Address linter warnings in JGDAS_ATMOS_GLDAS

Refs NOAA-EMC#1014

jobs/JGDAS_ATMOS_GLDAS

@@ -5,45 +5,46 @@ source "${HOMEgfs:?}/ush/preamble.sh"
 #############################
 # Source relevant config files
 #############################
-export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
+export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
 configs="base gldas"
-config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
-for config in $configs; do
-    . $config_path/config.$config
+config_path=${EXPDIR:-${NWROOT}/gfs.${gfs_ver}/parm/config}
+for config in ${configs}; do
+    # shellcheck source=parm/config/${config}
+    . "${config_path}/config.${config}"
     status=$?
-    [[ $status -ne 0 ]] && exit $status
+    [[ ${status} -ne 0 ]] && exit "${status}"
 done
 
 
-if [ $cyc -ne $gldas_cyc ]; then
-    echo "GLDAS only runs for $gldas_cyc cycle; Skip GLDAS step for cycle $cyc"
+if [ "${cyc:?}" -ne "${gldas_cyc:?}" ]; then
+    echo "GLDAS only runs for ${gldas_cyc} cycle; Skip GLDAS step for cycle ${cyc}"
     exit 0   
 fi
 
 xtime=$((gldas_spinup_hours+12))
-if [ $CDATE -le $($NDATE +$xtime $SDATE) ]; then
-    echo "GLDAS needs fluxes as forcing from cycles in previous $xtime hours"
-    echo "starting from $SDATE. This gldas cycle is skipped" 
+if [ "${CDATE}" -le "$(${NDATE:?} +"${xtime}" "${SDATE:?}")" ]; then
+    echo "GLDAS needs fluxes as forcing from cycles in previous ${xtime} hours"
+    echo "starting from ${SDATE}. This gldas cycle is skipped" 
     exit 0   
 fi
 
 ##########################################
 # Source machine runtime environment
 ##########################################
-. $HOMEgfs/env/${machine}.env gldas
+. "${HOMEgfs}/env/${machine:?}.env gldas"
 status=$?
-[[ $status -ne 0 ]] && exit $status
+[[ ${status} -ne 0 ]] && exit "${status}"
 
 
 ##############################################
 # Obtain unique process id (pid) and make temp directory
 ##############################################
 export pid=${pid:-$$}
-export outid=${outid:-"LL$job"}
+export outid=${outid:-"LL${job}"}
 
 export DATA=${DATA:-${DATAROOT}/${jobid:?}}
-mkdir -p $DATA
-cd $DATA
+mkdir -p "${DATA}"
+cd "${DATA}" || exit
 
 
 ##############################################
@@ -73,35 +74,35 @@ export COMPONENT=${COMPONENT:-atmos}
 # Begin JOB SPECIFIC work
 ##############################################
 export gldas_ver=${gldas_ver:-v2.3.0}
-export HOMEgldas=${HOMEgldas:-$HOMEgfs}
-export FIXgldas=${FIXgldas:-$HOMEgldas/fix/fix_gldas}
-export PARMgldas=${PARMgldas:-$HOMEgldas/parm/gldas}
-export EXECgldas=${EXECgldas:-$HOMEgldas/exec}
-export USHgldas=${USHgldas:-$HOMEgldas/ush}
-export PARA_CONFIG=$HOMEgfs/parm/config/config.gldas
-
-if [ $RUN_ENVIR = "nco" ]; then
-    export COMIN=${COMIN:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
-    export COMOUT=${COMOUT:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+export HOMEgldas=${HOMEgldas:-${HOMEgfs}}
+export FIXgldas=${FIXgldas:-${HOMEgldas}/fix/fix_gldas}
+export PARMgldas=${PARMgldas:-${HOMEgldas}/parm/gldas}
+export EXECgldas=${EXECgldas:-${HOMEgldas}/exec}
+export USHgldas=${USHgldas:-${HOMEgldas}/ush}
+export PARA_CONFIG=${HOMEgfs}/parm/config/config.gldas
+
+if [ "${RUN_ENVIR:?}" = "nco" ]; then
+    export COMIN=${COMIN:-${ROTDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
+    export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
 else
-    export COMIN="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
-    export COMOUT="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
+    export COMIN="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
+    export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
 fi
-[[ ! -d $COMOUT ]] && mkdir -m 775 -p $COMOUT
+[[ ! -d ${COMOUT} ]] && mkdir -m 775 -p "${COMOUT}"
 
-export COMINgdas=${COMINgdas:-$ROTDIR}
+export COMINgdas=${COMINgdas:-${ROTDIR}}
 export DCOMIN=${DCOMIN:-${DCOMROOT:-"/lfs/h1/ops/prod/dcom"}}
 
 export model=${model:-noah}
-export MODEL=${MODEL:-$(echo $model |tr '[a-z]' '[A-Z]')}
+export MODEL=${MODEL:-$(echo "${model} |tr 'a-z' 'A-Z'")}
 
 
 ###############################################################
 # Run relevant exglobal script
 
-${GLDASSH:-$HOMEgldas/scripts/exgdas_atmos_gldas.sh}
+${GLDASSH:-${HOMEgldas}/scripts/exgdas_atmos_gldas.sh}
 status=$?
-[[ $status -ne 0 ]] && exit $status
+[[ ${status} -ne 0 ]] && exit "${status}"
 
 ##############################################
 # End JOB SPECIFIC work
@@ -110,15 +111,15 @@ status=$?
 ##############################################
 # Final processing
 ##############################################
-if [ -e "$pgmout" ] ; then
-  cat $pgmout
+if [ -e "${pgmout}" ] ; then
+  cat "${pgmout}"
 fi
 
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd $DATAROOT
-[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+cd "${DATAROOT}" || exit
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
 
 exit 0