replace run_bufr2ioda.sh with run_bufr2ioda.py

parm/ioda/bufr2ioda/bufr2ioda_satwind_amv_goes.json

@@ -1,7 +1,7 @@
 {
   "data_format"      : "bufr_d",
   "data_type"        : "satwnd",
-  "cycle_type"       : "{{ DUMP }}",
+  "cycle_type"       : "{{ RUN }}",
   "cycle_datetime"   : "{{ current_cycle | to_YMDH }}",
   "dump_directory"   : "{{ DMPDIR }}",
   "ioda_directory"   : "{{ COM_OBS }}",

ush/ioda/bufr2ioda/bufr2ioda_satwind_amv_goes.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python3
 import argparse
 import numpy as np
 import numpy.ma as ma

ush/ioda/bufr2ioda/gen_bufr2ioda_json.py

@@ -6,8 +6,7 @@
 import argparse
 import json
 import os
-from wxflow import Logger, parse_j2yaml, cast_strdict_as_dtypedict
-from wxflow import add_to_datetime, to_timedelta
+from wxflow import Logger, parse_j2yaml
 
 # Initialize root logger
 logger = Logger('gen_bufr2ioda_json.py', level='INFO', colored_log=True)
@@ -29,9 +28,4 @@ def gen_bufr_json(config, template, output):
     parser.add_argument('-t', '--template', type=str, help='Input JSON template', required=True)
     parser.add_argument('-o', '--output', type=str, help='Output JSON file', required=True)
     args = parser.parse_args()
-    # get the config from your environment
-    config = cast_strdict_as_dtypedict(os.environ)
-    # we need to add in current cycle from PDYcyc
-    config['current_cycle'] = add_to_datetime(config['PDY'], to_timedelta(f"{config['cyc']}H"))
-    # call the parsing function
     gen_bufr_json(config, args.template, args.output)

ush/ioda/bufr2ioda/run_bufr2ioda.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+import argparse
+import os
+from pathlib import Path
+from gen_bufr2ioda_json import gen_bufr_json
+from wxflow import (Logger, Executable, cast_as_dtype, logit,
+                    to_datetime, datetime_to_YMDH, Task, rm_p)
+
+# Initialize root logger
+logger = Logger('run_bufr2ioda.py', level='INFO', colored_log=True)
+
+
+@logit(logger)
+def bufr2ioda(current_cycle, RUN, DMPDIR, config_template_dir, COM_OBS):
+    logger.info(f"Process {current_cycle} {RUN} from {DMPDIR} to {COM_OBS} using {config_template_dir}")
+
+    # Get gdasapp root directory
+    DIR_ROOT = os.path.realpath(os.path.join(os.path.dirname(os.path.realpath(__file__)), "../../.."))
+    USH_IODA = os.path.join(DIR_ROOT, "ush", "ioda", "bufr2ioda")
+
+    # Create output directory if it doesn't exist
+    os.makedirs(COM_OBS, exist_ok=True)
+
+    # Load configuration
+    config = {
+        'RUN': RUN,
+        'current_cycle': current_cycle,
+        'DMPDIR': DMPDIR,
+        'COM_OBS': COM_OBS
+    }
+
+    # Specify observation types to be processed by a script
+    BUFR_py = ["satwind_amv_goes"]
+
+    for obtype in BUFR_py:
+        logger.info(f"Convert {obtype}...")
+        json_output_file = os.path.join(COM_OBS, f"{obtype}_{datetime_to_YMDH(current_cycle)}.json")
+        filename = 'bufr2ioda_' + obtype + '.json'
+        template = os.path.join(config_template_dir, filename)
+        gen_bufr_json(config, template, json_output_file)
+
+        # Use the converter script for the ob type
+        bufr2iodapy = USH_IODA + '/bufr2ioda_' + obtype + ".py"
+        cmd = Executable(bufr2iodapy)
+        cmd.add_default_arg('-c')
+        cmd.add_default_arg(json_output_file)
+        logger.info(f"Executing {cmd}")
+        cmd()
+
+        # Check if the converter was successful
+        if os.path.exists(json_output_file):
+            rm_p(json_output_file)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Convert bufr dump file to ioda format')
+    parser.add_argument('current_cycle', help='current cycle to process', type=lambda dd: to_datetime(dd))
+    parser.add_argument('RUN', type=str, help='dump to process, either gdas or gdas')
+    parser.add_argument('DMPDIR', type=Path, help='path to bufr dump files')
+    parser.add_argument('config_template_dir', type=Path, help='path to templates')
+    parser.add_argument('COM_OBS', type=Path, help='path to output ioda format dump files')
+    args = parser.parse_args()
+    bufr2ioda(args.current_cycle, args.RUN, args.DMPDIR, args.config_template_dir, args.COM_OBS)