From 4139e079f4440bab034fb2d20f4cb096d9ff0863 Mon Sep 17 00:00:00 2001 From: Xuwznln <18435084+Xuwznln@users.noreply.github.com> Date: Sun, 22 Jun 2025 18:33:08 +0800 Subject: [PATCH] Dev (#52) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add biomek.py demo implementation * 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。 * Test * fix biomek success type * Convert LH action to biomek. * Update biomek.py * 注册表上报handle和schema (param input) * 修复biomek缺少的字段 * delete 's' * Remove warnings * Update biomek.py * Biomek test * Update biomek.py * 新增transfer_biomek的msg * New transfer_biomek * Updated transfer_biomek * 更新transfer_biomek的msg * 更新transfer_biomek的msg * 支持Biomek创建 * new action * fix key name typo * New parameter for biomek to run. * Refine * Update * new actions * new actions * 1 * registry * fix biomek startup add action handles * fix handles not as default entry * biomek_test.py biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json * Update biomek.py * biomek_test.py * fix liquid_handler.biomek handles * host node新增resource add时间统计 create_resource新增handle bump version to 0.9.2 * 修正物料上传时间 改用biomek_test 增加ResultInfoEncoder 支持返回结果上传 * 正确发送return_info结果 * 同步执行状态信息 * 取消raiseValueError提示 * Update biomek_test.py * 0608 DONE * 同步了Biomek.py 现在应可用 * biomek switch back to non-test * temp disable initialize resource * 37-biomek-i5i7 (#40) * add biomek.py demo implementation * 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。 * Test * fix biomek success type * Convert LH action to biomek. * Update biomek.py * 注册表上报handle和schema (param input) * 修复biomek缺少的字段 * delete 's' * Remove warnings * Update biomek.py * Biomek test * Update biomek.py * 新增transfer_biomek的msg * New transfer_biomek * Updated transfer_biomek * 更新transfer_biomek的msg * 更新transfer_biomek的msg * 支持Biomek创建 * new action * fix key name typo * New parameter for biomek to run. * Refine * Update * new actions * new actions * 1 * registry * fix biomek startup add action handles * fix handles not as default entry * biomek_test.py biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json * Update biomek.py * biomek_test.py * fix liquid_handler.biomek handles * host node新增resource add时间统计 create_resource新增handle bump version to 0.9.2 * 修正物料上传时间 改用biomek_test 增加ResultInfoEncoder 支持返回结果上传 * 正确发送return_info结果 * 同步执行状态信息 * 取消raiseValueError提示 * Update biomek_test.py * 0608 DONE * 同步了Biomek.py 现在应可用 * biomek switch back to non-test * temp disable initialize resource * Refine biomek * Refine copy issue * Refine --------- Co-authored-by: Junhan Chang Co-authored-by: Guangxin Zhang Co-authored-by: qxw138 * Device visualization (#39) * Update README and MQTTClient for installation instructions and code improvements * feat: 支持local_config启动 add: 增加对crt path的说明，为传入config.py的相对路径 move: web component * add: registry description * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * feat: node_info_update srv fix: OTDeck cant create * close #12 feat: slave node registry * feat: show machine name fix: host node registry not uploaded * feat: add hplc registry * feat: add hplc registry * fix: hplc status typo * fix: devices/ * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * fix: device.class possible null * fix: HPLC additions with online service * fix: slave mode spin not working * fix: slave mode spin not working * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * feat: 多ProtocolNode 允许子设备ID相同 feat: 上报发现的ActionClient feat: Host重启动，通过discover机制要求slaveNode重新注册，实现信息及时上报 * feat: 支持env设置config * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * Device visualization (#14) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: missing hostname in devices_names fix: upload_file for model file * fix: missing paho-mqtt package bump version to 0.9.0 * fix startup add ResourceCreateFromOuter.action * fix type hint * update actions * update actions * host node add_resource_from_outer fix cmake list * pass device config to device class * add: bind_parent_ids to resource create action fix: message convert string * fix: host node should not be re_discovered * feat: resource tracker support dict * feat: add more necessary params * feat: fix boolean null in registry action data * feat: add outer resource * 编写mesh添加action * feat: append resource * add action * feat: vis 2d for plr * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate * Device visualization (#22) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * 编写mesh添加action * add action * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: multi channel * fix: aspirate * fix: aspirate * fix: aspirate * fix: aspirate * 提交 * fix: jobadd * fix: jobadd * fix: msg converter * tijiao * add resource creat easy action * identify debug msg * mq client id * 提取lh的joint发布 * unify liquid_handler definition * 修改物料跟随与物料添加逻辑 修改物料跟随与物料添加逻辑 将joint_publisher类移出lh的backends，但仍需要对lh的backends进行一些改写 * Revert "修改物料跟随与物料添加逻辑" This reverts commit 498c997ad764263366f6d6207e0722fbc7a909a8. * Reapply "修改物料跟随与物料添加逻辑" This reverts commit 3a60d2ae8125a7b24506bb681e3baaf69f2ebf6b. * Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization" This reverts commit fa727220afa8546b84f1763730818d6360c26251, reversing changes made to 498c997ad764263366f6d6207e0722fbc7a909a8. * 修改物料放下时的方法，如果选择 修改物料放下时的方法， 如果选择drop_trash，则删除物料显示 如果选择drop，则让其解除连接 * add biomek.py demo implementation * 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。 * Test * fix biomek success type * Convert LH action to biomek. * Update biomek.py * 注册表上报handle和schema (param input) * 修复biomek缺少的字段 * delete 's' * Remove warnings * Update biomek.py * Biomek test * Update biomek.py * 新增transfer_biomek的msg * New transfer_biomek * Updated transfer_biomek * 更新transfer_biomek的msg * 更新transfer_biomek的msg * 支持Biomek创建 * new action * fix key name typo * New parameter for biomek to run. * Refine * Update * new actions * new actions * 1 * registry * fix biomek startup add action handles * fix handles not as default entry * unilab添加moveit启动 1,整合所有moveit节点到一个move_group中，并整合所有的controller依次激活 2,添加pymoveit2的节点，使用json可直接启动 3,修改机械臂规划方式，添加约束，让冗余关节不会进行过多移动 * biomek_test.py biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json * Update biomek.py * biomek_test.py * fix liquid_handler.biomek handles * 修改物体attach时，多次赋值当前时间导致卡顿问题， * Revert "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit 56d45b94f55d1339d54d9725ffe3c8cca7cbb73a. * Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit 07d9db20c3b43bc8af048b9e2c4af210ec16d446. * 添加缺少物料："plate_well_G12", * host node新增resource add时间统计 create_resource新增handle bump version to 0.9.2 * 修正物料上传时间 改用biomek_test 增加ResultInfoEncoder 支持返回结果上传 * 正确发送return_info结果 * 同步执行状态信息 * 取消raiseValueError提示 * Update biomek_test.py * 0608 DONE * 同步了Biomek.py 现在应可用 * biomek switch back to non-test * temp disable initialize resource * add * fix tip resource data * liquid states * change to debug level * Revert "change to debug level" This reverts commit 5d9953c3e58d9f33818f21232c3fdcc30a4f766c. * Reapply "change to debug level" This reverts commit 2487bb6ffc6590b2da13a3dd5226825e0a164993. * fix tip resource data * add full device * add moveit yaml * 修复moveit 增加post_init阶段，给予ros_node反向 * remove necessary node * fix moveit action client * remove necessary imports * Update moveit_interface.py * fix handler_key uppercase * json add