From fb584ef76bf0690a888995e3bb9d81be253d5e38 Mon Sep 17 00:00:00 2001
From: "Donald.E.Lippi" <donald.e.lippi@noaa.gov>
Date: Fri, 24 Jan 2025 17:23:45 +0000
Subject: [PATCH 1/3] Add logic for running offline IODA tools.

---
 scripts/exrrfs_ioda_bufr.sh | 34 ++++++++++++++++++++--------------
 1 file changed, 20 insertions(+), 14 deletions(-)

diff --git a/scripts/exrrfs_ioda_bufr.sh b/scripts/exrrfs_ioda_bufr.sh
index 8dff7448f..460c71009 100755
--- a/scripts/exrrfs_ioda_bufr.sh
+++ b/scripts/exrrfs_ioda_bufr.sh
@@ -13,20 +13,16 @@ execfile=${HOMErrfs}/sorc/RDASApp/build/bin/bufr2ioda.x
 # generate the namelist on the fly
 REFERENCE_TIME="${CDATE:0:4}-${CDATE:4:2}-${CDATE:6:2}T${CDATE:8:2}:00:00Z"
 yaml_list=(
-"prepbufr_aircraft.yaml" 
+"prepbufr_aircraft.yaml"
+#"prepbufr_ascatw.yaml"
+#"prepbufr_gpsipw.yaml"
+#"prepbufr_mesonet.yaml"
+#"prepbufr_profiler.yaml"
+#"prepbufr_rassda.yaml"
+#"prepbufr_satwnd.yaml"
+#"prepbufr_adpsfc.yaml"
 "prepbufr_adpupa.yaml"
 )
-#yaml_list=(
-#"prepbufr_aircraft.yaml" 
-#"prepbufr_ascatw.yaml" 
-#"prepbufr_gpsipw.yaml" 
-#"prepbufr_mesonet.yaml" 
-#"prepbufr_profiler.yaml" 
-#"prepbufr_rassda.yaml" 
-#"prepbufr_satwnd.yaml" 
-#"prepbufr_adpsfc.yaml" 
-#"prepbufr_adpupa.yaml"
-#)
 
 # run bufr2ioda.x
 for yaml in ${yaml_list[@]}; do
@@ -35,9 +31,19 @@ for yaml in ${yaml_list[@]}; do
  ${MPI_RUN_CMD} ${execfile} ${yaml}
  # some data may not be available at all cycles, so we don't check whether bufr2ioda.x runs successfully
 done
-ls ./ioda*nc  
+
+# run offline IODA tools
+${cpreq} ${HOMErrfs}/sorc/RDASApp/rrfs-test/IODA/offline_add_var_to_ioda.py .
+ioda_files=$(ls ioda*nc)
+for ioda_file in ${ioda_files[@]}; do
+  python offline_add_var_to_ioda.py -o ${ioda_file}
+  base_name=$(basename "$ioda_file" .nc)
+  mv  ${base_name}_llp.nc ${base_name}.nc
+done
+
+# file count sanity check and copy to COMOUT
+ls ./ioda*nc
 if (( $? == 0 )); then
-  # copy ioda*.nc to COMOUT
   ${cpreq} ${DATA}/ioda*.nc ${COMOUT}/ioda_bufr/
 else
   echo "WARNING: no ioda files generated."

From 8d06d4029946f01e84527901f3b9c2faaaa2c30e Mon Sep 17 00:00:00 2001
From: "Donald.E.Lippi" <donald.e.lippi@noaa.gov>
Date: Fri, 24 Jan 2025 20:04:48 +0000
Subject: [PATCH 2/3] remove leading "python" to run *.py tool

---
 scripts/exrrfs_ioda_bufr.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/exrrfs_ioda_bufr.sh b/scripts/exrrfs_ioda_bufr.sh
index 460c71009..cf8b9c78c 100755
--- a/scripts/exrrfs_ioda_bufr.sh
+++ b/scripts/exrrfs_ioda_bufr.sh
@@ -36,7 +36,7 @@ done
 ${cpreq} ${HOMErrfs}/sorc/RDASApp/rrfs-test/IODA/offline_add_var_to_ioda.py .
 ioda_files=$(ls ioda*nc)
 for ioda_file in ${ioda_files[@]}; do
-  python offline_add_var_to_ioda.py -o ${ioda_file}
+  offline_add_var_to_ioda.py -o ${ioda_file}
   base_name=$(basename "$ioda_file" .nc)
   mv  ${base_name}_llp.nc ${base_name}.nc
 done

From a7b5660fba2d75217f6002334d28cd7f34a8df42 Mon Sep 17 00:00:00 2001
From: "Donald.E.Lippi" <donald.e.lippi@noaa.gov>
Date: Fri, 24 Jan 2025 20:56:46 +0000
Subject: [PATCH 3/3] Add "./" before executing python script

---
 scripts/exrrfs_ioda_bufr.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/exrrfs_ioda_bufr.sh b/scripts/exrrfs_ioda_bufr.sh
index cf8b9c78c..5fa6562a6 100755
--- a/scripts/exrrfs_ioda_bufr.sh
+++ b/scripts/exrrfs_ioda_bufr.sh
@@ -36,7 +36,7 @@ done
 ${cpreq} ${HOMErrfs}/sorc/RDASApp/rrfs-test/IODA/offline_add_var_to_ioda.py .
 ioda_files=$(ls ioda*nc)
 for ioda_file in ${ioda_files[@]}; do
-  offline_add_var_to_ioda.py -o ${ioda_file}
+  ./offline_add_var_to_ioda.py -o ${ioda_file}
   base_name=$(basename "$ioda_file" .nc)
   mv  ${base_name}_llp.nc ${base_name}.nc
 done