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 <changjh@pku.edu.cn>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>

unilabos/app/main.py

@@ -10,6 +10,8 @@ from copy import deepcopy
 
 import yaml
 
+from unilabos.resources.graphio import tree_to_list
+
 # 首先添加项目根目录到路径
 current_dir = os.path.dirname(os.path.abspath(__file__))
 unilabos_dir = os.path.dirname(os.path.dirname(current_dir))
@@ -144,19 +146,19 @@ def main():
             else read_graphml(args_dict["graph"])
         )
         devices_and_resources = dict_from_graph(graph_res.physical_setup_graph)
-        args_dict["resources_config"] = initialize_resources(list(deepcopy(devices_and_resources).values()))
+        # args_dict["resources_config"] = initialize_resources(list(deepcopy(devices_and_resources).values()))
+        args_dict["resources_config"] = list(devices_and_resources.values())
         args_dict["devices_config"] = dict_to_nested_dict(deepcopy(devices_and_resources), devices_only=False)
-        # args_dict["resources_config"] = dict_to_tree(devices_and_resources, devices_only=False)
-
         args_dict["graph"] = graph_res.physical_setup_graph
     else:
         if args_dict["devices"] is None or args_dict["resources"] is None:
             print_status("Either graph or devices and resources must be provided.", "error")
             sys.exit(1)
         args_dict["devices_config"] = json.load(open(args_dict["devices"], encoding="utf-8"))
-        args_dict["resources_config"] = initialize_resources(
-            list(json.load(open(args_dict["resources"], encoding="utf-8")).values())
-        )
+        # args_dict["resources_config"] = initialize_resources(
+        #     list(json.load(open(args_dict["resources"], encoding="utf-8")).values())
+        # )
+        args_dict["resources_config"] = list(json.load(open(args_dict["resources"], encoding="utf-8")).values())
 
     print_status(f"{len(args_dict['resources_config'])} Resources loaded:", "info")
     for i in args_dict["resources_config"]:

unilabos/app/mq.py

@@ -1,6 +1,7 @@
 import json
 import time
 import traceback
+from typing import Optional
 import uuid
 
 import paho.mqtt.client as mqtt
@@ -163,10 +164,12 @@ class MQTTClient:
         self.client.publish(address, json.dumps(status), qos=2)
         logger.critical(f"Device status published: address: {address}, {status}")
 
-    def publish_job_status(self, feedback_data: dict, job_id: str, status: str):
+    def publish_job_status(self, feedback_data: dict, job_id: str, status: str, return_info: Optional[str] = None):
         if self.mqtt_disable:
             return
-        jobdata = {"job_id": job_id, "data": feedback_data, "status": status}
+        if return_info is None:
+            return_info = "{}"
+        jobdata = {"job_id": job_id, "data": feedback_data, "status": status, "return_info": return_info}
         self.client.publish(f"labs/{MQConfig.lab_id}/job/list/", json.dumps(jobdata), qos=2)
 
     def publish_registry(self, device_id: str, device_info: dict):

unilabos/app/web/client.py

@@ -30,18 +30,18 @@ class HTTPClient:
             self.auth = MQConfig.lab_id
         info(f"HTTPClient 初始化完成: remote_addr={self.remote_addr}")
 
-    def resource_add(self, resources: List[Dict[str, Any]]) -> requests.Response:
+    def resource_add(self, resources: List[Dict[str, Any]], database_process_later:bool) -> requests.Response:
         """
         添加资源
 
         Args:
             resources: 要添加的资源列表
-
+            database_process_later: 后台处理资源
         Returns:
             Response: API响应对象
         """
         response = requests.post(
-            f"{self.remote_addr}/lab/resource/",
+            f"{self.remote_addr}/lab/resource/?database_process_later={1 if database_process_later else 0}",
             json=resources,
             headers={"Authorization": f"lab {self.auth}"},
             timeout=5,