fix serialization error

nmdc_automation/import_automation/activity_mapper.py

@@ -4,14 +4,11 @@
 import logging
 import datetime
 import pytz
-import json
 import yaml
 
 from typing import List, Dict, Union, Tuple
 from nmdc_schema import nmdc
 
-
-from linkml_runtime.dumpers import json_dumper
 from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_automation.models.nmdc import DataObject, workflow_process_factory
 from .utils import object_action, file_link, get_md5, filter_import_by_type

nmdc_automation/workflow_automation/watch_nmdc.py

@@ -6,6 +6,8 @@
 from json import loads
 from pathlib import Path
 from typing import List, Dict, Any, Optional, Union, Tuple
+from linkml_runtime.dumpers import yaml_dumper
+import yaml
 
 from nmdc_schema.nmdc import Database
 from nmdc_automation.api import NmdcRuntimeApi
@@ -286,7 +288,7 @@ def cycle(self):
         successful_jobs, failed_jobs = self.job_manager.get_finished_jobs()
         for job in successful_jobs:
             job_database = self.job_manager.process_successful_job(job)
-            job_dict = json.loads(job_database.json(exclude_unset=True))
+            job_dict = yaml.safe_load(yaml_dumper.dumps(job_database))
 
             # post workflow execution and data objects to the runtime api
             resp = self.runtime_api_handler.post_objects(job_dict)