assign方法
                 other_calling_param["slot"] = slot
             # 本地拿到这个物料，可能需要先做初始化?
@@ -362,6 +364,28 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                 if initialize_full:
                     resources = initialize_resources([resources])
                 request.resources = [convert_to_ros_msg(Resource, resources)]
+            if len(LIQUID_INPUT_SLOT) and LIQUID_INPUT_SLOT[0] == -1:
+                container_instance = request.resources[0]
+                container_query_dict: dict = resources
+                found_resources = self.resource_tracker.figure_resource({"id": container_query_dict["name"]}, try_mode=True)
+                if not len(found_resources):
+                    self.resource_tracker.add_resource(container_instance)
+                    logger.info(f"添加物料{container_query_dict['name']}到资源跟踪器")
+                else:
+                    assert len(found_resources) == 1, f"找到多个同名物料: {container_query_dict['name']}, 请检查物料系统"
+                    resource = found_resources[0]
+                    if isinstance(resource, Resource):
+                        regular_container = RegularContainer(resource.id)
+                        regular_container.ulr_resource = resource
+                        regular_container.ulr_resource_data.update(json.loads(container_instance.data))
+                        logger.info(f"更新物料{container_query_dict['name']}的数据{resource.data} ULR")
+                    elif isinstance(resource, dict):
+                        if "data" not in resource:
+                            resource["data"] = {}
+                        resource["data"].update(json.loads(container_instance.data))
+                        logger.info(f"更新物料{container_query_dict['name']}的数据{resource['data']} dict")
+                    else:
+                        logger.info(f"更新物料{container_query_dict['name']}出现不支持的数据类型{type(resource)} {resource}")
             response = rclient.call(request)
             # 应该先add_resource了
             res.response = "OK"
@@ -385,7 +409,8 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                     res.response = serialize_result_info(traceback.format_exc(), False, {})
                 return res
             # 接下来该根据bind_parent_id进行assign了，目前只有plr可以进行assign，不然没有办法输入到物料系统中
-            resource = self.resource_tracker.figure_resource({"name": bind_parent_id})
+            if bind_parent_id != self.node_name:
+                resource = self.resource_tracker.figure_resource({"name": bind_parent_id})  # 拿到父节点，进行具体assign等操作
             # request.resources = [convert_to_ros_msg(Resource, resources)]
 
             try:
@@ -435,7 +460,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         "bind_parent_id": bind_parent_id,
                     }
                 )
-                future = action_client.send_goal_async(goal, goal_uuid=uuid.uuid4())
+                future = action_client.send_goal_async(goal)
 
                 def done_cb(*args):
                     self.lab_logger().info(f"向meshmanager发送新增resource完成")
@@ -901,9 +926,9 @@ class ROS2DeviceNode:
             from unilabos.ros.nodes.presets.protocol_node import ROS2ProtocolNode
 
             if self._driver_class is ROS2ProtocolNode:
-                self._driver_creator = ProtocolNodeCreator(driver_class, children=children)
+                self._driver_creator = ProtocolNodeCreator(driver_class, children=children, resource_tracker=self.resource_tracker)
             else:
-                self._driver_creator = DeviceClassCreator(driver_class)
+                self._driver_creator = DeviceClassCreator(driver_class, children=children, resource_tracker=self.resource_tracker)
 
         if driver_is_ros:
             driver_params["device_id"] = device_id

unilabos/ros/nodes/presets/host_node.py

@@ -383,18 +383,24 @@ class HostNode(BaseROS2DeviceNode):
         liquid_volume: list[int],
         slot_on_deck: str,
     ):
-        init_new_res = initialize_resource(
+        res_creation_input = {
-            {
+            "name": res_id,
-                "name": res_id,
+            "class": class_name,
-                "class": class_name,
+            "parent": parent,
-                "parent": parent,
+            "position": {
-                "position": {
+                "x": bind_locations.x,
-                    "x": bind_locations.x,
+                "y": bind_locations.y,
-                    "y": bind_locations.y,
+                "z": bind_locations.z,
-                    "z": bind_locations.z,
+            },
-                },
+        }
-            }
+        if len(liquid_input_slot) and liquid_input_slot[0] == -1:  # 目前container只逐个创建
-        )  # flatten的格式
+            res_creation_input.update({
+                "data": {
+                    "liquid_type": liquid_type[0] if liquid_type else None,
+                    "liquid_volume": liquid_volume[0] if liquid_volume else None,
+                }
+            })
+        init_new_res = initialize_resource(res_creation_input)  # flatten的格式
         resources = init_new_res  # initialize_resource已经返回list[dict]
         device_ids = [device_id]
         bind_parent_id = [parent]

unilabos/ros/nodes/resource_tracker.py

@@ -25,7 +25,7 @@ class DeviceNodeResourceTracker(object):
     def clear_resource(self):
         self.resources = []
 
