Remove existing directory if it exists when getic runs (#1165)

If getic is run with an existing `$ROTDIR` (possibly because it failed the first time), it would fail because the directory already exists. Now any existing directory is deleted before attempting to move the ICs.

Fixes #1156

jobs/rocoto/getic.sh

@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 
-source "$HOMEgfs/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
 ###############################################################
 ## Abstract:
@@ -16,75 +16,75 @@ source "$HOMEgfs/ush/preamble.sh"
 
 ###############################################################
 # Source FV3GFS workflow modules
-. $HOMEgfs/ush/load_fv3gfs_modules.sh
+. "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
 status=$?
-[[ $status -ne 0 ]] && exit $status
+[[ ${status} -ne 0 ]] && exit "${status}"
 
 ###############################################################
 # Source relevant configs
 configs="base getic init"
-for config in $configs; do
-    . $EXPDIR/config.${config}
+for config in ${configs}; do
+    . "${EXPDIR}/config.${config}"
     status=$?
-    [[ $status -ne 0 ]] && exit $status
+    [[ ${status} -ne 0 ]] && exit "${status}"
 done
 
 ###############################################################
 # Source machine runtime environment
-. $BASE_ENV/${machine}.env getic
+. ${BASE_ENV}/${machine}.env getic
 status=$?
-[[ $status -ne 0 ]] && exit $status
+[[ ${status} -ne 0 ]] && exit "${status}"
 
 ###############################################################
 # Set script and dependency variables
 
-export yy=$(echo $CDATE | cut -c1-4)
-export mm=$(echo $CDATE | cut -c5-6)
-export dd=$(echo $CDATE | cut -c7-8)
-export hh=${cyc:-$(echo $CDATE | cut -c9-10)}
-export GDATE=$($NDATE -${assim_freq:-"06"} $CDATE)
-export gyy=$(echo $GDATE | cut -c1-4)
-export gmm=$(echo $GDATE | cut -c5-6)
-export gdd=$(echo $GDATE | cut -c7-8)
-export ghh=$(echo $GDATE | cut -c9-10)
+export yy="$(echo ${CDATE} | cut -c1-4)"
+export mm="$(echo ${CDATE} | cut -c5-6)"
+export dd="$(echo ${CDATE} | cut -c7-8)"
+export hh="${cyc:-$(echo ${CDATE} | cut -c9-10)}"
+export GDATE="$(${NDATE} -${assim_freq:-"06"} ${CDATE})"
+export gyy="$(echo ${GDATE} | cut -c1-4)"
+export gmm="$(echo ${GDATE} | cut -c5-6)"
+export gdd="$(echo ${GDATE} | cut -c7-8)"
+export ghh="$(echo ${GDATE} | cut -c9-10)"
 
 export DATA=${DATA:-${DATAROOT}/getic}
-export EXTRACT_DIR=${DATA:-$EXTRACT_DIR}
+export EXTRACT_DIR=${DATA:-${EXTRACT_DIR}}
 export PRODHPSSDIR=${PRODHPSSDIR:-/NCEPPROD/hpssprod/runhistory}
 export COMPONENT="atmos"
 export gfs_ver=${gfs_ver:-"v16"}
 export OPS_RES=${OPS_RES:-"C768"}
 export GETICSH=${GETICSH:-${GDASINIT_DIR}/get_v16.data.sh}
 
 # Create ROTDIR/EXTRACT_DIR
-if [ ! -d $ROTDIR ]; then mkdir -p $ROTDIR ; fi
-if [ ! -d $EXTRACT_DIR ]; then mkdir -p $EXTRACT_DIR ; fi
-cd $EXTRACT_DIR
+if [[ ! -d ${ROTDIR} ]]; then mkdir -p "${ROTDIR}" ; fi
+if [[ ! -d ${EXTRACT_DIR} ]]; then mkdir -p "${EXTRACT_DIR}" ; fi
+cd "${EXTRACT_DIR}"
 
 # Check version, cold/warm start, and resolution
-if [[ $gfs_ver = "v16" && $EXP_WARM_START = ".true." && $CASE = $OPS_RES ]]; then # Pull warm start ICs - no chgres
+if [[ ${gfs_ver} = "v16" && ${EXP_WARM_START} = ".true." && ${CASE} = ${OPS_RES} ]]; then # Pull warm start ICs - no chgres
 
   # Pull RESTART files off HPSS
-  if [ ${RETRO:-"NO"} = "YES" ]; then # Retrospective parallel input
+  if [[ ${RETRO:-"NO"} = "YES" ]]; then # Retrospective parallel input
 
     # Pull prior cycle restart files
     htar -xvf ${HPSSDIR}/${GDATE}/gdas_restartb.tar
     status=$?
-    [[ $status -ne 0 ]] && exit $status
+    [[ ${status} -ne 0 ]] && exit "${status}"
 
     # Pull current cycle restart files
     htar -xvf ${HPSSDIR}/${CDATE}/gfs_restarta.tar
     status=$?
-    [[ $status -ne 0 ]] && exit $status
+    [[ ${status} -ne 0 ]] && exit "${status}"
 
