From 15814cbd4b3a71e2f2d5dc768d607b77f04d8510 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 3 May 2023 12:17:14 -0400
Subject: [PATCH 1/4] removed tmpl, added com_obs

---
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT | 4 ++--
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST  | 4 ++--
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP  | 8 ++++----
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN   | 5 ++++-
 4 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
index f157488a595..c5c4a9575d5 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
@@ -23,8 +23,8 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_ANALYSIS
 
 
 ##############################################
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
index 9b3467feec3..b1977a2cb62 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -14,7 +14,7 @@ export CDATE=${CDATE:-${PDY}${cyc}}
 export GDUMP=${GDUMP:-"gdas"}
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS
 RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_ICE_RESTART
 
 mkdir -p "${COM_OCEAN_ANALYSIS}"
@@ -42,6 +42,6 @@ status=$?
 # Remove the Temporary working directory
 ##########################################
 cd "${DATAROOT}" || exit 1
-[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
+#[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
 exit 0
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
index c4843c596d4..6966f72b62c 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -22,10 +22,10 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_OCEAN_HISTORY:COM_OCEAN_HISTORY_TMPL
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_HISTORY:COM_ICE_HISTORY_TMPL
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_RESTART:COM_ICE_RESTART_TMPL
-
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_OCEAN_HISTORY
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_HISTORY
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_RESTART
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 
 
 ##############################################
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
index c89f8b273bc..87ca5560c41 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
@@ -6,11 +6,14 @@ export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
 
 
+##############################################
+# Set variables used in the script
+##############################################
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
 
 ###############################################################
 # Run relevant script

From 3fe0e21a146120416b404f3b50eeeb94659b43a1 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 3 May 2023 16:55:24 -0400
Subject: [PATCH 2/4] fixed confusion in com def

---
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT | 4 ++--
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST  | 5 ++---
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP  | 9 +++++----
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
index c5c4a9575d5..68ba3f012df 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
@@ -23,8 +23,8 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_ANALYSIS
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL \
+                                                     COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL
 
 
 ##############################################
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
index b1977a2cb62..32e18e60f6c 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -2,7 +2,7 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
-DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
+export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalpost" -c "base ocnanalpost"
 
 
@@ -14,8 +14,7 @@ export CDATE=${CDATE:-${PDY}${cyc}}
 export GDUMP=${GDUMP:-"gdas"}
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS
-RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_ICE_RESTART
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS COM_ICE_RESTART
 
 mkdir -p "${COM_OCEAN_ANALYSIS}"
 mkdir -p "${COM_ICE_RESTART}"
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
index 6966f72b62c..c3fd5b5d656 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -22,11 +22,12 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_OCEAN_HISTORY
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_HISTORY
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_RESTART
-RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
+   COM_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
+   COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
+   COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
 
 ##############################################
 # Begin JOB SPECIFIC work

From ff4d35d5784926131cf6da30f865ad5ea39519be Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 3 May 2023 17:37:44 -0400
Subject: [PATCH 3/4] oops

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

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
index 32e18e60f6c..eb9607ad21a 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -41,6 +41,6 @@ status=$?
 # Remove the Temporary working directory
 ##########################################
 cd "${DATAROOT}" || exit 1
-#[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
 exit 0

From 68840f145886ba4252457f227e16e38c66c85470 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 3 May 2023 17:55:16 -0400
Subject: [PATCH 4/4] wrong atmos ana com

---
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
index 68ba3f012df..7e4294bd7ca 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
@@ -23,8 +23,9 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL \
-                                                     COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
+
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
 
 
 ##############################################