From b67ec89958f93db768c9bd278bd4f34e0f132831 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue, 6 Dec 2022 13:07:31 -0500
Subject: [PATCH 1/3] make ocean analysis j-jobs consistent

---
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST | 27 +++++++++++-
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP | 59 +++++++++++++--------------
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN  | 57 ++++++++++++--------------
 3 files changed, 80 insertions(+), 63 deletions(-)

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
index 6b64e5ab8a..98385ddfe4 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -2,14 +2,37 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 
+##############################################
+# make temp directory
+##############################################
+export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+mkdir -p ${DATA}
+cd ${DATA} || (echo "${DATA} does not exist. ABORT!"; exit 1)
+
+
+##############################################
+# Run setpdy and initialize PDY variables
+##############################################
+export cycle="t${cyc}z"
+setpdy.sh
+. ./PDY
+
+
+##############################################
+# Determine Job Output Name on System
+##############################################
+export pid=${pid:-$$}
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+
+
 #############################
 # Source relevant config files
 #############################
 export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
 configs="base ocnanalpost"
-config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
 for config in ${configs}; do
-    . "${config_path}"/config."${config}"
+    . ${EXPDIR}/config.${config}
     status=$?
     [[ "${status}" -ne 0 ]] && exit "${status}"
 done
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
index 9ba0a96ae5..07be734626 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -2,36 +2,13 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 
-#############################
-# Source relevant config files
-#############################
-export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
-configs="base ocnanal ocnanalprep"
-config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
-for config in ${configs}; do
-    . "${config_path}"/config."${config}"
-    status=$?
-    [[ ${status} -ne 0 ]] && exit "${status}"
-done
-
-
-##########################################
-# Source machine runtime environment
-##########################################
-. "${HOMEgfs}"/env/"${machine}".env ocnanalprep
-status=$?
-[[ ${status} -ne 0 ]] && exit "${status}"
-
-
 ##############################################
-# Obtain unique process id (pid) and make temp directory
+# make temp directory
 ##############################################
-export pid=${pid:-$$}
-export outid=${outid:-"LL${job}"}
-
-export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}}
-mkdir -p "${DATA}"
-cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
+export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+rm -rf ${DATA}  # Ensure starting with a clean DATA
+mkdir -p ${DATA}
+cd ${DATA} || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
 
 ##############################################
@@ -45,23 +22,43 @@ setpdy.sh
 ##############################################
 # Determine Job Output Name on System
 ##############################################
+export pid=${pid:-$$}
 export pgmout="OUTPUT.${pid}"
 export pgmerr=errfile
 
 
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
+configs="base ocnanal ocnanalprep"
+for config in ${configs}; do
+    . ${EXPDIR}/config.${config}
+    status=$?
+    [[ ${status} -ne 0 ]] && exit "${status}"
+done
+
+
+##########################################
+# Source machine runtime environment
+##########################################
+. ${HOMEgfs}/env/${machine}.env ocnanalprep
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+
 ##############################################
 # Set variables used in the script
 ##############################################
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT=${COMPONENT:-ocean}
+export COMPONENT="ocean"
 
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
-GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
-export GDATE
+export GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}
 export gcyc=${GDATE:8:2}
 export GDUMP=${GDUMP:-"gdas"}
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
index 374d889ee6..a41117cf40 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
@@ -2,36 +2,13 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 
-#############################
-# Source relevant config files
-#############################
-export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
-configs="base ocnanal ocnanalrun"
-config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
-for config in ${configs}; do
-    . "${config_path}"/config."${config}"
-    status=$?
-    [[ ${status} -ne 0 ]] && exit "${status}"
-done
-
-
-##########################################
-# Source machine runtime environment
-##########################################
-. "${HOMEgfs}"/env/"${machine}".env ocnanalrun
-status=$?
-[[ ${status} -ne 0 ]] && exit "${status}"
-
 
 ##############################################
-# Obtain unique process id (pid) and make temp directory
+# make temp directory
 ##############################################
-export pid=${pid:-$$}
-export outid=${outid:-"LL${job}"}
-
-export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}}
-mkdir -p "${DATA}"
-cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
+export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+mkdir -p ${DATA}
+cd ${DATA} || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
 
 ##############################################
@@ -45,16 +22,37 @@ setpdy.sh
 ##############################################
 # Determine Job Output Name on System
 ##############################################
+export pid=${pid:-$$}
 export pgmout="OUTPUT.${pid}"
 export pgmerr=errfile
 
