From fa2db5270b93e83330336c5349a10aa63e10d934 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Wed, 23 Aug 2023 18:52:44 +0000
Subject: [PATCH 1/8] initial commit of bufr2ioda job (#1820)

---
 jobs/JGLOBAL_PREP_IODA_OBS          | 36 +++++++++++++++++++++++++++++
 jobs/rocoto/prepiodaobs.sh          | 25 ++++++++++++++++++++
 parm/config/gfs/config.prepiodaobs  | 14 +++++++++++
 parm/config/gfs/config.resources    | 10 +++++++-
 workflow/applications/gfs_cycled.py |  4 ++--
 workflow/rocoto/gfs_tasks.py        | 16 +++++++++++--
 workflow/rocoto/tasks.py            |  2 +-
 7 files changed, 101 insertions(+), 6 deletions(-)
 create mode 100755 jobs/JGLOBAL_PREP_IODA_OBS
 create mode 100755 jobs/rocoto/prepiodaobs.sh
 create mode 100644 parm/config/gfs/config.prepiodaobs

diff --git a/jobs/JGLOBAL_PREP_IODA_OBS b/jobs/JGLOBAL_PREP_IODA_OBS
new file mode 100755
index 0000000000..ff22289f44
--- /dev/null
+++ b/jobs/JGLOBAL_PREP_IODA_OBS
@@ -0,0 +1,36 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "prepiodaobs" -c "base prepiodaobs"
+
+##############################################
+# Set variables used in the script
+##############################################
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+# Generate COM variables from templates
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
+
+
+###############################################################
+# Run relevant script
+EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/${HOMEgfs}/ush/ioda/bufr2ioda/run_bufr2ioda.sh}
+${EXSCRIPT} "${PDY}${cyc}" "${CDUMP}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
+status=$?
+[[ ${status} -ne 0 ]] && (echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}")
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0
diff --git a/jobs/rocoto/prepiodaobs.sh b/jobs/rocoto/prepiodaobs.sh
new file mode 100755
index 0000000000..aa523ee26d
--- /dev/null
+++ b/jobs/rocoto/prepiodaobs.sh
@@ -0,0 +1,25 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="prepatmobs"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+##wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+##gdasappPATH="${HOMEgfs}/sorc/gdas.cd/iodaconv/src:${HOMEgfs}/sorc/gdas.cd/build/lib/python3.7"
+##PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}:${gdasappPATH}"
+##export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_PREP_IODA_OBS"
+status=$?
+exit "${status}"
diff --git a/parm/config/gfs/config.prepiodaobs b/parm/config/gfs/config.prepiodaobs
new file mode 100644
index 0000000000..c95fcf08b7
--- /dev/null
+++ b/parm/config/gfs/config.prepiodaobs
@@ -0,0 +1,14 @@
+#! /usr/bin/env bash
+
+########## config.prepiodaobs ##########
+# Atm Obs Prep specific
+
+echo "BEGIN: config.prepiodaobs"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" prepiodaobs
+
+export BUFR2IODASH="${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.sh"
+export IODAPARM="${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda"
+
+echo "END: config.prepiodaobs"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index 6844802a0b..c9bba96839 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -9,7 +9,7 @@ if [[ $# -ne 1 ]]; then
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
     echo "coupled_ic aerosol_init"
-    echo "prep preplandobs"
+    echo "prep preplandobs prepiodaobs"
     echo "atmanlinit atmanlrun atmanlfinal"
     echo "atmensanlinit atmensanlrun atmensanlfinal"
     echo "landanl"
@@ -73,6 +73,14 @@ elif [[ "${step}" = "preplandobs" ]]; then
     npe_node_preplandobs=1
     export npe_node_preplandobs
 
+elif [[ "${step}" = "prepiodaobs" ]]; then
+    export wtime_prepiodaobs="00:05:00"
+    npe_prepiodaobs=1
+    export npe_prepiodaobs
+    export nth_prepiodaobs=1
+    npe_node_prepiodaobs=1
+    export npe_node_prepiodaobs
+
 elif [[ "${step}" = "aerosol_init" ]]; then
     export wtime_aerosol_init="00:05:00"
     export npe_aerosol_init=1
diff --git a/workflow/applications/gfs_cycled.py b/workflow/applications/gfs_cycled.py
index 3478d563a3..08324d91ac 100644
--- a/workflow/applications/gfs_cycled.py
+++ b/workflow/applications/gfs_cycled.py
@@ -37,7 +37,7 @@ def _get_app_configs(self):
         configs = ['prep']
 
         if self.do_jediatmvar:
-            configs += ['atmanlinit', 'atmanlrun', 'atmanlfinal']
+            configs += ['prepiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             configs += ['anal', 'analdiag']
 
@@ -109,7 +109,7 @@ def get_task_names(self):
         gdas_gfs_common_cleanup_tasks = ['arch']
 
         if self.do_jediatmvar:
-            gdas_gfs_common_tasks_before_fcst += ['atmanlinit', 'atmanlrun', 'atmanlfinal']
+            gdas_gfs_common_tasks_before_fcst += ['prepiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             gdas_gfs_common_tasks_before_fcst += ['anal']
 
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index 726f7e67fb..6b43f6859b 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -245,11 +245,23 @@ def analdiag(self):
 
         return task
 
-    def atmanlinit(self):
+    def prepiodaobs(self):
 
         deps = []
         dep_dict = {'type': 'task', 'name': f'{self.cdump}prep'}
         deps.append(rocoto.add_dependency(dep_dict))
+        dependencies = rocoto.create_dependency(dep=deps)
+
+        resources = self.get_resource('prepiodaobs')
+        task = create_wf_task('prepiodaobs', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
+
+        return task
+
+    def atmanlinit(self):
+
+        deps = []
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}prepiodaobs'}
+        deps.append(rocoto.add_dependency(dep_dict))
         if self.app_config.do_hybvar:
             dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
             deps.append(rocoto.add_dependency(dep_dict))
@@ -993,7 +1005,7 @@ def eupd(self):
 
     def atmensanlinit(self):
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.cdump.replace("enkf","")}prep'}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump.replace("enkf","")}prepiodaobs'}
         deps.append(rocoto.add_dependency(dep_dict))
         dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
diff --git a/workflow/rocoto/tasks.py b/workflow/rocoto/tasks.py
index 2a1ac1842b..46f468efca 100644
--- a/workflow/rocoto/tasks.py
+++ b/workflow/rocoto/tasks.py
@@ -12,7 +12,7 @@ class Tasks:
     SERVICE_TASKS = ['arch', 'earc']
     VALID_TASKS = ['aerosol_init', 'coupled_ic',
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch',
-                   'atmanlinit', 'atmanlrun', 'atmanlfinal',
+                   'prepiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal',
                    'ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',

From 3d614c2365b397d68db537b78a7fa204da0adbe4 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Thu, 31 Aug 2023 10:07:35 +0000
Subject: [PATCH 2/8] clean up prepiodaobs scripting (#1820)

---
 jobs/JGLOBAL_PREP_IODA_OBS       | 2 +-
 jobs/rocoto/prepiodaobs.sh       | 7 -------
 parm/config/gfs/config.resources | 7 +++----
 3 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/jobs/JGLOBAL_PREP_IODA_OBS b/jobs/JGLOBAL_PREP_IODA_OBS
index ff22289f44..08d828b95c 100755
--- a/jobs/JGLOBAL_PREP_IODA_OBS
+++ b/jobs/JGLOBAL_PREP_IODA_OBS
@@ -17,7 +17,7 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 
 ###############################################################
 # Run relevant script
-EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/${HOMEgfs}/ush/ioda/bufr2ioda/run_bufr2ioda.sh}
+EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/ioda/bufr2ioda/run_bufr2ioda.sh}
 ${EXSCRIPT} "${PDY}${cyc}" "${CDUMP}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
 status=$?
 [[ ${status} -ne 0 ]] && (echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}")
diff --git a/jobs/rocoto/prepiodaobs.sh b/jobs/rocoto/prepiodaobs.sh
index aa523ee26d..22e502cf57 100755
--- a/jobs/rocoto/prepiodaobs.sh
+++ b/jobs/rocoto/prepiodaobs.sh
@@ -11,13 +11,6 @@ status=$?
 export job="prepatmobs"
 export jobid="${job}.$$"
 
