Fixes GSI monitor undefined and error exits

After moving the GSI monitor scripts to workflow, several of the scripts would fail because set -eu is on, either due to undefined variables or trying to operate on non-existent files. This corrects some of those issues. Some of the non-existent files were globs, for these the bash built-in `compgen -G` is used to check if it resolves to any files. Refs: #967
NOAA-EMC · Aug 19, 2022 · cb29351 · cb29351
1 parent 4a22035
commit cb29351
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Showing 7 changed files with 92 additions and 68 deletions.
diff --git a/scripts/exgdas_atmos_verfrad.sh b/scripts/exgdas_atmos_verfrad.sh
@@ -147,12 +147,20 @@ if [[ -s ${radstat} && -s ${biascr} ]]; then
          netcdf=1
       fi
 
-      mv diag_${type}_ges.${PDATE}*.${Z} ${type}.${Z}
-      ${UNCOMPRESS} ./${type}.${Z}
+      if [[ -f "diag_${type}_ges.${PDATE}*.${Z}" ]]; then
+        mv diag_${type}_ges.${PDATE}*.${Z} ${type}.${Z}
+        ${UNCOMPRESS} ./${type}.${Z}
+      else
+        echo "WARNING: diag_${type}_ges.${PDATE}*.${Z} not available, skipping"
+      fi
 
       if [[ $USE_ANL -eq 1 ]]; then
-         mv diag_${type}_anl.${PDATE}*.${Z} ${type}_anl.${Z}
-         ${UNCOMPRESS} ./${type}_anl.${Z}
+        if [[ -f "diag_${type}_anl.${PDATE}*.${Z}" ]]; then
+          mv diag_${type}_anl.${PDATE}*.${Z} ${type}_anl.${Z}
+          ${UNCOMPRESS} ./${type}_anl.${Z}
+        else
+          echo "WARNING: diag_${type}_anl.${PDATE}*.${Z} not available, skipping"
+        fi
       fi
    done
 
@@ -177,7 +185,7 @@ if [[ -s ${radstat} && -s ${biascr} ]]; then
     #--------------------------------------
     #  optionally run clean_tankdir script
     #
-    if [[ ${CLEAN_TANKVERF} -eq 1 ]]; then
+    if [[ ${CLEAN_TANKVERF:-0} -eq 1 ]]; then
        ${USHradmon}/clean_tankdir.sh glb 60
        rc_clean_tankdir=$?
        echo "rc_clean_tankdir = $rc_clean_tankdir"
@@ -208,7 +216,9 @@ fi
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 rlist="saphir"
 for rtype in $rlist; do
+  if compgen -G "$TANKverf_rad/*${rtype}*" > /dev/null; then
     ${CHGRP_CMD} $TANKverf_rad/*${rtype}*
+  fi
 done
 
 exit ${err}

diff --git a/ush/ozn_xtrct.sh b/ush/ozn_xtrct.sh
@@ -40,8 +40,7 @@ check_diag_files() {
    echo ""; echo ""; echo "--> check_diag_files"
 
    for type in ${found_satype}; do
-      check=$(echo ${avail_satype} | grep ${type})    
-      len_check=$(echo -n "${check}" | wc -c)
+      len_check=$(echo ${avail_satype} | grep ${type} | wc -c)
 
       if [[ ${len_check} -le 1 ]]; then
          echo "missing diag file -- diag_${type}_ges.${pdate}.gz not found " >> ./${out_file}   
@@ -153,9 +152,11 @@ else
       echo "ptype = ${ptype}"
 
 
-      for type in ${satype}; do
-         mv diag_${type}_${ptype}.${PDATE}.gz ${type}.${ptype}.gz
-         gunzip ./${type}.${ptype}.gz
+      for type in ${avail_satype}; do
+         if [[ -f "diag_${type}_${ptype}.${PDATE}.gz" ]]; then
+            mv diag_${type}_${ptype}.${PDATE}.gz ${type}.${ptype}.gz
+            gunzip ./${type}.${ptype}.gz
+         fi
       done
 
 
@@ -167,7 +168,7 @@ else
       idd=$(echo ${PDATE} | cut -c7-8)
       ihh=$(echo ${PDATE} | cut -c9-10)
 
-      for type in ${satype}; do
+      for type in ${avail_satype}; do
          echo "processing ptype, type:  ${ptype}, ${type}"
          rm -f input
 
@@ -258,7 +259,7 @@ fi
 #-------------------------------------------------------
 # Conditionally remove data files older than 40 days
 #
-if [[ ${CLEAN_TANKDIR} -eq 1 ]]; then
+if [[ ${CLEAN_TANKDIR:-0} -eq 1 ]]; then
    ${HOMEoznmon}/ush/clean_tankdir.sh glb 40
 fi 
 

diff --git a/ush/radmon_verf_angle.sh b/ush/radmon_verf_angle.sh
@@ -225,20 +225,22 @@ EOF
 
    ${USHradmon}/rstprod.sh
 
-   tar_file=radmon_angle.tar 
-   tar -cf $tar_file angle*.ieee_d* angle*.ctl*
-   ${COMPRESS} ${tar_file}
-   mv $tar_file.${Z} ${TANKverf_rad}/.
-
-   if [[ $RAD_AREA = "rgn" ]]; then
-      cwd=$(pwd)
-      cd ${TANKverf_rad}
-      tar -xf ${tar_file}.${Z}
-      rm ${tar_file}.${Z}
-      cd ${cwd}
-   fi   
-
-   if [[ $fail -eq $ctr || $fail -gt $ctr ]]; then
+   tar_file=radmon_angle.tar
+   if compgen -G "angle*.ieee_d* angle*.ctl*" > /dev/null; then
+      tar -cf $tar_file angle*.ieee_d* angle*.ctl*
+      ${COMPRESS} ${tar_file}
+      mv $tar_file.${Z} ${TANKverf_rad}/.
+
+     if [[ $RAD_AREA = "rgn" ]]; then
+        cwd=$(pwd)
+        cd ${TANKverf_rad}
+        tar -xf ${tar_file}.${Z}
+        rm ${tar_file}.${Z}
+        cd ${cwd}
+     fi
+   fi
+
+   if [[ $ctr -gt 0 && $fail -eq $ctr || $fail -gt $ctr ]]; then
       err=3
    fi
 fi

diff --git a/ush/radmon_verf_bcoef.sh b/ush/radmon_verf_bcoef.sh
@@ -206,20 +206,22 @@ EOF
 
    ${USHradmon}/rstprod.sh
 
-   tar_file=radmon_bcoef.tar
-   tar -cf $tar_file bcoef*.ieee_d* bcoef*.ctl*
-   ${COMPRESS} ${tar_file}
-   mv $tar_file.${Z} ${TANKverf_rad}
-
-   if [[ $RAD_AREA = "rgn" ]]; then
-      cwd=$(pwd)
-      cd ${TANKverf_rad}
-      tar -xf ${tar_file}.${Z}
-      rm ${tar_file}.${Z}
-      cd ${cwd}
+   if compgen -G "bcoef*.ieee_d* bcoef*.ctl*" > /dev/null; then
+     tar_file=radmon_bcoef.tar
+     tar -cf $tar_file bcoef*.ieee_d* bcoef*.ctl*
+     ${COMPRESS} ${tar_file}
+     mv $tar_file.${Z} ${TANKverf_rad}
+
+     if [[ $RAD_AREA = "rgn" ]]; then
+        cwd=$(pwd)
+        cd ${TANKverf_rad}
+        tar -xf ${tar_file}.${Z}
+        rm ${tar_file}.${Z}
+        cd ${cwd}
+     fi
    fi
 
-   if [[ $fail -eq $ctr || $fail -gt $ctr ]]; then
+   if [[ $ctr -gt 0 && $fail -eq $ctr || $fail -gt $ctr ]]; then
       err=5
    fi
 fi

diff --git a/ush/radmon_verf_bcor.sh b/ush/radmon_verf_bcor.sh
@@ -146,7 +146,7 @@ else
             input_file=${type}
          fi
 
-         rm input
+         if [[ -f input ]]; then rm input; fi
 
       # Check for 0 length input file here and avoid running 
       # the executable if $input_file doesn't exist or is 0 bytes
@@ -200,19 +200,21 @@ EOF
    ${USHradmon}/rstprod.sh
    tar_file=radmon_bcor.tar
 
-   tar -cf $tar_file bcor*.ieee_d* bcor*.ctl*
-   ${COMPRESS} ${tar_file}
-   mv $tar_file.${Z} ${TANKverf_rad}/.
-
-   if [[ $RAD_AREA = "rgn" ]]; then
-      cwd=$(pwd)
-      cd ${TANKverf_rad}
-      tar -xf ${tar_file}.${Z}
-      rm ${tar_file}.${Z}
-      cd ${cwd}
+   if compgen -G "bcor*.ieee_d* bcor*.ctl*" > /dev/null; then
+     tar -cf $tar_file bcor*.ieee_d* bcor*.ctl*
+     ${COMPRESS} ${tar_file}
+     mv $tar_file.${Z} ${TANKverf_rad}/.
+
+     if [[ $RAD_AREA = "rgn" ]]; then
+        cwd=$(pwd)
+        cd ${TANKverf_rad}
+        tar -xf ${tar_file}.${Z}
+        rm ${tar_file}.${Z}
+        cd ${cwd}
+     fi
    fi
 
-   if [[ $fail -eq $ctr || $fail -gt $ctr ]]; then
+   if [[ $ctr -gt 0 && $fail -eq $ctr || $fail -gt $ctr ]]; then
       err=7
    fi
 fi

diff --git a/ush/radmon_verf_time.sh b/ush/radmon_verf_time.sh
@@ -259,20 +259,22 @@ EOF
 
    ${USHradmon}/rstprod.sh
 
-   tar_file=radmon_time.tar
-   tar -cf $tar_file time*.ieee_d* time*.ctl*
-   ${COMPRESS} ${tar_file}
-   mv $tar_file.${Z} ${TANKverf_rad}/.
-
-   if [[ $RAD_AREA = "rgn" ]]; then
-      cwd=$(pwd)
-      cd ${TANKverf_rad}
-      tar -xf ${tar_file}.${Z}
-      rm ${tar_file}.${Z}
-      cd ${cwd}
+   if compgen -G "time*.ieee_d* time*.ctl*" > /dev/null; then
+     tar_file=radmon_time.tar
+     tar -cf $tar_file time*.ieee_d* time*.ctl*
+     ${COMPRESS} ${tar_file}
+     mv $tar_file.${Z} ${TANKverf_rad}/.
+
+     if [[ $RAD_AREA = "rgn" ]]; then
+        cwd=$(pwd)
+        cd ${TANKverf_rad}
+        tar -xf ${tar_file}.${Z}
+        rm ${tar_file}.${Z}
+        cd ${cwd}
+     fi
    fi
 
-   if [[ $fail -eq $ctr || $fail -gt $ctr  ]]; then
+   if [[ $ctr -gt 0 && $fail -eq $ctr || $fail -gt $ctr  ]]; then
       echo "fail, ctr = $fail, $ctr"
       err=10
    fi
@@ -407,11 +409,14 @@ EOF
    #--------------------------------------------------------------------
    #  Remove extra spaces in new bad_pen & low_count files
    #
-   gawk '{$1=$1}1' $bad_pen > tmp.bad_pen
-   mv -f tmp.bad_pen $bad_pen
-
-   gawk '{$1=$1}1' $low_count > tmp.low_count
-   mv -f tmp.low_count $low_count
+   if [[ -s ${bad_pen} ]]; then
+     gawk '{$1=$1}1' $bad_pen > tmp.bad_pen
+     mv -f tmp.bad_pen $bad_pen
+   fi
+   if [[ -s ${low_count} ]]; then
+     gawk '{$1=$1}1' $low_count > tmp.low_count
+     mv -f tmp.low_count $low_count
+   fi
 
    echo " do_pen, do_chan, do_cnt = $do_pen, $do_chan, $do_cnt"
    echo " diag_report = $diag_report "

diff --git a/ush/rstprod.sh b/ush/rstprod.sh
@@ -13,5 +13,7 @@ source "$HOMEgfs/ush/preamble.sh"
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 rlist="saphir abi_g16"
 for rtype in $rlist; do
-    ${CHGRP_CMD} *${rtype}*
+    if compgen -G "*${rtype}*" > /dev/null; then
+        ${CHGRP_CMD} *${rtype}*
+    fi
 done