 
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
+configs="base ocnanal ocnanalrun"
+for config in ${configs}; do
+    . ${EXPDIR}/config.${config}
+    status=$?
+    [[ ${status} -ne 0 ]] && exit "${status}"
+done
+
+
+##########################################
+# Source machine runtime environment
+##########################################
+. ${HOMEgfs}/env/${machine}.env ocnanalrun
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+
 ##############################################
 # Set variables used in the script
 ##############################################
 
 export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT=${COMPONENT:-ocean}
+export COMPONENT="ocean"
 
 ##############################################
 # Begin JOB SPECIFIC work
@@ -82,9 +80,8 @@ if [[ -e "${pgmout}" ]] ; then
 fi
 
 ##########################################
-# Remove the Temporary working directory
+# Do not remove the Temporary working directory (do this in POST)
 ##########################################
 cd "${DATAROOT}" || exit 1
-[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
 
 exit 0

From c2fb077274a0d833f4586c2c2ff44522dd27ce99 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue, 6 Dec 2022 13:45:57 -0500
Subject: [PATCH 2/3] fix SC2155

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

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
index 07be734626..b43d9c4fbe 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -58,8 +58,9 @@ export COMPONENT="ocean"
 # Begin JOB SPECIFIC work
 ##############################################
 
-export GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
-gPDY=${GDATE:0:8}
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+export GDATE
+export gPDY=${GDATE:0:8}
 export gcyc=${GDATE:8:2}
 export GDUMP=${GDUMP:-"gdas"}
 

From 72f28488a9c436b1bda7500182c4dfb652fe4e9c Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue, 6 Dec 2022 14:05:23 -0500
Subject: [PATCH 3/3] fix SC2086 in the canonical form

---
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST |  8 ++++----
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP | 10 +++++-----
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN  |  8 ++++----
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
index 98385ddfe4..00526d45e7 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -6,8 +6,8 @@ source "${HOMEgfs}/ush/preamble.sh"
 # make temp directory
 ##############################################
 export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
-mkdir -p ${DATA}
-cd ${DATA} || (echo "${DATA} does not exist. ABORT!"; exit 1)
+mkdir -p "${DATA}"
+cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
 
 ##############################################
@@ -32,7 +32,7 @@ export pgmerr=errfile
 export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
 configs="base ocnanalpost"
 for config in ${configs}; do
-    . ${EXPDIR}/config.${config}
+    . "${EXPDIR}/config.${config}"
     status=$?
     [[ "${status}" -ne 0 ]] && exit "${status}"
 done
@@ -41,6 +41,6 @@ done
 # Remove the Temporary working directory
 ##########################################
 cd "${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 b43d9c4fbe..3c036674fa 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -6,9 +6,9 @@ source "${HOMEgfs}/ush/preamble.sh"
 # make temp directory
 ##############################################
 export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
-rm -rf ${DATA}  # Ensure starting with a clean DATA
-mkdir -p ${DATA}
-cd ${DATA} || (echo "${DATA} does not exist. ABORT!"; exit 1)
+rm -rf "${DATA}"  # Ensure starting with a clean DATA
+mkdir -p "${DATA}"
+cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
 
 ##############################################
@@ -33,7 +33,7 @@ export pgmerr=errfile
 export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
 configs="base ocnanal ocnanalprep"
 for config in ${configs}; do
-    . ${EXPDIR}/config.${config}
+    . "${EXPDIR}/config.${config}"
     status=$?
     [[ ${status} -ne 0 ]] && exit "${status}"
 done
@@ -42,7 +42,7 @@ done
 ##########################################
 # Source machine runtime environment
 ##########################################
-. ${HOMEgfs}/env/${machine}.env ocnanalprep
+. "${HOMEgfs}/env/${machine}.env ocnanalprep"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
index a41117cf40..25941d1784 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
@@ -7,8 +7,8 @@ source "${HOMEgfs}/ush/preamble.sh"
 # make temp directory
 ##############################################
 export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
-mkdir -p ${DATA}
-cd ${DATA} || (echo "${DATA} does not exist. ABORT!"; exit 1)
+mkdir -p "${DATA}"
+cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
 
 ##############################################
@@ -33,7 +33,7 @@ export pgmerr=errfile
 export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
 configs="base ocnanal ocnanalrun"
 for config in ${configs}; do
-    . ${EXPDIR}/config.${config}
+    . "${EXPDIR}/config.${config}"
     status=$?
     [[ ${status} -ne 0 ]] && exit "${status}"
 done
@@ -42,7 +42,7 @@ done
 ##########################################
 # Source machine runtime environment
 ##########################################
-. ${HOMEgfs}/env/${machine}.env ocnanalrun
+. "${HOMEgfs}/env/${machine}.env ocnanalrun"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"