-###############################################################
-# setup python path for workflow utilities and tasks
-##wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
-##gdasappPATH="${HOMEgfs}/sorc/gdas.cd/iodaconv/src:${HOMEgfs}/sorc/gdas.cd/build/lib/python3.7"
-##PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}:${gdasappPATH}"
-##export PYTHONPATH
-
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_PREP_IODA_OBS"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index c9bba96839..d79d341aa1 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -74,11 +74,10 @@ elif [[ "${step}" = "preplandobs" ]]; then
     export npe_node_preplandobs
 
 elif [[ "${step}" = "prepiodaobs" ]]; then
-    export wtime_prepiodaobs="00:05:00"
-    npe_prepiodaobs=1
-    export npe_prepiodaobs
+    export wtime_prepiodaobs="00:10:00"
+    export npe_prepiodaobs=1
     export nth_prepiodaobs=1
-    npe_node_prepiodaobs=1
+    npe_node_prepiodaobs=$(echo "${npe_node_max} / ${nth_prepiodaobs}" | bc)
     export npe_node_prepiodaobs
 
 elif [[ "${step}" = "aerosol_init" ]]; then

From 7af58ee3b083e66e55eccfff5e4bea6f6dc57849 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Thu, 31 Aug 2023 15:50:36 +0000
Subject: [PATCH 3/8] replace prepiodaobs with prepatmiodaobs, add soft link
 for bufr2ioda run script (#1820)

---
 jobs/JGLOBAL_PREP_IODA_OBS            |  4 ++--
 parm/config/gfs/config.prepatmiodaobs | 14 ++++++++++++++
 parm/config/gfs/config.prepiodaobs    | 14 --------------
 parm/config/gfs/config.resources      | 14 +++++++-------
 sorc/link_workflow.sh                 |  1 +
 workflow/applications/gfs_cycled.py   |  4 ++--
 workflow/rocoto/gfs_tasks.py          | 10 +++++-----
 workflow/rocoto/tasks.py              |  2 +-
 8 files changed, 32 insertions(+), 31 deletions(-)
 create mode 100644 parm/config/gfs/config.prepatmiodaobs
 delete mode 100644 parm/config/gfs/config.prepiodaobs

diff --git a/jobs/JGLOBAL_PREP_IODA_OBS b/jobs/JGLOBAL_PREP_IODA_OBS
index 08d828b95c..ef2fc8a7cc 100755
--- a/jobs/JGLOBAL_PREP_IODA_OBS
+++ b/jobs/JGLOBAL_PREP_IODA_OBS
@@ -1,7 +1,7 @@
 #! /usr/bin/env bash
 
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "prepiodaobs" -c "base prepiodaobs"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "prepatmiodaobs" -c "base prepatmiodaobs"
 
 ##############################################
 # Set variables used in the script
@@ -17,7 +17,7 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 
 ###############################################################
 # Run relevant script
-EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/ioda/bufr2ioda/run_bufr2ioda.sh}
+EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/run_bufr2ioda.sh}
 ${EXSCRIPT} "${PDY}${cyc}" "${CDUMP}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
 status=$?
 [[ ${status} -ne 0 ]] && (echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}")
diff --git a/parm/config/gfs/config.prepatmiodaobs b/parm/config/gfs/config.prepatmiodaobs
new file mode 100644
index 0000000000..63c979d377
--- /dev/null
+++ b/parm/config/gfs/config.prepatmiodaobs
@@ -0,0 +1,14 @@
+#! /usr/bin/env bash
+
+########## config.prepatmiodaobs ##########
+# Atm Obs Prep specific
+
+echo "BEGIN: config.prepatmiodaobs"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" prepatmiodaobs
+
+export BUFR2IODASH="${HOMEgfs}/ush/run_bufr2ioda.sh"
+export IODAPARM="${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda"
+
+echo "END: config.prepatmiodaobs"
diff --git a/parm/config/gfs/config.prepiodaobs b/parm/config/gfs/config.prepiodaobs
deleted file mode 100644
index c95fcf08b7..0000000000
--- a/parm/config/gfs/config.prepiodaobs
+++ /dev/null
@@ -1,14 +0,0 @@
-#! /usr/bin/env bash
-
-########## config.prepiodaobs ##########
-# Atm Obs Prep specific
-
-echo "BEGIN: config.prepiodaobs"
-
-# Get task specific resources
-. "${EXPDIR}/config.resources" prepiodaobs
-
-export BUFR2IODASH="${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.sh"
-export IODAPARM="${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda"
-
-echo "END: config.prepiodaobs"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index d79d341aa1..76ebdf0cdb 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -9,7 +9,7 @@ if [[ $# -ne 1 ]]; then
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
     echo "coupled_ic aerosol_init"
-    echo "prep preplandobs prepiodaobs"
+    echo "prep preplandobs prepatmiodaobs"
     echo "atmanlinit atmanlrun atmanlfinal"
     echo "atmensanlinit atmensanlrun atmensanlfinal"
     echo "landanl"
@@ -73,12 +73,12 @@ elif [[ "${step}" = "preplandobs" ]]; then
     npe_node_preplandobs=1
     export npe_node_preplandobs
 