liquids * fix setup * add * change to "sources" and "targets" for lh * bump version * remove parent's parent link --------- Co-authored-by: Harvey Que Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: Junhan Chang Co-authored-by: Guangxin Zhang Co-authored-by: qxw138 * Device visualization (#41) * Update README and MQTTClient for installation instructions and code improvements * feat: 支持local_config启动 add: 增加对crt path的说明，为传入config.py的相对路径 move: web component * add: registry description * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * feat: node_info_update srv fix: OTDeck cant create * close #12 feat: slave node registry * feat: show machine name fix: host node registry not uploaded * feat: add hplc registry * feat: add hplc registry * fix: hplc status typo * fix: devices/ * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * fix: device.class possible null * fix: HPLC additions with online service * fix: slave mode spin not working * fix: slave mode spin not working * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * feat: 多ProtocolNode 允许子设备ID相同 feat: 上报发现的ActionClient feat: Host重启动，通过discover机制要求slaveNode重新注册，实现信息及时上报 * feat: 支持env设置config * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * Device visualization (#14) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: missing hostname in devices_names fix: upload_file for model file * fix: missing paho-mqtt package bump version to 0.9.0 * fix startup add ResourceCreateFromOuter.action * fix type hint * update actions * update actions * host node add_resource_from_outer fix cmake list * pass device config to device class * add: bind_parent_ids to resource create action fix: message convert string * fix: host node should not be re_discovered * feat: resource tracker support dict * feat: add more necessary params * feat: fix boolean null in registry action data * feat: add outer resource * 编写mesh添加action * feat: append resource * add action * feat: vis 2d for plr * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate * Device visualization (#22) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * 编写mesh添加action * add action * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: multi channel * fix: aspirate * fix: aspirate * fix: aspirate * fix: aspirate * 提交 * fix: jobadd * fix: jobadd * fix: msg converter * tijiao * add resource creat easy action * identify debug msg * mq client id * 提取lh的joint发布 * unify liquid_handler definition * 修改物料跟随与物料添加逻辑 修改物料跟随与物料添加逻辑 将joint_publisher类移出lh的backends，但仍需要对lh的backends进行一些改写 * Revert "修改物料跟随与物料添加逻辑" This reverts commit 498c997ad764263366f6d6207e0722fbc7a909a8. * Reapply "修改物料跟随与物料添加逻辑" This reverts commit 3a60d2ae8125a7b24506bb681e3baaf69f2ebf6b. * Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization" This reverts commit fa727220afa8546b84f1763730818d6360c26251, reversing changes made to 498c997ad764263366f6d6207e0722fbc7a909a8. * 修改物料放下时的方法，如果选择 修改物料放下时的方法， 如果选择drop_trash，则删除物料显示 如果选择drop，则让其解除连接 * add biomek.py demo implementation * 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。 * Test * fix biomek success type * Convert LH action to biomek. * Update biomek.py * 注册表上报handle和schema (param input) * 修复biomek缺少的字段 * delete 's' * Remove warnings * Update biomek.py * Biomek test * Update biomek.py * 新增transfer_biomek的msg * New transfer_biomek * Updated transfer_biomek * 更新transfer_biomek的msg * 更新transfer_biomek的msg * 支持Biomek创建 * new action * fix key name typo * New parameter for biomek to run. * Refine * Update * new actions * new actions * 1 * registry * fix biomek startup add action handles * fix handles not as default entry * unilab添加moveit启动 1,整合所有moveit节点到一个move_group中，并整合所有的controller依次激活 2,添加pymoveit2的节点，使用json可直接启动 3,修改机械臂规划方式，添加约束，让冗余关节不会进行过多移动 * biomek_test.py biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json * Update biomek.py * biomek_test.py * fix liquid_handler.biomek handles * 修改物体attach时，多次赋值当前时间导致卡顿问题， * Revert "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit 56d45b94f55d1339d54d9725ffe3c8cca7cbb73a. * Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit 07d9db20c3b43bc8af048b9e2c4af210ec16d446. * 添加缺少物料："plate_well_G12", * host node新增resource add时间统计 create_resource新增handle bump version to 0.9.2 * 修正物料上传时间 改用biomek_test 增加ResultInfoEncoder 支持返回结果上传 * 正确发送return_info结果 * 同步执行状态信息 * 取消raiseValueError提示 * Update biomek_test.py * 0608 DONE * 同步了Biomek.py 现在应可用 * biomek switch back to non-test * temp disable initialize resource * add * fix tip resource data * liquid states * change to debug level * Revert "change to debug level" This reverts commit 5d9953c3e58d9f33818f21232c3fdcc30a4f766c. * Reapply "change to debug level" This reverts commit 2487bb6ffc6590b2da13a3dd5226825e0a164993. * fix tip resource data * add full device * add moveit yaml * 修复moveit 增加post_init阶段，给予ros_node反向 * remove necessary node * fix moveit action client * remove necessary imports * Update moveit_interface.py * fix handler_key uppercase * json add liquids * fix setup * add * change to "sources" and "targets" for lh * bump version * remove parent's parent link * change arm's name * change name --------- Co-authored-by: Harvey Que Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com> Co-authored-by: Junhan Chang Co-authored-by: Guangxin Zhang Co-authored-by: qxw138 * fix move it * fix move it * create_resource * bump ver modify slot type * 增加modbus支持 调整protocol node以更好支持多种类型的read和write * 调整protocol node以更好支持多种类型的read和write * 补充日志 * Device visualization (#42) * Update README and MQTTClient for installation instructions and code improvements * feat: 支持local_config启动 add: 增加对crt path的说明，为传入config.py的相对路径 move: web component * add: registry description * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * feat: node_info_update srv fix: OTDeck cant create * close #12 feat: slave node registry * feat: show machine name fix: host node registry not uploaded * feat: add hplc registry * feat: add hplc registry * fix: hplc status typo * fix: devices/ * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * fix: device.class possible null * fix: HPLC additions with online service * fix: slave mode spin not working * fix: slave mode spin not working * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * feat: 多ProtocolNode 允许子设备ID相同 feat: 上报发现的ActionClient feat: Host重启动，通过discover机制要求slaveNode重新注册，实现信息及时上报 * feat: 支持env设置config * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * Device visualization (#14) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: missing hostname in devices_names fix: upload_file for model file * fix: missing paho-mqtt package bump version to 0.9.0 * fix startup add ResourceCreateFromOuter.action * fix type hint * update actions * update actions * host node add_resource_from_outer fix cmake list * pass device config to device class * add: bind_parent_ids to resource create action fix: message convert string * fix: host node should not be re_discovered * feat: resource tracker support dict * feat: add more necessary params * feat: fix boolean null in registry action data * feat: add outer resource * 编写mesh添加action * feat: append resource * add action * feat: vis 2d for plr * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate * Device visualization (#22) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * 编写mesh添加action * add action * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: multi channel * fix: aspirate * fix: aspirate * fix: aspirate * fix: aspirate * 提交 * fix: jobadd * fix: jobadd * fix: msg converter * tijiao * add resource creat easy action * identify debug msg * mq client id * 提取lh的joint发布 * unify liquid_handler definition * 修改物料跟随与物料添加逻辑 修改物料跟随与物料添加逻辑 将joint_publisher类移出lh的backends，但仍需要对lh的backends进行一些改写 * Revert "修改物料跟随与物料添加逻辑" This reverts commit 498c997ad764263366f6d6207e0722fbc7a909a8. * Reapply "修改物料跟随与物料添加逻辑" This reverts commit 3a60d2ae8125a7b24506bb681e3baaf69f2ebf6b. * Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization" This reverts commit fa727220afa8546b84f1763730818d6360c26251, reversing changes made to 498c997ad764263366f6d6207e0722fbc7a909a8. * 修改物料放下时的方法，如果选择 修改物料放下时的方法， 如果选择drop_trash，则删除物料显示 如果选择drop，则让其解除连接 * unilab添加moveit启动 1,整合所有moveit节点到一个move_group中，并整合所有的controller依次激活 2,添加pymoveit2的节点，使用json可直接启动 3,修改机械臂规划方式，添加约束，让冗余关节不会进行过多移动 * 修改物体attach时，多次赋值当前时间导致卡顿问题， * Revert "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit 56d45b94f55d1339d54d9725ffe3c8cca7cbb73a. * Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit 07d9db20c3b43bc8af048b9e2c4af210ec16d446. * 添加缺少物料："plate_well_G12", * add * fix tip resource data * liquid states * change to debug level * Revert "change to debug level" This reverts commit 5d9953c3e58d9f33818f21232c3fdcc30a4f766c. * Reapply "change to debug level" This reverts commit 2487bb6ffc6590b2da13a3dd5226825e0a164993. * fix tip resource data * add full device * add moveit yaml * 修复moveit 增加post_init阶段，给予ros_node反向 * remove necessary node * fix moveit action client * remove necessary imports * Update moveit_interface.py * fix handler_key uppercase * json add liquids * fix setup * add * change to "sources" and "targets" for lh * bump version * remove parent's parent link * change arm's name * change name * fix ik error --------- Co-authored-by: Harvey Que Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com> Co-authored-by: Junhan Chang * Add Mock Device for Organic Synthesis\添加有机合成的虚拟仪器和Protocol (#43) * Add Device MockChiller Add device MockChiller * Add Device MockFilter * Add Device MockPump * Add Device MockRotavap * Add Device MockSeparator * Add Device MockStirrer * Add Device MockHeater * Add Device MockVacuum * Add Device MockSolenoidValve * Add Device Mock \_init_.py * 规范模拟设备代码与注册表信息 * 更改Mock大写文件夹名 * 删除大写目录 * Edited Mock device json * Match mock device with action * Edit mock device yaml * Add new action * Add Virtual Device, Action, YAML, Protocol for Organic Syn * 单独分类测试的protocol文件夹 * 更名Action --------- Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com> * bump version & protocol fix * hotfix: Add macos_sdk_config (#46) Co-authored-by: quehh * include device_mesh when pip install * 测试自动构建 * try build fix * try build * test artifacts * hotfix: Add .certs in .gitignore * create container * container 添加和更新完成 * Device registry port (#49) * Update README and MQTTClient for installation instructions and code improvements * feat: 支持local_config启动 add: 增加对crt path的说明，为传入config.py的相对路径 move: web component * add: registry description * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * feat: node_info_update srv fix: OTDeck cant create * close #12 feat: slave node registry * feat: show machine name fix: host node registry not uploaded * feat: add hplc registry * feat: add hplc registry * fix: hplc status typo * fix: devices/ * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * fix: device.class possible null * fix: HPLC additions with online service * fix: slave mode spin not working * fix: slave mode spin not working * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * feat: 多ProtocolNode 允许子设备ID相同 feat: 上报发现的ActionClient feat: Host重启动，通过discover机制要求slaveNode重新注册，实现信息及时上报 * feat: 支持env设置config * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * Device visualization (#14) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: missing hostname in devices_names fix: upload_file for model file * fix: missing paho-mqtt package bump version to 0.9.0 * fix startup add ResourceCreateFromOuter.action * fix type hint * update actions * update actions * host node add_resource_from_outer fix cmake list * pass device config to device class * add: bind_parent_ids to resource create action fix: message convert string * fix: host node should not be re_discovered * feat: resource tracker support dict * feat: add more necessary params * feat: fix boolean null in registry action data * feat: add outer resource * 编写mesh添加action * feat: append resource * add action * feat: vis 2d for plr * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate * Device visualization (#22) * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * add 3d visualization * 完成在main中启动设备可视化 完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model 添加物料模型管理类，遍历物料与resource_model，完成TF数据收集 * 完成TF发布 * 修改模型方向，在yaml中添加变换属性 * 添加物料tf变化时，发送topic到前端 另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题 * 添加关节发布节点与物料可视化节点进入unilab * 使用json启动plr与3D模型仿真 * 完成启动OT并联动rviz * 修复rviz位置问题, 修复rviz位置问题, 在无tf变动时减缓发送频率 在backend中添加物料跟随方法 * fix: running logic * fix: running logic * fix: missing ot * 在main中直接初始化republisher和物料的mesh节点 * 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中 * 编写mesh添加action * add action * fix * fix: browser on rviz * fix: cloud bridge error fallback to local * fix: salve auto run rviz * 初始化两个plate --------- Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> * fix: multi channel * fix: aspirate * fix: aspirate * fix: aspirate * fix: aspirate * 提交 * fix: jobadd * fix: jobadd * fix: msg converter * tijiao * add resource creat easy action * identify debug msg * mq client id * unify liquid_handler definition * Update virtual_device.yaml * 更正了stir和heater的连接方式 * 区分了虚拟仪器中的八通阀和电磁阀，添加了两个阀门的驱动 * 修改了add protocol * 修复了阀门更新版的bug * 修复了添加protocol前缀导致的不能启动的bug * Fix handles * bump version to 0.9.6 * add resource edge upload * update container registry and handles * add virtual_separator virtual_rotavap fix transfer_pump * fix container value add parent_name to edge device id * 大图的问题都修复好了，添加了gassource和vacuum pump的驱动以及注册表 * default resource upload mode is false * 添加了icon的文件名在注册表里面 * 修改了json图中link的格式 * fix resource and edge upload * fix device ports * Fix edge id * 移除device的父节点关联 * separate registry sync and resource_add * 默认不进行注册表报送，通过命令unilabos-register或者增加启动参数 * 完善tip * protocol node不再嵌套显示 * bump version to 0.9.7 新增一个测试PumpTransferProtocol的teststation，亲测可以运行，将八通阀们和转移泵与pump_protocol适配 * protocol node 执行action不应携带自身device id * 添加了一套简易双八通阀工作站JSON，亲测能跑 * 修复了很多protocol，亲测能跑 * 添加了run column和filter through的protocol，亲测能跑 * fix mock_reactor * 修改了大图和小图的json，但是在前端上没看到改变 --------- Co-authored-by: Harvey Que Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com> Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com> Co-authored-by: Junhan Chang * 更新workstation注册表 * 添加了两个protocol的检索功能 (#51) * 添加了两个protocol的检索liquid type功能 * fix workstation registry * 修复了没连接的几个仪器的link，添加了container的icon * 修改了json和注册表，现在大图全部的device都链接上了 * 修复了小图的json图，线全部连上了 * add work_station protocol handles (ports) * fix workstation action handle --------- Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com> Co-authored-by: Junhan Chang --------- Co-authored-by: Junhan Chang Co-authored-by: Guangxin Zhang Co-authored-by: qxw138 Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com> Co-authored-by: Harvey Que Co-authored-by: Kongchang Feng <2100011801@stu.pku.edu.cn> Co-authored-by: hh. <103566763+Mile-Away@users.noreply.github.com> Co-authored-by: quehh Co-authored-by: Harvey Que Co-authored-by: Junhan Chang --- .../clean_vessel_protocol_test_station.json | 86 ++- .../comprehensive_station.json | 98 ++- unilabos/compile/__init__.py | 25 +- unilabos/compile/add_protocol.py | 316 ++++++++- unilabos/compile/clean_vessel_protocol.py | 163 ++++- unilabos/registry/devices/virtual_device.yaml | 8 + unilabos/registry/devices/work_station.yaml | 622 +++++++++++++++++- .../registry/resources/organic/container.yaml | 1 + 8 files changed, 1203 insertions(+), 116 deletions(-) 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 index f4200f71..6d793453 100644 --- a/test/experiments/Protocol_Test_Station/clean_vessel_protocol_test_station.json +++ b/test/experiments/Protocol_Test_Station/clean_vessel_protocol_test_station.json @@ -301,9 +301,9 @@ } } ], - "links": [ + "links": [ { - "id": "link_pump1_valve1", + "id": "link_pump1_to_valve1", "source": "transfer_pump_1", "target": "multiway_valve_1", "type": "fluid", @@ -313,7 +313,7 @@ } }, { - "id": "link_pump2_valve2", + "id": "link_pump2_to_valve2", "source": "transfer_pump_2", "target": "multiway_valve_2", "type": "fluid", @@ -323,17 +323,7 @@ } }, { - "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", + "id": "link_valve1_to_water", "source": "multiway_valve_1", "target": "flask_water", "type": "fluid", @@ -343,7 +333,7 @@ } }, { - "id": "link_valve1_acetone", + "id": "link_valve1_to_acetone", "source": "multiway_valve_1", "target": "flask_acetone", "type": "fluid", @@ -353,7 +343,7 @@ } }, { - "id": "link_valve1_ethanol", + "id": "link_valve1_to_ethanol", "source": "multiway_valve_1", "target": "flask_ethanol", "type": "fluid", @@ -363,17 +353,27 @@ } }, { - "id": "link_valve1_valve2", + "id": "link_valve1_to_air", + "source": "multiway_valve_1", + "target": "flask_air", + "type": "fluid", + "port": { + "multiway_valve_1": "6", + "flask_air": "top" + } + }, + { + "id": "link_valve1_to_valve2_for_cleaning", "source": "multiway_valve_1", "target": "multiway_valve_2", "type": "fluid", "port": { - "multiway_valve_1": "5", - "multiway_valve_2": "1" + "multiway_valve_1": "1", + "multiway_valve_2": "8" } }, { - "id": "link_valve2_main_reactor", + "id": "link_valve2_to_main_reactor_in", "source": "multiway_valve_2", "target": "main_reactor", "type": "fluid", @@ -383,7 +383,7 @@ } }, { - "id": "link_valve2_secondary_reactor", + "id": "link_valve2_to_secondary_reactor_in", "source": "multiway_valve_2", "target": "secondary_reactor", "type": "fluid", @@ -393,7 +393,27 @@ } }, { - "id": "link_valve2_waste", + "id": "link_main_reactor_out_to_valve2", + "source": "main_reactor", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "main_reactor": "bottom", + "multiway_valve_2": "6" + } + }, + { + "id": "link_secondary_reactor_out_to_valve2", + "source": "secondary_reactor", + "target": "multiway_valve_2", + "type": "fluid", + "port": { + "secondary_reactor": "bottom", + "multiway_valve_2": "7" + } + }, + { + "id": "link_valve2_to_waste", "source": "multiway_valve_2", "target": "waste_workup", "type": "fluid", @@ -403,17 +423,7 @@ } }, { - "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", + "id": "link_heatchill1_to_main_reactor", "source": "heatchill_1", "target": "main_reactor", "type": "mechanical", @@ -421,6 +431,16 @@ "heatchill_1": "heatchill", "main_reactor": "bind" } + }, + { + "id": "link_heatchill1_to_secondary_reactor", + "source": "heatchill_1", + "target": "secondary_reactor", + "type": "mechanical", + "port": { + "heatchill_1": "heatchill", + "secondary_reactor": "bind" + } } ] } \ No newline at end of file diff --git a/test/experiments/comprehensive_protocol/comprehensive_station.json b/test/experiments/comprehensive_protocol/comprehensive_station.json index b0f1a1bd..071d9137 100644 --- a/test/experiments/comprehensive_protocol/comprehensive_station.json +++ b/test/experiments/comprehensive_protocol/comprehensive_station.json @@ -1,8 +1,8 @@ { "nodes": [ { - "id": "ComprehensiveProtocolStation", - "name": "综合协议测试工作站", + "id": "OrganicSynthesisStation", + "name": "有机化学流程综合测试工作站", "children": [ "multiway_valve_1", "multiway_valve_2", @@ -69,7 +69,7 @@ "id": "multiway_valve_1", "name": "八通阀门1", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_multiway_valve", "position": { @@ -89,7 +89,7 @@ "id": "multiway_valve_2", "name": "八通阀门2", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_multiway_valve", "position": { @@ -109,7 +109,7 @@ "id": "transfer_pump_1", "name": "转移泵1", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_transfer_pump", "position": { @@ -130,7 +130,7 @@ "id": "transfer_pump_2", "name": "转移泵2", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_transfer_pump", "position": { @@ -151,7 +151,7 @@ "id": "reagent_bottle_1", "name": "试剂瓶1-DMF", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -172,7 +172,7 @@ "id": "reagent_bottle_2", "name": "试剂瓶2-乙酸乙酯", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -193,7 +193,7 @@ "id": "reagent_bottle_3", "name": "试剂瓶3-己烷", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -214,7 +214,7 @@ "id": "reagent_bottle_4", "name": "试剂瓶4-甲醇", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -235,7 +235,7 @@ "id": "reagent_bottle_5", "name": "试剂瓶5-水", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -256,7 +256,7 @@ "id": "centrifuge_1", "name": "离心机", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_centrifuge", "position": { @@ -278,7 +278,7 @@ "id": "rotavap_1", "name": "旋转蒸发仪", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_rotavap", "position": { @@ -300,7 +300,7 @@ "id": "main_reactor", "name": "主反应器", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -324,7 +324,7 @@ "id": "heater_1", "name": "加热器", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_heatchill", "position": { @@ -345,7 +345,7 @@ "id": "stirrer_1", "name": "搅拌器1", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_stirrer", "position": { @@ -365,7 +365,7 @@ "id": "stirrer_2", "name": "搅拌器2", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_stirrer", "position": { @@ -385,7 +385,7 @@ "id": "waste_bottle_1", "name": "废液瓶1", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -404,7 +404,7 @@ "id": "waste_bottle_2", "name": "废液瓶2", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -423,7 +423,7 @@ "id": "solenoid_valve_1", "name": "电磁阀1", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_solenoid_valve", "position": { @@ -444,7 +444,7 @@ "id": "solenoid_valve_2", "name": "电磁阀2", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_solenoid_valve", "position": { @@ -465,7 +465,7 @@ "id": "vacuum_pump_1", "name": "真空泵", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_vacuum_pump", "position": { @@ -486,7 +486,7 @@ "id": "gas_source_1", "name": "气源", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_gas_source", "position": { @@ -504,7 +504,7 @@ "id": "filter_1", "name": "过滤器", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_filter", "position": { @@ -525,7 +525,7 @@ "id": "column_1", "name": "洗脱柱", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_column", "position": { @@ -547,7 +547,7 @@ "id": "separator_1", "name": "分液器", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "device", "class": "virtual_separator", "position": { @@ -568,7 +568,7 @@ "id": "collection_bottle_1", "name": "接收瓶1", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -587,7 +587,7 @@ "id": "collection_bottle_2", "name": "接收瓶2", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -606,7 +606,7 @@ "id": "collection_bottle_3", "name": "接收瓶3", "children": [], - "parent": "ComprehensiveProtocolStation", + "parent": "OrganicSynthesisStation", "type": "container", "class": "container", "position": { @@ -852,6 +852,46 @@ "heater_1": "heatchill", "main_reactor": "bind" } + }, + { + "id": "link_separator_waste2", + "source": "separator_1", + "target": "waste_bottle_2", + "type": "fluid", + "port": { + "separator_1": "top_phase_out", + "waste_bottle_2": "top" + } + }, + { + "id": "mech_stirrer2_separator", + "source": "stirrer_2", + "target": "separator_1", + "type": "mechanical", + "port": { + "stirrer_2": "stirrer", + "separator_1": "bind" + } + }, + { + "id": "link_filter_filtrate_to_collection1", + "source": "filter_1", + "target": "collection_bottle_1", + "type": "transport", + "port": { + "filter_1": "filtrate_out", + "collection_bottle_1": "top" + } + }, + { + "id": "link_filter_retentate_to_waste1", + "source": "filter_1", + "target": "waste_bottle_1", + "type": "transport", + "port": { + "filter_1": "retentate_out", + "waste_bottle_1": "top" + } } ] } \ No newline at end of file diff --git a/unilabos/compile/__init__.py b/unilabos/compile/__init__.py index 0b56a5d2..98ea8a28 100644 --- a/unilabos/compile/__init__.py +++ b/unilabos/compile/__init__.py @@ -25,26 +25,25 @@ from .wash_solid_protocol import generate_wash_solid_protocol # Define a dictionary of protocol generators. action_protocol_generators = { - PumpTransferProtocol: generate_pump_protocol_with_rinsing, - CleanProtocol: generate_clean_protocol, - SeparateProtocol: generate_separate_protocol, - EvaporateProtocol: generate_evaporate_protocol, - EvacuateAndRefillProtocol: generate_evacuateandrefill_protocol, + AddProtocol: generate_add_protocol, AGVTransferProtocol: generate_agv_transfer_protocol, CentrifugeProtocol: generate_centrifuge_protocol, - AddProtocol: generate_add_protocol, + CleanProtocol: generate_clean_protocol, + CleanVesselProtocol: generate_clean_vessel_protocol, + DissolveProtocol: generate_dissolve_protocol, + EvacuateAndRefillProtocol: generate_evacuateandrefill_protocol, + EvaporateProtocol: generate_evaporate_protocol, FilterProtocol: generate_filter_protocol, + FilterThroughProtocol: generate_filter_through_protocol, 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, + PumpTransferProtocol: generate_pump_protocol_with_rinsing, + RunColumnProtocol: generate_run_column_protocol, + SeparateProtocol: generate_separate_protocol, StartStirProtocol: generate_start_stir_protocol, + StirProtocol: generate_stir_protocol, StopStirProtocol: generate_stop_stir_protocol, 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, -} +} \ No newline at end of file diff --git a/unilabos/compile/add_protocol.py b/unilabos/compile/add_protocol.py index a1398e68..144ec96f 100644 --- a/unilabos/compile/add_protocol.py +++ b/unilabos/compile/add_protocol.py @@ -5,7 +5,10 @@ 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 + 根据试剂名称查找对应的试剂瓶，支持多种匹配模式： + 1. 容器名称匹配（如 flask_DMF, reagent_bottle_1-DMF） + 2. 容器内液体类型匹配（如 liquid_type: "DMF", name: "ethanol"） + 3. 试剂名称匹配（如 reagent_name: "DMF", config.reagent: "ethyl_acetate"） Args: G: 网络图 @@ -17,23 +20,184 @@ def find_reagent_vessel(G: nx.DiGraph, reagent: str) -> str: 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}" + print(f"ADD_PROTOCOL: 正在查找试剂 '{reagent}' 的容器...") - if reagent_vessel_id in G.nodes(): - return reagent_vessel_id + # 第一步：通过容器名称匹配 + possible_names = [ + f"flask_{reagent}", # flask_DMF, flask_ethanol + f"bottle_{reagent}", # bottle_DMF, bottle_ethanol + f"vessel_{reagent}", # vessel_DMF, vessel_ethanol + f"{reagent}_flask", # DMF_flask, ethanol_flask + f"{reagent}_bottle", # DMF_bottle, ethanol_bottle + f"{reagent}", # 直接用试剂名 + f"reagent_{reagent}", # reagent_DMF, reagent_ethanol + f"reagent_bottle_{reagent}", # reagent_bottle_DMF + ] - # 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 + # 尝试名称匹配 + for vessel_name in possible_names: + if vessel_name in G.nodes(): + print(f"ADD_PROTOCOL: 通过名称匹配找到容器: {vessel_name}") + return vessel_name - # 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'] + # 第二步：通过模糊名称匹配（名称中包含试剂名） + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + # 检查节点ID或名称中是否包含试剂名 + node_name = G.nodes[node_id].get('name', '').lower() + if (reagent.lower() in node_id.lower() or + reagent.lower() in node_name): + print(f"ADD_PROTOCOL: 通过模糊名称匹配找到容器: {node_id} (名称: {node_name})") + return node_id - raise ValueError(f"找不到试剂 '{reagent}' 对应的试剂瓶。可用试剂瓶: {available_flasks}") + # 第三步：通过液体类型匹配 + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + vessel_data = G.nodes[node_id].get('data', {}) + liquids = vessel_data.get('liquid', []) + + for liquid in liquids: + if isinstance(liquid, dict): + # 支持两种格式的液体类型字段 + liquid_type = liquid.get('liquid_type') or liquid.get('name', '') + reagent_name = vessel_data.get('reagent_name', '') + config_reagent = G.nodes[node_id].get('config', {}).get('reagent', '') + + # 检查多个可能的字段 + if (liquid_type.lower() == reagent.lower() or + reagent_name.lower() == reagent.lower() or + config_reagent.lower() == reagent.lower()): + print(f"ADD_PROTOCOL: 通过液体类型匹配找到容器: {node_id}") + print(f" - liquid_type: {liquid_type}") + print(f" - reagent_name: {reagent_name}") + print(f" - config.reagent: {config_reagent}") + return node_id + + # 第四步：列出所有可用的容器信息帮助调试 + available_containers = [] + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + vessel_data = G.nodes[node_id].get('data', {}) + config_data = G.nodes[node_id].get('config', {}) + liquids = vessel_data.get('liquid', []) + + container_info = { + 'id': node_id, + 'name': G.nodes[node_id].get('name', ''), + 'liquid_types': [], + 'reagent_name': vessel_data.get('reagent_name', ''), + 'config_reagent': config_data.get('reagent', '') + } + + for liquid in liquids: + if isinstance(liquid, dict): + liquid_type = liquid.get('liquid_type') or liquid.get('name', '') + if liquid_type: + container_info['liquid_types'].append(liquid_type) + + available_containers.append(container_info) + + print(f"ADD_PROTOCOL: 可用容器列表:") + for container in available_containers: + print(f" - {container['id']}: {container['name']}") + print(f" 液体类型: {container['liquid_types']}") + print(f" 试剂名称: {container['reagent_name']}") + print(f" 配置试剂: {container['config_reagent']}") + + raise ValueError(f"找不到试剂 '{reagent}' 对应的试剂瓶。