initial changes for bufr conversion refactor

parm/ioda/bufr2ioda/bufr2ioda_insitu_profile_argo.yaml

@@ -0,0 +1,10 @@
+cycle_datetime: '{{ current_cycle | to_YMDH }}'
+cycle_type: '{{ RUN }}'
+data_description: 6-hrly in situ ARGO profiles
+data_format: subpfl
+data_provider: U.S. NOAA
+data_type: argo
+dump_directory: '{{ DMPDIR }}'
+ioda_directory: '{{ COM_OBS }}'
+source: NCEP data tank
+subsets: SUBPFL

parm/ioda/bufr2ioda/j2y.py

@@ -0,0 +1,24 @@
+import json
+import yaml
+import argparse
+
+def convert_json_to_yaml(input_file, output_file):
+ # Load the JSON data from the input file
+ with open(input_file, 'r') as json_file:
+ json_data = json.load(json_file)
+
+ # Convert and save as YAML in the output file
+ with open(output_file, 'w') as yaml_file:
+ yaml.dump(json_data, yaml_file, default_flow_style=False)
+
+if __name__ == '__main__':
+ # Set up argument parser
+ parser = argparse.ArgumentParser(description='Convert JSON to YAML.')
+ parser.add_argument('input_file', help='Path to the input JSON file')
+ parser.add_argument('output_file', help='Path to the output YAML file')
+
+ args = parser.parse_args()
+
+ # Perform the conversion
+ convert_json_to_yaml(args.input_file, args.output_file)
+

ush/soca/prep_ocean_obs.py

@@ -10,6 +10,7 @@
 from wxflow import (chdir,
  FileHandler,
  logit,
+ parse_j2yaml,
  save_as_yaml,
  Task,
  YAMLFile)
@@ -91,7 +92,8 @@ def initialize(self):
  raise FileNotFoundError
 
  JSON_TMPL_DIR = self.task_config.JSON_TMPL_DIR
- BUFR2IODA_PY_DIR = self.task_config.BUFR2IODA_PY_DIR
+# BUFR2IODA_PY_DIR = self.task_config.BUFR2IODA_PY_DIR
+ BUFR2IODA_PY_DIR = os.path.join(self.task_config.HOMEgfs, 'sorc/gdas.cd/ush/ioda/bufr2ioda/marine/b2i')
 
  COMIN_OBS = self.task_config.COMIN_OBS
  COMOUT_OBS = self.task_config['COMOUT_OBS']
@@ -150,19 +152,22 @@ def initialize(self):
  # set up the config file for conversion to IODA for bufr and
  # netcdf files respectively
  if obsprep_space['type'] == 'bufr':
- gen_bufr_json_config = {'RUN': RUN,
+ gen_bufr_yaml_config = {'RUN': RUN,
  'current_cycle': cdate,
  'DMPDIR': COMIN_OBS,
  'COM_OBS': COMIN_OBS}
- json_config_file = os.path.join(COMIN_OBS,
- f"{obtype}_{cdatestr}.json")
- obsprep_space['conversion config file'] = json_config_file
+ yaml_config_file = os.path.join(COMIN_OBS,
+ f"{obtype}_{cdatestr}.yaml")
+ obsprep_space['conversion config file'] = yaml_config_file
  bufr2iodapy = BUFR2IODA_PY_DIR + '/bufr2ioda_' + obtype + '.py'
  obsprep_space['bufr2ioda converter'] = bufr2iodapy
- tmpl_filename = 'bufr2ioda_' + obtype + '.json'
+ tmpl_filename = 'bufr2ioda_' + obtype + '.yaml'
  template = os.path.join(JSON_TMPL_DIR, tmpl_filename)
+
  try:
- gen_bufr_json(gen_bufr_json_config, template, json_config_file)
+# gen_bufr_json(gen_bufr_json_config, template, yaml_config_file)
+ myyaml = parse_j2yaml(template, gen_bufr_yaml_config, yaml_config_file)
+ myyaml.save(yaml_config_file)
  except Exception as e:
  logger.warning(f"An exeception {e} occured while trying to run gen_bufr_json")
  logger.warning(f"obtype {obtype} will be skipped")