-elif [[ "${step}" = "prepiodaobs" ]]; then
-    export wtime_prepiodaobs="00:10:00"
-    export npe_prepiodaobs=1
-    export nth_prepiodaobs=1
-    npe_node_prepiodaobs=$(echo "${npe_node_max} / ${nth_prepiodaobs}" | bc)
-    export npe_node_prepiodaobs
+elif [[ "${step}" = "prepatmiodaobs" ]]; then
+    export wtime_prepatmiodaobs="00:10:00"
+    export npe_prepatmiodaobs=1
+    export nth_prepatmiodaobs=1
+    npe_node_prepatmiodaobs=$(echo "${npe_node_max} / ${nth_prepatmiodaobs}" | bc)
+    export npe_node_prepatmiodaobs
 
 elif [[ "${step}" = "aerosol_init" ]]; then
     export wtime_aerosol_init="00:05:00"
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 3c1d19f740..05be37183b 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -203,6 +203,7 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
   cd "${HOMEgfs}/ush" || exit 1
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ufsda"                              .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/jediinc2fv3.py"                     .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.sh"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
 fi
 
diff --git a/workflow/applications/gfs_cycled.py b/workflow/applications/gfs_cycled.py
index 08324d91ac..633e93bac0 100644
--- a/workflow/applications/gfs_cycled.py
+++ b/workflow/applications/gfs_cycled.py
@@ -37,7 +37,7 @@ def _get_app_configs(self):
         configs = ['prep']
 
         if self.do_jediatmvar:
-            configs += ['prepiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
+            configs += ['prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             configs += ['anal', 'analdiag']
 
@@ -109,7 +109,7 @@ def get_task_names(self):
         gdas_gfs_common_cleanup_tasks = ['arch']
 
         if self.do_jediatmvar:
-            gdas_gfs_common_tasks_before_fcst += ['prepiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
+            gdas_gfs_common_tasks_before_fcst += ['prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             gdas_gfs_common_tasks_before_fcst += ['anal']
 
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index 6b43f6859b..8f91abae75 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -245,22 +245,22 @@ def analdiag(self):
 
         return task
 
-    def prepiodaobs(self):
+    def prepatmiodaobs(self):
 
         deps = []
         dep_dict = {'type': 'task', 'name': f'{self.cdump}prep'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)
 
-        resources = self.get_resource('prepiodaobs')
-        task = create_wf_task('prepiodaobs', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
+        resources = self.get_resource('prepatmiodaobs')
+        task = create_wf_task('prepatmiodaobs', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
 
         return task
 
     def atmanlinit(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.cdump}prepiodaobs'}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}prepatmiodaobs'}
         deps.append(rocoto.add_dependency(dep_dict))
         if self.app_config.do_hybvar:
             dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
@@ -1005,7 +1005,7 @@ def eupd(self):
 
     def atmensanlinit(self):
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.cdump.replace("enkf","")}prepiodaobs'}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump.replace("enkf","")}prepatmiodaobs'}
         deps.append(rocoto.add_dependency(dep_dict))
         dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
diff --git a/workflow/rocoto/tasks.py b/workflow/rocoto/tasks.py
index 46f468efca..1eba5a2652 100644
--- a/workflow/rocoto/tasks.py
+++ b/workflow/rocoto/tasks.py
@@ -12,7 +12,7 @@ class Tasks:
     SERVICE_TASKS = ['arch', 'earc']
     VALID_TASKS = ['aerosol_init', 'coupled_ic',
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch',
-                   'prepiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal',
+                   'prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal',
                    'ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',

From cd6972d42fed85c96bae1acde5b2d6ea060d9c0f Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Thu, 31 Aug 2023 16:33:20 +0000
Subject: [PATCH 4/8] rename rotoco job prepiodaobs.sh as prepatmiodaobs.sh
 (#1820)

---
 jobs/rocoto/{prepiodaobs.sh => prepatmiodaobs.sh} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename jobs/rocoto/{prepiodaobs.sh => prepatmiodaobs.sh} (100%)

diff --git a/jobs/rocoto/prepiodaobs.sh b/jobs/rocoto/prepatmiodaobs.sh
similarity index 100%
rename from jobs/rocoto/prepiodaobs.sh
rename to jobs/rocoto/prepatmiodaobs.sh

From f6d63e11dd5ff21820905689a12acc6189411033 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Thu, 31 Aug 2023 18:05:11 +0000
Subject: [PATCH 5/8] rename prep_ioda_obs j-job to be consistent with other
 prepatmiodaobs files (#1820)

---
 jobs/{JGLOBAL_PREP_IODA_OBS => JGLOBAL_ATM_PREP_IODA_OBS} | 0
 jobs/rocoto/prepatmiodaobs.sh                             | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename jobs/{JGLOBAL_PREP_IODA_OBS => JGLOBAL_ATM_PREP_IODA_OBS} (100%)

diff --git a/jobs/JGLOBAL_PREP_IODA_OBS b/jobs/JGLOBAL_ATM_PREP_IODA_OBS
similarity index 100%
rename from jobs/JGLOBAL_PREP_IODA_OBS
rename to jobs/JGLOBAL_ATM_PREP_IODA_OBS
diff --git a/jobs/rocoto/prepatmiodaobs.sh b/jobs/rocoto/prepatmiodaobs.sh
index 22e502cf57..477c040805 100755
--- a/jobs/rocoto/prepatmiodaobs.sh
+++ b/jobs/rocoto/prepatmiodaobs.sh
@@ -13,6 +13,6 @@ export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}/jobs/JGLOBAL_PREP_IODA_OBS"
+"${HOMEgfs}/jobs/JGLOBAL_ATM_PREP_IODA_OBS"
 status=$?
 exit "${status}"

From 92bdd9a49c30c9303df95feb5c11dac6b2f3d8ba Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Tue, 5 Sep 2023 13:20:14 +0000
Subject: [PATCH 6/8] replace run_bufr2ioda.sh with run_bufr2ioda.py, add
 run_bufr2ioda.py to .gitignore (#1820)

---
 .gitignore                            | 1 +
 jobs/JGLOBAL_ATM_PREP_IODA_OBS        | 2 +-
 parm/config/gfs/config.prepatmiodaobs | 2 +-
 sorc/link_workflow.sh                 | 2 +-
 4 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index c2e98c210d..9ac9ece1dd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -144,6 +144,7 @@ ush/make_tif.sh
 ush/month_name.sh
 ush/imsfv3_scf2ioda.py
 ush/atparse.bash
+ush/run_bufr2ioda.py
 
 # version files
 versions/build.ver
diff --git a/jobs/JGLOBAL_ATM_PREP_IODA_OBS b/jobs/JGLOBAL_ATM_PREP_IODA_OBS
index ef2fc8a7cc..a38945da4d 100755
--- a/jobs/JGLOBAL_ATM_PREP_IODA_OBS
+++ b/jobs/JGLOBAL_ATM_PREP_IODA_OBS
@@ -17,7 +17,7 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 
 ###############################################################
 # Run relevant script
-EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/run_bufr2ioda.sh}
+EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/run_bufr2ioda.py}
 ${EXSCRIPT} "${PDY}${cyc}" "${CDUMP}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
 status=$?
 [[ ${status} -ne 0 ]] && (echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}")
diff --git a/parm/config/gfs/config.prepatmiodaobs b/parm/config/gfs/config.prepatmiodaobs
index 63c979d377..ed9b246120 100644
--- a/parm/config/gfs/config.prepatmiodaobs
+++ b/parm/config/gfs/config.prepatmiodaobs
@@ -8,7 +8,7 @@ echo "BEGIN: config.prepatmiodaobs"
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepatmiodaobs
 
-export BUFR2IODASH="${HOMEgfs}/ush/run_bufr2ioda.sh"
+export BUFR2IODASH="${HOMEgfs}/ush/run_bufr2ioda.py"
 export IODAPARM="${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda"
 
 echo "END: config.prepatmiodaobs"
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 05be37183b..0e2cdf5edd 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -203,7 +203,7 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
   cd "${HOMEgfs}/ush" || exit 1
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ufsda"                              .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/jediinc2fv3.py"                     .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.sh"    .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
 fi
 

From 13c1f478729c3d2cfe6fcd3b0531a82d89db7f64 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Wed, 6 Sep 2023 01:19:40 +0000
Subject: [PATCH 7/8] replace CDUMP with RUN in JGLOBAL_ATM_PREP_IODA_OBS,
 update PYTHONPATH in prepatmiodaobs.sh (#1820)

---
 jobs/JGLOBAL_ATM_PREP_IODA_OBS | 2 +-
 jobs/rocoto/prepatmiodaobs.sh  | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/jobs/JGLOBAL_ATM_PREP_IODA_OBS b/jobs/JGLOBAL_ATM_PREP_IODA_OBS
index a38945da4d..ef0e682468 100755
--- a/jobs/JGLOBAL_ATM_PREP_IODA_OBS
+++ b/jobs/JGLOBAL_ATM_PREP_IODA_OBS
@@ -18,7 +18,7 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 ###############################################################
 # Run relevant script
 EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/run_bufr2ioda.py}
-${EXSCRIPT} "${PDY}${cyc}" "${CDUMP}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
+${EXSCRIPT} "${PDY}${cyc}" "${RUN}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
 status=$?
 [[ ${status} -ne 0 ]] && (echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}")
 
diff --git a/jobs/rocoto/prepatmiodaobs.sh b/jobs/rocoto/prepatmiodaobs.sh
index 477c040805..d424df9261 100755
--- a/jobs/rocoto/prepatmiodaobs.sh
+++ b/jobs/rocoto/prepatmiodaobs.sh
@@ -11,6 +11,13 @@ status=$?
 export job="prepatmobs"
 export jobid="${job}.$$"
 
+###############################################################
+# setup python path for workflow and ioda utilities
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYIODALIB="${HOMEgfs}/sorc/gdas.cd/build/lib/python3.7"
+PYTHONPATH="${PYIODALIB}:${wxflowPATH}:${PYTHONPATH}"
+export PYTHONPATH
+
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_ATM_PREP_IODA_OBS"

From 339c6a02bb73c393b2abbbbfa61e56e90c29aaae Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <russ.treadon@noaa.gov>
Date: Thu, 7 Sep 2023 09:47:18 +0000
Subject: [PATCH 8/8] update GDASApp hash to support prepatmiodaobs (#1820)

---
 Externals.cfg    | 2 +-
 sorc/checkout.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index fee84e957a..159432fda7 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -57,7 +57,7 @@ protocol = git
 required = False
 
 [GDASApp]
-hash = f614cc2
+hash = ac8fdb1
 local_path = sorc/gdas.cd
 repo_url = https://github.com/NOAA-EMC/GDASApp.git
 protocol = git
diff --git a/sorc/checkout.sh b/sorc/checkout.sh
index 98873ea6f1..d69cfec208 100755
--- a/sorc/checkout.sh
+++ b/sorc/checkout.sh
@@ -160,7 +160,7 @@ if [[ ${checkout_gsi} == "YES" ]]; then
 fi
 
 if [[ ${checkout_gdas} == "YES" ]]; then
-  checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "f614cc2"; errs=$((errs + $?))
+  checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "ac8fdb1"; errs=$((errs + $?))
 fi
 
 if [[ ${checkout_gsi} == "YES" || ${checkout_gdas} == "YES" ]]; then