尝试了名称匹配: {possible_names}") + + +def find_reagent_vessel_by_any_match(G: nx.DiGraph, reagent: str) -> str: + """ + 增强版试剂容器查找，支持各种匹配方式的别名函数 + """ + return find_reagent_vessel(G, reagent) + + +def get_vessel_reagent_volume(G: nx.DiGraph, vessel: str) -> float: + """获取容器中的试剂体积""" + 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 get_vessel_reagent_types(G: nx.DiGraph, vessel: str) -> List[str]: + """获取容器中所有试剂的类型""" + if vessel not in G.nodes(): + return [] + + vessel_data = G.nodes[vessel].get('data', {}) + liquids = vessel_data.get('liquid', []) + + reagent_types = [] + for liquid in liquids: + if isinstance(liquid, dict): + # 支持两种格式的试剂类型字段 + reagent_type = liquid.get('liquid_type') or liquid.get('name', '') + if reagent_type: + reagent_types.append(reagent_type) + + # 同时检查配置中的试剂信息 + config_reagent = G.nodes[vessel].get('config', {}).get('reagent', '') + reagent_name = vessel_data.get('reagent_name', '') + + if config_reagent and config_reagent not in reagent_types: + reagent_types.append(config_reagent) + if reagent_name and reagent_name not in reagent_types: + reagent_types.append(reagent_name) + + return reagent_types + + +def find_vessels_by_reagent(G: nx.DiGraph, reagent: str) -> List[str]: + """ + 根据试剂类型查找所有匹配的容器 + 返回匹配容器的ID列表 + """ + matching_vessels = [] + + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + # 检查容器名称匹配 + node_name = G.nodes[node_id].get('name', '').lower() + if reagent.lower() in node_id.lower() or reagent.lower() in node_name: + matching_vessels.append(node_id) + continue + + # 检查试剂类型匹配 + vessel_data = G.nodes[node_id].get('data', {}) + liquids = vessel_data.get('liquid', []) + config_data = G.nodes[node_id].get('config', {}) + + # 检查 reagent_name 和 config.reagent + reagent_name = vessel_data.get('reagent_name', '').lower() + config_reagent = config_data.get('reagent', '').lower() + + if (reagent.lower() == reagent_name or + reagent.lower() == config_reagent): + matching_vessels.append(node_id) + continue + + # 检查液体列表 + for liquid in liquids: + if isinstance(liquid, dict): + liquid_type = liquid.get('liquid_type') or liquid.get('name', '') + if liquid_type.lower() == reagent.lower(): + matching_vessels.append(node_id) + break + + return matching_vessels def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str: @@ -49,7 +213,7 @@ def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str: """ # 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'] + 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: @@ -74,10 +238,10 @@ def generate_add_protocol( purpose: str = "添加试剂" ) -> List[Dict[str, Any]]: """ - 生成添加试剂的协议序列 + 生成添加试剂的协议序列，支持智能试剂匹配 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 + 1. 智能查找试剂瓶（支持名称匹配、液体类型匹配、试剂配置匹配） 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 @@ -102,24 +266,41 @@ def generate_add_protocol( """ action_sequence = [] + print(f"ADD_PROTOCOL: 开始生成添加试剂协议") + print(f" - 目标容器: {vessel}") + print(f" - 试剂: {reagent}") + print(f" - 体积: {volume} mL") + print(f" - 质量: {mass} g") + print(f" - 搅拌: {stir} (速度: {stir_speed} RPM)") + print(f" - 粘稠: {viscous}") + print(f" - 目的: {purpose}") + # 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 + # 2. 智能查找试剂瓶 try: reagent_vessel = find_reagent_vessel(G, reagent) + print(f"ADD_PROTOCOL: 找到试剂容器: {reagent_vessel}") 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 + # 3. 验证试剂容器中的试剂体积 + available_volume = get_vessel_reagent_volume(G, reagent_vessel) + print(f"ADD_PROTOCOL: 试剂容器 {reagent_vessel} 中有 {available_volume} mL 试剂") + + if available_volume < volume: + print(f"ADD_PROTOCOL: 警告 - 试剂容器中的试剂不足！需要 {volume} mL，可用 {available_volume} mL") + + # 4. 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！ + # 5. **先启动搅拌** - 关键改进！ if stir: try: stirrer_id = find_connected_stirrer(G, vessel) @@ -140,15 +321,21 @@ def generate_add_protocol( action_sequence.append(stir_action) print(f"ADD_PROTOCOL: 已添加搅拌动作，速度 {stir_speed} RPM") + + # 等待搅拌稳定 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 5} + }) 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") 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 + # 6. 如果指定了体积，执行液体转移 if volume > 0: - # 5.1 计算流速参数 + # 6.1 计算流速参数 if time > 0: # 根据时间计算流速 transfer_flowrate = volume / time @@ -165,7 +352,7 @@ def generate_add_protocol( 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 + # 6.2 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, @@ -190,6 +377,8 @@ def generate_add_protocol( 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") + print(f"ADD_PROTOCOL: 添加试剂协议生成完成") + return action_sequence @@ -210,7 +399,7 @@ def generate_add_protocol_with_cleaning( cleaning_repeats: int = 1 ) -> List[Dict[str, Any]]: """ - 生成带清洗的添加试剂协议 + 生成带清洗的添加试剂协议，支持智能试剂匹配 与普通添加协议的区别是会在添加后进行管道清洗 @@ -235,7 +424,7 @@ def generate_add_protocol_with_cleaning( """ action_sequence = [] - # 1. 查找试剂瓶 + # 1. 智能查找试剂瓶 reagent_vessel = find_reagent_vessel(G, reagent) # 2. **先启动搅拌** @@ -251,6 +440,12 @@ def generate_add_protocol_with_cleaning( "purpose": f"{purpose}: 启动搅拌，准备添加 {reagent}" } }) + + # 等待搅拌稳定 + action_sequence.append({ + "action_name": "wait", + "action_kwargs": {"time": 5} + }) # 3. 计算流速 if time > 0: @@ -296,7 +491,7 @@ def generate_sequential_add_protocol( final_stir_time: float = 300.0 ) -> List[Dict[str, Any]]: """ - 生成连续添加多种试剂的协议 + 生成连续添加多种试剂的协议，支持智能试剂匹配 Args: G: 网络图 @@ -313,13 +508,13 @@ def generate_sequential_add_protocol( Example: reagents = [ { - "reagent": "DMF", + "reagent": "DMF", # 会匹配 reagent_bottle_1 (reagent_name: "DMF") "volume": 10.0, "viscous": False, "stir_speed": 300.0 }, { - "reagent": "ethyl_acetate", + "reagent": "ethyl_acetate", # 会匹配 reagent_bottle_2 (reagent_name: "ethyl_acetate") "volume": 5.0, "viscous": False, "stir_speed": 350.0 @@ -328,14 +523,17 @@ def generate_sequential_add_protocol( """ action_sequence = [] + print(f"ADD_PROTOCOL: 开始连续添加 {len(reagents)} 种试剂到容器 {vessel}") + 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')}") + reagent_name = reagent_params.get('reagent') + print(f"ADD_PROTOCOL: 处理第 {i+1}/{len(reagents)} 个试剂: {reagent_name}") # 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'), + reagent=reagent_name, volume=reagent_params.get('volume', 0.0), mass=reagent_params.get('mass', 0.0), amount=reagent_params.get('amount', ''), @@ -343,7 +541,7 @@ def generate_sequential_add_protocol( 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}') + purpose=reagent_params.get('purpose', f'添加试剂 {reagent_name} ({i+1}/{len(reagents)})') ) action_sequence.extend(add_actions) @@ -352,17 +550,23 @@ def generate_sequential_add_protocol( if i < len(reagents) - 1: # 不是最后一个试剂 action_sequence.append({ "action_name": "wait", - "action_kwargs": {"time": 2} + "action_kwargs": {"time": 10} # 试剂混合时间 }) # 最终搅拌 if final_stir: stirrer_id = find_connected_stirrer(G, vessel) if stirrer_id: + print(f"ADD_PROTOCOL: 添加最终搅拌动作，速度 {final_stir_speed} RPM，时间 {final_stir_time} 秒") action_sequence.extend([ { - "action_name": "wait", - "action_kwargs": {"time": final_stir_time} + "device_id": stirrer_id, + "action_name": "stir", + "action_kwargs": { + "stir_time": final_stir_time, + "stir_speed": final_stir_speed, + "settling_time": 30.0 + } } ]) @@ -370,10 +574,52 @@ def generate_sequential_add_protocol( return action_sequence +# 便捷函数：常用添加方案 +def generate_organic_add_protocol( + G: nx.DiGraph, + vessel: str, + organic_reagent: str, + volume: float, + stir_speed: float = 400.0 +) -> List[Dict[str, Any]]: + """有机试剂添加：慢速、搅拌""" + return generate_add_protocol( + G, vessel, organic_reagent, volume, 0.0, "", 0.0, + True, stir_speed, False, f"添加有机试剂 {organic_reagent}" + ) + + +def generate_viscous_add_protocol( + G: nx.DiGraph, + vessel: str, + viscous_reagent: str, + volume: float, + addition_time: float = 120.0 +) -> List[Dict[str, Any]]: + """粘稠试剂添加：慢速、长时间""" + return generate_add_protocol( + G, vessel, viscous_reagent, volume, 0.0, "", addition_time, + True, 250.0, True, f"缓慢添加粘稠试剂 {viscous_reagent}" + ) + + +def generate_solvent_add_protocol( + G: nx.DiGraph, + vessel: str, + solvent: str, + volume: float +) -> List[Dict[str, Any]]: + """溶剂添加：快速、无需特殊处理""" + return generate_add_protocol( + G, vessel, solvent, volume, 0.0, "", 0.0, + False, 300.0, False, f"添加溶剂 {solvent}" + ) + + # 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("=== ADD PROTOCOL 智能匹配测试 ===") print("测试完成") diff --git a/unilabos/compile/clean_vessel_protocol.py b/unilabos/compile/clean_vessel_protocol.py index cf752fae..28abc954 100644 --- a/unilabos/compile/clean_vessel_protocol.py +++ b/unilabos/compile/clean_vessel_protocol.py @@ -5,9 +5,13 @@ 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 + 查找溶剂容器，支持多种匹配模式： + 1. 