     # Pull IAU increment files
     htar -xvf ${HPSSDIR}/${CDATE}/gfs_netcdfa.tar
     status=$?
-    [[ $status -ne 0 ]] && exit $status
+    [[ ${status} -ne 0 ]] && exit "${status}"
 
   else # Opertional input - warm starts
 
-    cd $ROTDIR
+    cd "${ROTDIR}"
     # Pull CDATE gfs restart tarball
     htar -xvf ${PRODHPSSDIR}/rh${yy}/${yy}${mm}/${yy}${mm}${dd}/com_gfs_prod_gfs.${yy}${mm}${dd}_${hh}.gfs_restart.tar
     # Pull GDATE gdas restart tarball
@@ -96,53 +96,57 @@ else # Pull chgres cube inputs for cold start IC generation
   # Run UFS_UTILS GETICSH
   sh ${GETICSH} ${CDUMP}
   status=$?
-  [[ $status -ne 0 ]] && exit $status
+  [[ ${status} -ne 0 ]] && exit "${status}"
 
 fi
 
 # Move extracted data to ROTDIR
-if [ ! -d ${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT} ]; then mkdir -p ${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT} ; fi
-if [ $gfs_ver = v16 -a $RETRO = "YES" ]; then
+if [[ -d ${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT} ]]; then
+  rm -rf "${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT}"
+fi
+mkdir -p "${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT}"
+
+if [ ${gfs_ver} = v16 -a ${RETRO} = "YES" ]; then
   mv ${EXTRACT_DIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/* ${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT}
 else
   mv ${EXTRACT_DIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/* ${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}
 fi
 
 # Pull pgbanl file for verification/archival - v14+
-if [ $gfs_ver = v14 -o $gfs_ver = v15 -o $gfs_ver = v16 ]; then
+if [ ${gfs_ver} = v14 -o ${gfs_ver} = v15 -o ${gfs_ver} = v16 ]; then
   for grid in 0p25 0p50 1p00
   do
     file=gfs.t${hh}z.pgrb2.${grid}.anl
 
-    if [ $gfs_ver = v14 ]; then # v14 production source
+    if [[ ${gfs_ver} = v14 ]]; then # v14 production source
 
-      cd $ROTDIR/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT}
+      cd "${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT}"
       export tarball="gpfs_hps_nco_ops_com_gfs_prod_gfs.${yy}${mm}${dd}${hh}.pgrb2_${grid}.tar"
       htar -xvf ${PRODHPSSDIR}/rh${yy}/${yy}${mm}/${yy}${mm}${dd}/${tarball} ./${file}
 
-    elif [ $gfs_ver = v15 ]; then # v15 production source
+    elif [[ ${gfs_ver} = v15 ]]; then # v15 production source
 
-      cd $EXTRACT_DIR
+      cd "${EXTRACT_DIR}"
       export tarball="com_gfs_prod_gfs.${yy}${mm}${dd}_${hh}.gfs_pgrb2.tar"
       htar -xvf ${PRODHPSSDIR}/rh${yy}/${yy}${mm}/${yy}${mm}${dd}/${tarball} ./${CDUMP}.${yy}${mm}${dd}/${hh}/${file}
       mv ${EXTRACT_DIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${file} ${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT}/${file}
 
-    elif [ $gfs_ver = v16 ]; then # v16 - determine RETRO or production source next
+    elif [[ ${gfs_ver} = v16 ]]; then # v16 - determine RETRO or production source next
 
-      if [ $RETRO = "YES" ]; then # Retrospective parallel source
+      if [[ ${RETRO} = "YES" ]]; then # Retrospective parallel source
 
-        cd $EXTRACT_DIR
-        if [ $grid = "0p25" ]; then # anl file spread across multiple tarballs
+        cd ${EXTRACT_DIR}
+        if [[ ${grid} = "0p25" ]]; then # anl file spread across multiple tarballs
           export tarball="gfsa.tar"
-        elif [ $grid = "0p50" -o $grid = "1p00" ]; then
+        elif [ ${grid} = "0p50" -o ${grid} = "1p00" ]; then
           export tarball="gfsb.tar"
         fi
         htar -xvf ${HPSSDIR}/${yy}${mm}${dd}${hh}/${tarball} ./${CDUMP}.${yy}${mm}${dd}/${hh}/${file}
         mv ${EXTRACT_DIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${file} ${ROTDIR}/${CDUMP}.${yy}${mm}${dd}/${hh}/${COMPONENT}/${file}
 
       else # Production source
 
-        cd $ROTDIR
+        cd "${ROTDIR}"
         export tarball="com_gfs_prod_gfs.${yy}${mm}${dd}_${hh}.gfs_pgrb2.tar"
         htar -xvf ${PRODHPSSDIR}/rh${yy}/${yy}${mm}/${yy}${mm}${dd}/${tarball} ./${CDUMP}.${yy}${mm}${dd}/${hh}/atmos/${file}
 
@@ -155,8 +159,8 @@ fi # v14-v16 pgrb anl file pull
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd $DATAROOT
-[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+cd "${DATAROOT}"
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
 
 ###############################################################
 # Exit out cleanly