From 4f1e2a8cbe7385e72582cecff6163d1fed7e0796 Mon Sep 17 00:00:00 2001
From: ShastriPaturi <shastri.paturi@noaa.gov>
Date: Wed, 28 Feb 2024 20:03:27 +0000
Subject: [PATCH 01/11] fix path

---
 jobs/JGLOBAL_PREP_OCEAN_OBS | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jobs/JGLOBAL_PREP_OCEAN_OBS b/jobs/JGLOBAL_PREP_OCEAN_OBS
index a6fcf9c9b32..fde61dcd89d 100755
--- a/jobs/JGLOBAL_PREP_OCEAN_OBS
+++ b/jobs/JGLOBAL_PREP_OCEAN_OBS
@@ -20,7 +20,7 @@ export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush:${PYTHONPATH}
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPOCNOBSPY:-${HOMEgfs}/ush/exglobal_prep_ocean_obs.py}
+EXSCRIPT=${GDASPREPOCNOBSPY:-${HOMEgfs}/scripts/exglobal_prep_ocean_obs.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

From 30b2294c5d9d0904ec058fbcc2a19c96a2afa84c Mon Sep 17 00:00:00 2001
From: ShastriPaturi <shastri.paturi@noaa.gov>
Date: Mon, 4 Mar 2024 16:45:43 -0600
Subject: [PATCH 02/11] insitu BUFR2IODA related

---
 jobs/JGLOBAL_PREP_OCEAN_OBS         | 2 ++
 parm/config/gfs/config.prepoceanobs | 4 ++++
 2 files changed, 6 insertions(+)

diff --git a/jobs/JGLOBAL_PREP_OCEAN_OBS b/jobs/JGLOBAL_PREP_OCEAN_OBS
index fde61dcd89d..acc5a53f5f7 100755
--- a/jobs/JGLOBAL_PREP_OCEAN_OBS
+++ b/jobs/JGLOBAL_PREP_OCEAN_OBS
@@ -16,6 +16,8 @@ YMD=${PDY} HH=${cyc} generate_com -rx COMOUT_OBS:COM_OBS_TMPL
 
 # Add prep_marine_obs.py to PYTHONPATH
 export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush:${PYTHONPATH}
+# Add gen_bufr2ioda.py to PYTHONPATH
+export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda:${PYTHONPATH}
 
 ###############################################################
 # Run relevant script
diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index 56fc349ce23..b6b8e0657ef 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -15,6 +15,10 @@ export OBS_YAML=${OBS_LIST}
 # ocean analysis needs own dmpdir until standard dmpdir has full ocean obs
 export DMPDIR=@DMPDIR@
 
+# For BUFR2IODA json and python scripts
+export JSON_TMPL_DIR=${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda
+export BUFR2IODA_PY_DIR=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda
+export KEEPDATA='YES'
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepoceanobs
 echo "END: config.prepoceanobs"

From 81015c58db5d9a54c4df365af1fe07ccd1902074 Mon Sep 17 00:00:00 2001
From: ShastriPaturi <shastri.paturi@noaa.gov>
Date: Tue, 19 Mar 2024 12:18:48 -0500
Subject: [PATCH 03/11] path to bufr2ioda

---
 jobs/JGLOBAL_PREP_OCEAN_OBS | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jobs/JGLOBAL_PREP_OCEAN_OBS b/jobs/JGLOBAL_PREP_OCEAN_OBS
index acc5a53f5f7..c459a45dbaa 100755
--- a/jobs/JGLOBAL_PREP_OCEAN_OBS
+++ b/jobs/JGLOBAL_PREP_OCEAN_OBS
@@ -22,7 +22,7 @@ export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda:${PYTHONPATH}
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPOCNOBSPY:-${HOMEgfs}/scripts/exglobal_prep_ocean_obs.py}
+EXSCRIPT=${GDASPREPOCNOBSPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exglobal_prep_ocean_obs.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

From e43ce9ad7fd3840f9b6ae6611ee7e61d2f856ffe Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA <andrew.eichmann@noaa.gov>
Date: Thu, 4 Apr 2024 19:03:53 +0000
Subject: [PATCH 04/11] redo