容器名称匹配（如 flask_water, reagent_bottle_1-DMF） + 2. 容器内液体类型匹配（如 liquid_type: "DMF", "ethanol"） """ - # 可能的溶剂容器命名模式 + print(f"CLEAN_VESSEL: 正在查找溶剂 '{solvent}' 的容器...") + + # 第一步：通过容器名称匹配 possible_names = [ f"flask_{solvent}", # flask_water, flask_ethanol f"bottle_{solvent}", # bottle_water, bottle_ethanol @@ -16,13 +20,87 @@ def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str: f"{solvent}_bottle", # water_bottle, ethanol_bottle f"{solvent}", # 直接用溶剂名 f"solvent_{solvent}", # solvent_water, solvent_ethanol + f"reagent_bottle_{solvent}", # reagent_bottle_DMF ] + # 尝试名称匹配 for vessel_name in possible_names: if vessel_name in G.nodes(): + print(f"CLEAN_VESSEL: 通过名称匹配找到容器: {vessel_name}") return vessel_name - raise ValueError(f"未找到溶剂 '{solvent}' 的容器。尝试了以下名称: {possible_names}") + # 第二步：通过模糊名称匹配（名称中包含溶剂名） + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + # 检查节点ID或名称中是否包含溶剂名 + node_name = G.nodes[node_id].get('name', '').lower() + if (solvent.lower() in node_id.lower() or + solvent.lower() in node_name): + print(f"CLEAN_VESSEL: 通过模糊名称匹配找到容器: {node_id} (名称: {node_name})") + return node_id + + # 第三步：通过液体类型匹配 + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + vessel_data = G.nodes[node_id].get('data', {}) + liquids = vessel_data.get('liquid', []) + + for liquid in liquids: + if isinstance(liquid, dict): + # 支持两种格式的液体类型字段 + liquid_type = liquid.get('liquid_type') or liquid.get('name', '') + reagent_name = vessel_data.get('reagent_name', '') + config_reagent = G.nodes[node_id].get('config', {}).get('reagent', '') + + # 检查多个可能的字段 + if (liquid_type.lower() == solvent.lower() or + reagent_name.lower() == solvent.lower() or + config_reagent.lower() == solvent.lower()): + print(f"CLEAN_VESSEL: 通过液体类型匹配找到容器: {node_id}") + print(f" - liquid_type: {liquid_type}") + print(f" - reagent_name: {reagent_name}") + print(f" - config.reagent: {config_reagent}") + return node_id + + # 第四步：列出所有可用的容器信息帮助调试 + available_containers = [] + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + vessel_data = G.nodes[node_id].get('data', {}) + config_data = G.nodes[node_id].get('config', {}) + liquids = vessel_data.get('liquid', []) + + container_info = { + 'id': node_id, + 'name': G.nodes[node_id].get('name', ''), + 'liquid_types': [], + 'reagent_name': vessel_data.get('reagent_name', ''), + 'config_reagent': config_data.get('reagent', '') + } + + for liquid in liquids: + if isinstance(liquid, dict): + liquid_type = liquid.get('liquid_type') or liquid.get('name', '') + if liquid_type: + container_info['liquid_types'].append(liquid_type) + + available_containers.append(container_info) + + print(f"CLEAN_VESSEL: 可用容器列表:") + for container in available_containers: + print(f" - {container['id']}: {container['name']}") + print(f" 液体类型: {container['liquid_types']}") + print(f" 试剂名称: {container['reagent_name']}") + print(f" 配置试剂: {container['config_reagent']}") + + raise ValueError(f"未找到溶剂 '{solvent}' 的容器。尝试了名称匹配: {possible_names}") + + +def find_solvent_vessel_by_any_match(G: nx.DiGraph, solvent: str) -> str: + """ + 增强版溶剂容器查找，支持各种匹配方式的别名函数 + """ + return find_solvent_vessel(G, solvent) def find_waste_vessel(G: nx.DiGraph) -> str: @@ -281,4 +359,81 @@ def generate_organic_clean_protocol( ) action_sequence.extend(water_actions) - return action_sequence \ No newline at end of file + return action_sequence + + +def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float: + """获取容器中的液体体积（修复版）""" + 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 get_vessel_liquid_types(G: nx.DiGraph, vessel: str) -> List[str]: + """获取容器中所有液体的类型""" + if vessel not in G.nodes(): + return [] + + vessel_data = G.nodes[vessel].get('data', {}) + liquids = vessel_data.get('liquid', []) + + liquid_types = [] + for liquid in liquids: + if isinstance(liquid, dict): + # 支持两种格式的液体类型字段 + liquid_type = liquid.get('liquid_type') or liquid.get('name', '') + if liquid_type: + liquid_types.append(liquid_type) + + return liquid_types + + +def find_vessel_by_content(G: nx.DiGraph, content: str) -> List[str]: + """ + 根据内容物查找所有匹配的容器 + 返回匹配容器的ID列表 + """ + matching_vessels = [] + + for node_id in G.nodes(): + if G.nodes[node_id].get('type') == 'container': + # 检查容器名称匹配 + node_name = G.nodes[node_id].get('name', '').lower() + if content.lower() in node_id.lower() or content.lower() in node_name: + matching_vessels.append(node_id) + continue + + # 检查液体类型匹配 + vessel_data = G.nodes[node_id].get('data', {}) + liquids = vessel_data.get('liquid', []) + config_data = G.nodes[node_id].get('config', {}) + + # 检查 reagent_name 和 config.reagent + reagent_name = vessel_data.get('reagent_name', '').lower() + config_reagent = config_data.get('reagent', '').lower() + + if (content.lower() == reagent_name or + content.lower() == config_reagent): + matching_vessels.append(node_id) + continue + + # 检查液体列表 + for liquid in liquids: + if isinstance(liquid, dict): + liquid_type = liquid.get('liquid_type') or liquid.get('name', '') + if liquid_type.lower() == content.lower(): + matching_vessels.append(node_id) + break + + return matching_vessels \ No newline at end of file diff --git a/unilabos/registry/devices/virtual_device.yaml b/unilabos/registry/devices/virtual_device.yaml index 26d620da..e25c0d6b 100644 --- a/unilabos/registry/devices/virtual_device.yaml +++ b/unilabos/registry/devices/virtual_device.yaml @@ -845,6 +845,14 @@ virtual_separator: data_source: executor data_key: top_outlet description: "上相（轻相）液体输出口" + - handler_key: bind + label: bind + io_type: target + data_type: mechanical + side: WEST + data_source: handle + data_key: mechanical_port + description: "用于连接搅拌器等机械设备的接口" schema: type: object properties: diff --git a/unilabos/registry/devices/work_station.yaml b/unilabos/registry/devices/work_station.yaml index d3a37338..c8c0324d 100644 --- a/unilabos/registry/devices/work_station.yaml +++ b/unilabos/registry/devices/work_station.yaml @@ -3,5 +3,623 @@ workstation: class: module: unilabos.ros.nodes.presets.protocol_node:ROS2ProtocolNode type: ros2 - schema: - properties: {} + action_value_mappings: + AddProtocol: + type: Add + goal: + vessel: vessel + reagent: reagent + volume: volume + mass: mass + amount: amount + time: time + stir: stir + stir_speed: stir_speed + viscous: viscous + purpose: purpose + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: reagent + label: Reagent + data_type: resource + data_source: handle + data_key: reagent + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + AGVTransferProtocol: + type: AGVTransfer + goal: + from_repo: from_repo + from_repo_position: from_repo_position + to_repo: to_repo + to_repo_position: to_repo_position + feedback: {} + result: {} + + CentrifugeProtocol: + type: Centrifuge + goal: + vessel: vessel + speed: speed + time: time + temp: temp + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + CleanProtocol: + type: Clean + goal: + vessel: vessel + solvent: solvent + volume: volume + temp: temp + repeats: repeats + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: solvent + label: Solvent + data_type: resource + data_source: handle + data_key: solvent + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + CleanVesselProtocol: + type: CleanVessel + goal: + vessel: vessel + solvent: solvent + volume: volume + temp: temp + repeats: repeats + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: solvent + label: Solvent + data_type: resource + data_source: handle + data_key: solvent + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + DissolveProtocol: + type: Dissolve + goal: + vessel: vessel + solvent: solvent + volume: volume + amount: amount + temp: temp + time: time + stir_speed: stir_speed + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: solvent + label: Solvent + data_type: resource + data_source: handle + data_key: solvent + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + EvacuateAndRefillProtocol: + type: EvacuateAndRefill + goal: + vessel: vessel + gas: gas + repeats: repeats + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + EvaporateProtocol: + type: Evaporate + goal: + vessel: vessel + pressure: pressure + temp: temp + time: time + stir_speed: stir_speed + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + FilterProtocol: + type: Filter + goal: + vessel: vessel + filtrate_vessel: filtrate_vessel + stir: stir + stir_speed: stir_speed + temp: temp + continue_heatchill: continue_heatchill + volume: volume + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: filtrate_vessel + label: Filtrate Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + - handler_key: filtrate_out + label: Filtrate Vessel + data_type: resource + data_source: executor + data_key: vessel + + FilterThroughProtocol: + type: FilterThrough + goal: + from_vessel: from_vessel + to_vessel: to_vessel + filter_through: filter_through + eluting_solvent: eluting_solvent + eluting_volume: eluting_volume + eluting_repeats: eluting_repeats + residence_time: residence_time + feedback: {} + result: {} + handles: + input: + - handler_key: from_vessel + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + - handler_key: solvent + label: Eluting Solvent + data_type: resource + data_source: handle + data_key: solvent + output: + - handler_key: from_vessel_out + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel_out + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + + HeatChillProtocol: + type: HeatChill + goal: + vessel: vessel + temp: temp + time: time + stir: stir + stir_speed: stir_speed + purpose: purpose + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + HeatChillStartProtocol: + type: HeatChillStart + goal: + vessel: vessel + temp: temp + purpose: purpose + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + HeatChillStopProtocol: + type: HeatChillStop + goal: + vessel: vessel + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + PumpTransferProtocol: + type: PumpTransfer + goal: + from_vessel: from_vessel + to_vessel: to_vessel + volume: volume + amount: amount + time: time + viscous: viscous + rinsing_solvent: rinsing_solvent + rinsing_volume: rinsing_volume + rinsing_repeats: rinsing_repeats + solid: solid + feedback: {} + result: {} + handles: + input: + - handler_key: from_vessel + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + - handler_key: solvent + label: Rinsing Solvent + data_type: resource + data_source: handle + data_key: solvent + output: + - handler_key: from_vessel_out + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel_out + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + + RunColumnProtocol: + type: RunColumn + goal: + from_vessel: from_vessel + to_vessel: to_vessel + column: column + feedback: {} + result: {} + handles: + input: + - handler_key: from_vessel + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + output: + - handler_key: from_vessel_out + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel_out + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + + SeparateProtocol: + 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: {} + result: {} + handles: + input: + - handler_key: from_vessel + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + - handler_key: solvent + label: Solvent + data_type: resource + data_source: handle + data_key: solvent + output: + - handler_key: from_vessel_out + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel_out + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + + StartStirProtocol: + type: StartStir + goal: + vessel: vessel + stir_speed: stir_speed + purpose: purpose + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + StirProtocol: + type: Stir + goal: + stir_time: stir_time + stir_speed: stir_speed + settling_time: settling_time + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + StopStirProtocol: + type: StopStir + goal: + vessel: vessel + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel + data_type: resource + data_source: executor + data_key: vessel + + TransferProtocol: + type: Transfer + goal: + from_vessel: from_vessel + to_vessel: to_vessel + volume: volume + amount: amount + time: time + viscous: viscous + rinsing_solvent: rinsing_solvent + rinsing_volume: rinsing_volume + rinsing_repeats: rinsing_repeats + solid: solid + feedback: {} + result: {} + handles: + input: + - handler_key: from_vessel + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + - handler_key: solvent + label: Rinsing Solvent + data_type: resource + data_source: handle + data_key: solvent + output: + - handler_key: from_vessel_out + label: From Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: to_vessel_out + label: To Vessel + data_type: resource + data_source: executor + data_key: vessel + + WashSolidProtocol: + type: WashSolid + goal: + vessel: vessel + solvent: solvent + volume: volume + filtrate_vessel: filtrate_vessel + temp: temp + stir: stir + stir_speed: stir_speed + time: time + repeats: repeats + feedback: {} + result: {} + handles: + input: + - handler_key: vessel + label: Vessel + data_type: resource + data_source: handle + data_key: vessel + - handler_key: solvent + label: Solvent + data_type: resource + data_source: handle + data_key: solvent + - handler_key: filtrate_vessel + label: Filtrate Vessel + data_type: resource + data_source: executor + data_key: vessel + output: + - handler_key: vessel_out + label: Vessel Out + data_type: resource + data_source: handle + data_key: vessel + - handler_key: filtrate_vessel_out + label: Filtrate Vessel + data_type: resource + data_source: executor + data_key: vessel \ No newline at end of file diff --git a/unilabos/registry/resources/organic/container.yaml b/unilabos/registry/resources/organic/container.yaml index bfdcba90..2186b700 100644 --- a/unilabos/registry/resources/organic/container.yaml +++ b/unilabos/registry/resources/organic/container.yaml @@ -1,5 +1,6 @@ container: description: regular organic container + icon: Flask.webp class: module: unilabos.resources.container:RegularContainer type: unilabos