-    def figure_resource(self, query_resource):
+    def figure_resource(self, query_resource, try_mode=False):
         if isinstance(query_resource, list):
             return [self.figure_resource(r) for r in query_resource]
         res_id = query_resource.id if hasattr(query_resource, "id") else (query_resource.get("id") if isinstance(query_resource, dict) else None)
@@ -45,10 +45,14 @@ class DeviceNodeResourceTracker(object):
                 res_list.extend(
                     self.loop_find_resource(r, resource_cls_type, identifier_key, getattr(query_resource, identifier_key))
                 )
-        assert len(res_list) == 1, f"{query_resource} 找到多个资源，请检查资源是否唯一: {res_list}"
+        if not try_mode:
+            assert len(res_list) > 0, f"没有找到资源 {query_resource}，请检查资源是否存在"
+            assert len(res_list) == 1, f"{query_resource} 找到多个资源，请检查资源是否唯一: {res_list}"
+        else:
+            return [i[1] for i in res_list]
+        # 后续加入其他对比方式
         self.resource2parent_resource[id(query_resource)] = res_list[0][0]
         self.resource2parent_resource[id(res_list[0][1])] = res_list[0][0]
-        # 后续加入其他对比方式
         return res_list[0][1]
 
     def loop_find_resource(self, resource, target_resource_cls_type, identifier_key, compare_value, parent_res=None) -> List[Tuple[Any, Any]]:
@@ -57,8 +61,12 @@ class DeviceNodeResourceTracker(object):
         children = getattr(resource, "children", [])
         for child in children:
             res_list.extend(self.loop_find_resource(child, target_resource_cls_type, identifier_key, compare_value, resource))
-        if target_resource_cls_type == type(resource) or target_resource_cls_type == dict:
+        if target_resource_cls_type == type(resource):
-            if hasattr(resource, identifier_key):
+            if target_resource_cls_type == dict:
+                if identifier_key in resource:
+                    if resource[identifier_key] == compare_value:
+                        res_list.append((parent_res, resource))
+            elif hasattr(resource, identifier_key):
                 if getattr(resource, identifier_key) == compare_value:
                     res_list.append((parent_res, resource))
         return res_list

unilabos/ros/utils/driver_creator.py

@@ -33,7 +33,7 @@ class DeviceClassCreator(Generic[T]):
     这个类提供了从任意类创建实例的通用方法。
     """
 
-    def __init__(self, cls: Type[T]):
+    def __init__(self, cls: Type[T], children: Dict[str, Any], resource_tracker: DeviceNodeResourceTracker):
         """
         初始化设备类创建器
 
@@ -42,6 +42,18 @@ class DeviceClassCreator(Generic[T]):
         """
         self.device_cls = cls
         self.device_instance: Optional[T] = None
+        self.children = children
+        self.resource_tracker = resource_tracker
+
+    def attach_resource(self):
+        """
+        附加资源到设备类实例
+        """
+        if self.device_instance is not None:
+            for c in self.children.values():
+                if c["type"] == "container":
+                    self.resource_tracker.add_resource(c)
+
 
     def create_instance(self, data: Dict[str, Any]) -> T:
         """
@@ -60,6 +72,7 @@ class DeviceClassCreator(Generic[T]):
             }
         )
         self.post_create()
+        self.attach_resource()
         return self.device_instance
 
     def get_instance(self) -> Optional[T]:
@@ -90,14 +103,15 @@ class PyLabRobotCreator(DeviceClassCreator[T]):
             cls: PyLabRobot设备类
             children: 子资源字典，用于资源替换
         """
-        super().__init__(cls)
+        super().__init__(cls, children, resource_tracker)
-        self.children = children
-        self.resource_tracker = resource_tracker
         # 检查类是否具有deserialize方法
         self.has_deserialize = hasattr(cls, "deserialize") and callable(getattr(cls, "deserialize"))
         if not self.has_deserialize:
             logger.warning(f"类 {cls.__name__} 没有deserialize方法，将使用标准构造函数")
 
+    def attach_resource(self):
+        pass  # 只能增加实例化物料，原来默认物料仅为字典查询
+
     def _process_resource_mapping(self, resource, source_type):
         if source_type == dict:
             from pylabrobot.resources.resource import Resource
@@ -260,7 +274,7 @@ class ProtocolNodeCreator(DeviceClassCreator[T]):
     这个类提供了针对ProtocolNode设备类的实例创建方法，处理children参数。
     """
 
-    def __init__(self, cls: Type[T], children: Dict[str, Any]):
+    def __init__(self, cls: Type[T], children: Dict[str, Any], resource_tracker: DeviceNodeResourceTracker):
         """
         初始化ProtocolNode设备类创建器
 
@@ -268,8 +282,7 @@ class ProtocolNodeCreator(DeviceClassCreator[T]):
             cls: ProtocolNode设备类
             children: 子资源字典，用于资源替换
         """
-        super().__init__(cls)
+        super().__init__(cls, children, resource_tracker)
-        self.children = children
 
     def create_instance(self, data: Dict[str, Any]) -> T:
         """
@@ -282,8 +295,7 @@ class ProtocolNodeCreator(DeviceClassCreator[T]):
             ProtocolNode设备类实例
         """
         try:
-
+            # 创建实例，额外补充一个给protocol node的字段，后面考虑取消
-            # 创建实例
             data["children"] = self.children
             self.device_instance = super(ProtocolNodeCreator, self).create_instance(data)
             self.post_create()