---
 jobs/JGLOBAL_PREP_OCEAN_OBS         | 2 +-
 parm/config/gfs/config.prepoceanobs | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/jobs/JGLOBAL_PREP_OCEAN_OBS b/jobs/JGLOBAL_PREP_OCEAN_OBS
index c459a45dbaa..2178c5fe2d2 100755
--- a/jobs/JGLOBAL_PREP_OCEAN_OBS
+++ b/jobs/JGLOBAL_PREP_OCEAN_OBS
@@ -22,7 +22,7 @@ export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda:${PYTHONPATH}
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPOCNOBSPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exglobal_prep_ocean_obs.py}
+EXSCRIPT=${GDASPREPOCNOBSPY:-${USHgfs}/exglobal_prep_ocean_obs.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index b6b8e0657ef..a13cb42dbad 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -6,6 +6,7 @@ echo "BEGIN: config.prepoceanobs"
 
 export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
 
+[[ -n "${JSON_TMPL_DIR}" ]] || export JSON_TMPL_DIR=${HOMEgfs}/parm/gdas/ioda/bufr2ioda
 export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
 export OBSPREP_YAML=@OBSPREP_YAML@
 export OBS_LIST=@SOCA_OBS_LIST@

From 38d4bcbbfd0f231c57c7fcfad9c06d393b6875e9 Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA
 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri, 5 Apr 2024 13:55:02 -0400
Subject: [PATCH 05/11] Update parm/config/gfs/config.prepoceanobs

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 parm/config/gfs/config.prepoceanobs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index a13cb42dbad..7780207c011 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -6,7 +6,7 @@ echo "BEGIN: config.prepoceanobs"
 
 export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
 
-[[ -n "${JSON_TMPL_DIR}" ]] || export JSON_TMPL_DIR=${HOMEgfs}/parm/gdas/ioda/bufr2ioda
+[[ -n "${JSON_TMPL_DIR}" ]] || export JSON_TMPL_DIR=${PARMgfs}/gdas/ioda/bufr2ioda
 export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
 export OBSPREP_YAML=@OBSPREP_YAML@
 export OBS_LIST=@SOCA_OBS_LIST@

From 084c151706cc3837c13f0942d2f78062072c2341 Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA <andrew.eichmann@noaa.gov>
Date: Fri, 5 Apr 2024 20:44:20 +0000
Subject: [PATCH 06/11] tweaks from review

---
 parm/config/gfs/config.prepoceanobs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index b06ee745f27..147f54e526f 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -18,8 +18,8 @@ export DMPDIR=@DMPDIR@
 
 # For BUFR2IODA json and python scripts
 [[ -n "${JSON_TMPL_DIR}" ]] || export JSON_TMPL_DIR=${PARMgfs}/gdas/ioda/bufr2ioda
-export BUFR2IODA_PY_DIR=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda
-export KEEPDATA='YES'
+export BUFR2IODA_PY_DIR=${HOMEgfs}/ush
+
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepoceanobs
 echo "END: config.prepoceanobs"

From 13c081efb0b818820be665a12034a014b7821b44 Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA <andrew.eichmann@noaa.gov>
Date: Fri, 5 Apr 2024 21:00:28 +0000
Subject: [PATCH 07/11] path wrangling

---
 jobs/JGLOBAL_PREP_OCEAN_OBS | 4 ++--
 sorc/link_workflow.sh       | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/jobs/JGLOBAL_PREP_OCEAN_OBS b/jobs/JGLOBAL_PREP_OCEAN_OBS
index 47b0ab901e0..bf9bde0d716 100755
--- a/jobs/JGLOBAL_PREP_OCEAN_OBS
+++ b/jobs/JGLOBAL_PREP_OCEAN_OBS
@@ -16,8 +16,8 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMOUT_OBS:COM_OBS_TMPL
 
 # Add prep_marine_obs.py to PYTHONPATH
 export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush:${PYTHONPATH}
-# Add gen_bufr2ioda.py to PYTHONPATH
-export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda:${PYTHONPATH}
+## Add gen_bufr2ioda.py to PYTHONPATH
+#export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda:${PYTHONPATH}
 
 ###############################################################
 # Run relevant script
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index b92ae0e757d..3b1a2d5dc77 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -225,6 +225,8 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
   cd "${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/gen_bufr2ioda_json.py"    .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_yaml.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/scripts/exglobal_prep_ocean_obs.py"           .

From 670bee6c5bd37f21dee1f9b2ee282e27f5ca0693 Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA
 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri, 5 Apr 2024 17:13:16 -0400
Subject: [PATCH 08/11] Update parm/config/gfs/config.prepoceanobs

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 parm/config/gfs/config.prepoceanobs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index 147f54e526f..58a25371492 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -17,8 +17,8 @@ export OBS_YAML=${OBS_LIST}
 export DMPDIR=@DMPDIR@
 
 # For BUFR2IODA json and python scripts
-[[ -n "${JSON_TMPL_DIR}" ]] || export JSON_TMPL_DIR=${PARMgfs}/gdas/ioda/bufr2ioda
-export BUFR2IODA_PY_DIR=${HOMEgfs}/ush
+[[ -n "${JSON_TMPL_DIR}" ]] || export JSON_TMPL_DIR="${PARMgfs}/gdas/ioda/bufr2ioda"
+export BUFR2IODA_PY_DIR="${USHgfs}"
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepoceanobs

From d40eeca153e1eaff64cff88c070db3b122936c44 Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA <andrew.eichmann@noaa.gov>
Date: Fri, 5 Apr 2024 21:59:41 +0000
Subject: [PATCH 09/11] more tweaks

---
 jobs/JGLOBAL_PREP_OCEAN_OBS         | 2 --
 parm/config/gfs/config.prepoceanobs | 9 +++++----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/jobs/JGLOBAL_PREP_OCEAN_OBS b/jobs/JGLOBAL_PREP_OCEAN_OBS
index bf9bde0d716..c3a0035ac67 100755
--- a/jobs/JGLOBAL_PREP_OCEAN_OBS
+++ b/jobs/JGLOBAL_PREP_OCEAN_OBS
@@ -16,8 +16,6 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMOUT_OBS:COM_OBS_TMPL
 
 # Add prep_marine_obs.py to PYTHONPATH
 export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush:${PYTHONPATH}
-## Add gen_bufr2ioda.py to PYTHONPATH
-#export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda:${PYTHONPATH}
 
 ###############################################################
 # Run relevant script
diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index 58a25371492..8a4286aa6b6 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -7,18 +7,19 @@ echo "BEGIN: config.prepoceanobs"
 export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
 
 export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
-export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
+
+export OBS_YAML_DIR=${OBS_YAML_DIR:-${PARMgfs}/gdas/soca/obs/config}
 export OBSPREP_YAML=@OBSPREP_YAML@
 export OBS_LIST=@SOCA_OBS_LIST@
-[[ -n "${OBS_LIST}" ]] || export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
+export OBS_LIST=${OBS_LIST:-${PARMgfs}/gdas/soca/obs/obs_list.yaml}
 export OBS_YAML=${OBS_LIST}
 
 # ocean analysis needs own dmpdir until standard dmpdir has full ocean obs
 export DMPDIR=@DMPDIR@
 
 # For BUFR2IODA json and python scripts
-[[ -n "${JSON_TMPL_DIR}" ]] || export JSON_TMPL_DIR="${PARMgfs}/gdas/ioda/bufr2ioda"
-export BUFR2IODA_PY_DIR="${USHgfs}"
+export JSON_TMPL_DIR=${JSON_TMPL_DIR:-"${PARMgfs}/gdas/ioda/bufr2ioda"}
+export BUFR2IODA_PY_DIR=${BUFR2IODA_PY_DIR:-"${USHgfs}"}
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepoceanobs

From 2df0dd3c8f19c54f798b666adbd1da455c5fb150 Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA <andrew.eichmann@noaa.gov>
Date: Mon, 8 Apr 2024 10:52:41 +0000
Subject: [PATCH 10/11] added bufr2ioda links to gitignore

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 2b6c8350458..9d085474406 100644
--- a/.gitignore
+++ b/.gitignore
@@ -168,6 +168,8 @@ ush/fv3gfs_driver_grid.sh
 ush/fv3gfs_filter_topo.sh
 ush/fv3gfs_make_grid.sh
 ush/fv3gfs_make_orog.sh
+ush/gen_bufr2ioda_json.py
+ush/gen_bufr2ioda_yaml.py
 ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh

From 3d7758da24e9473874bded0663e9bd74fe3fb789 Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA <andrew.eichmann@noaa.gov>
Date: Tue, 9 Apr 2024 15:18:29 +0000
Subject: [PATCH 11/11] simplified env var assignments

---
 parm/config/gfs/config.prepoceanobs | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index 8a4286aa6b6..746ce792575 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -8,18 +8,17 @@ export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
 
 export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
 
-export OBS_YAML_DIR=${OBS_YAML_DIR:-${PARMgfs}/gdas/soca/obs/config}
+export OBS_YAML_DIR="${PARMgfs}/gdas/soca/obs/config"
 export OBSPREP_YAML=@OBSPREP_YAML@
 export OBS_LIST=@SOCA_OBS_LIST@
-export OBS_LIST=${OBS_LIST:-${PARMgfs}/gdas/soca/obs/obs_list.yaml}
 export OBS_YAML=${OBS_LIST}
 
 # ocean analysis needs own dmpdir until standard dmpdir has full ocean obs
 export DMPDIR=@DMPDIR@
 
 # For BUFR2IODA json and python scripts
-export JSON_TMPL_DIR=${JSON_TMPL_DIR:-"${PARMgfs}/gdas/ioda/bufr2ioda"}
-export BUFR2IODA_PY_DIR=${BUFR2IODA_PY_DIR:-"${USHgfs}"}
+export JSON_TMPL_DIR="${PARMgfs}/gdas/ioda/bufr2ioda"
+export BUFR2IODA_PY_DIR="${USHgfs}"
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepoceanobs