Remove Direct Linking to COM from DATA for extractvars Job

ush/atmos_extractvars.sh

@@ -72,10 +72,16 @@ for outtype in "f2d" "f3d"; do
 
     for infile in "${infile1}" "${infile2}"; do
       if [[ -f "${infile}" ]]; then # check if input file exists before extraction
+        new_infile="${outdirpre}/$(basename "${infile}")_ext"
+        cpfs "${infile}" "${new_infile}"
         # shellcheck disable=SC2312
-        ${WGRIB2} "${infile}" | grep -F -f "${varlist}" | ${WGRIB2} -i "${infile}" -append -grib "${outfile}"
-      else
-        echo "WARNING: ${infile} does not exist."
+        ${WGRIB2} "${new_infile}" | grep -F -f "${varlist}" | ${WGRIB2} -i "${new_infile}" -append -grib "${outfile}"
+        elif [[ -f "${infile}" ]]; then
+          echo "WARNING: ${infile} does not exist in ${com_dir}."
+        elif [[ -f "${new_infile}" ]]; then
+          echo "WARNING: ${new_infile} does not exist in ${subdata}. Copying skipped."
+        else
+          echo "WARNING: ${infile} and ${new_infile} do not exist."
       fi
     done
 
@@ -87,10 +93,16 @@ for outtype in "f2d" "f3d"; do
       outfile=${subdata}/vartmp_raw_vari_ldy${dcnt}.grib2
       for infile in "${infile1}" "${infile2}"; do
         if [[ -f "${infile}" ]]; then # check if input file exists before extraction
+          new_infile="${outdirpre}/$(basename "${infile}")_ext"
+          cpfs "${infile}" "${new_infile}"
           # shellcheck disable=SC2312
-          ${WGRIB2} "${infile}" | grep -F -f "${varlist_d}" | ${WGRIB2} -i "${infile}" -append -grib "${outfile}"
+          ${WGRIB2} "${new_infile}" | grep -F -f "${varlist_d}" | ${WGRIB2} -i "${new_infile}" -append -grib "${outfile}"
+        elif [[ -f "${infile}" ]]; then
+          echo "WARNING: ${infile} does not exist in ${com_dir}."
+        elif [[ -f "${new_infile}" ]]; then
+          echo "WARNING: ${new_infile} does not exist in ${subdata}. Copying skipped."
         else
-          echo "WARNING: ${infile} does not exist."
+          echo "WARNING: ${infile} and ${new_infile} do not exist."
         fi
       done
       if [[ ${fcnt} -eq 4 ]]; then

ush/ocnice_extractvars.sh

@@ -26,49 +26,62 @@ for (( nh = FHMIN_GFS + fhout_ocnice; nh <= FHMAX_GFS; nh = nh + fhout_ocnice ))
 
   if [[ ${component_name} == "ocn" ]]; then
     if [[ "${datares}" == "native" ]]; then
-      infile="${COMIN_OCEAN_HISTORY}/${RUN}.ocean.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc"
+      com_dir=${COMIN_OCEAN_HISTORY}
+      infile="${com_dir}/${RUN}.ocean.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc"
+      new_infile=${subdata}/${RUN}.ocean.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}_ext.nc
     else
-      infile="${COMIN_OCEAN_NETCDF}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc"
+      com_dir=${COMIN_OCEAN_NETCDF}
+      infile="${com_dir}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc"
+      new_infile=${subdata}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}_ext.nc
     fi
     # For ocean products, add an argument to extract a subset of levels
     otherargs=(-d "${depthvar_name},""${zmin},""${zmax}")
   elif [[ ${component_name} == "ice" ]]; then
     if [[ "${datares}" == "native" ]]; then
-      infile="${COMIN_ICE_HISTORY}/${RUN}.ice.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc"
+      com_dir=${COMIN_ICE_HISTORY}
+      infile="${com_dir}/${RUN}.ice.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc"
+      new_infile=${subdata}/${RUN}.ice.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}_ext.nc
     else
-      infile="${COMIN_ICE_NETCDF}/${datares}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc"
+      com_dir=${COMIN_ICE_NETCDF}
+      infile="${com_dir}/${datares}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc"
+      new_infile=${subdata}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}_ext.nc
     fi
     otherargs=()
   fi
   outfile=${subdata}/${RUN}.${component_name}.t${cyc}z.${datares}.f${fnh}.nc
 
   if [[ -f "${infile}" ]]; then #check if input file exists before extraction
+    cpfs "${infile}" "${new_infile}" #copy infile to the subdata directory
     varsrequested=$(paste -s "${varlist}")
-    varsinfile=$(cdo -showname "${infile}")
+    varsinfile=$(cdo -showname "${new_infile}")
     varsavailable=""
     for i in ${varsrequested}; do
       # Check if variable from parm file is available in netcdf file. If variable is not in netcdf file, do not try to extract that variable.
       if [[ ${varsinfile} == *"${i}"* ]]; then
         varsavailable+="${i},"
       else
-        echo "WARNING: ${i} is not available in ${infile}."
+        echo "WARNING: ${i} is not available in ${new_infile}."
       fi
     done
     if [[ -z "${varsavailable}" ]]; then
-      echo "WARNING: No variables from parm file ${varlist} are available in netcdf file ${infile}."
+      echo "WARNING: No variables from parm file ${varlist} are available in netcdf file ${new_infile}."
     else
       ocnice_vars=${varsavailable::-1}
-      ncks -v "${ocnice_vars}" "${otherargs[@]}" "${infile}" "${outfile}"
+      ncks -v "${ocnice_vars}" "${otherargs[@]}" "${new_infile}" "${outfile}"
     fi
     if [[ ${datacompress} -eq 1 ]]; then
       ${COMPRSCMD} "${outfile}"
       copy_to_comout "${outfile}.bz2" "${comout_rfcst_prod_ocnice}"
     else
       copy_to_comout "${outfile}" "${comout_rfcst_prod_ocnice}"
-    fi 
+    fi
+  elif [[ -f "${infile}" ]]; then
+    echo "WARNING: ${infile} does not exist in ${com_dir}."
+  elif [[ -f "${new_infile}" ]]; then
+    echo "WARNING: ${new_infile} does not exist in ${subdata}. Copying skipped."
   else
-    echo "WARNING: ${infile} does not exist."
+    echo "WARNING: ${infile} and ${new_infile} do not exist."
   fi
 done # nh
 
-exit 0                                                                                                                                                                                        
+exit 0

ush/wave_extractvars.sh

@@ -1,4 +1,4 @@
-#! /usr/bin/env bash                                                                                                                                                                          
+#! /usr/bin/env bash
 
 ################################################################################
 ## UNIX Script Documentation Block
@@ -24,16 +24,22 @@ for (( nh = FHOUT_WAV_EXTRACT; nh <= FHMAX_WAV; nh = nh + FHOUT_WAV_EXTRACT ));
   fnh=$(printf "%3.3d" "${nh}")
 
   infile=${com_dir}/${RUN}wave.t${cyc}z.global.${wavres}.f${fnh}.grib2
+  new_infile=${subdata}/${RUN}wave.t${cyc}z.global.${wavres}.f${fnh}_ext.grib2
   outfile=${subdata}/${RUN}wave.t${cyc}z.global.${wavres}.f${fnh}.grib2
   rm -f "${outfile}" # Remove outfile if it already exists before extraction
 
   if [[ -f "${infile}" ]]; then # Check if input file exists before extraction
-    # shellcheck disable=SC2312 
-    ${WGRIB2} "${infile}" | grep -F -f "${varlist_wav}" | ${WGRIB2} -i "${infile}" -append -grib "${outfile}"
+    cpfs "${infile}" "${new_infile}" # Copy infile to the subdata directory
+    # shellcheck disable=SC2312
+    ${WGRIB2} "${new_infile}" | grep -F -f "${varlist_wav}" | ${WGRIB2} -i "${new_infile}" -append -grib "${outfile}"
+  elif [[ -f "${infile}" ]]; then
+    echo "WARNING: ${infile} does not exist in ${com_dir}."
+  elif [[ -f "${new_infile}" ]]; then
+    echo "WARNING: ${new_infile} does not exist in ${subdata}. Copying skipped."
   else
-    echo "WARNING: ${infile} does not exist."
-  fi 
+    echo "WARNING: ${infile} and ${new_infile} do not exist."
+  fi
   copy_to_comout "${outfile}" "${ARC_RFCST_PROD_WAV}"
 done # nh
 
-exit 0                                                                                                                                                                                        
+exit 0