Improving the scripts for CONUS II

Given that there might be descrepencies between various versions of the
CONUS II dataset files (what is locally available and what is offered by
NCAR,) minor changes are proposed to alleviate issues that may come up.

Reported-by: Logan Fang <[email protected]>
Signed-off-by: Kasra Keshavarz <[email protected]>

scripts/gwf-ncar-conus_ii/conus_ii.sh

@@ -312,8 +312,25 @@ function concat_files () {
   shift 2               # shift arguments by 2 positions
   local filesArr=("$@") # array of file names
 
-  # concatenating $files and producing a single $fName.nc
-  ncrcat "${filesArr[@]}" "${fTempDir}/${fName}_cat.nc"
+  # Create temp directory for intermediate files
+  local ctmpdir="${fTempDir}/tmp_concat_$$"
+  mkdir -p "$ctmpdir"
+
+  # Process each file to add Time variable
+  for f in "${filesArr[@]}"; do
+      if [ -f "$f" ]; then
+          local basename_f=$(basename "$f")
+          ncap2 -s 'Time=XTIME' "$f" "${ctmpdir}/${basename_f}"
+      else
+          echo "Warning: File $f does not exist, skipping"
+      fi
+  done
+
+  # Concatenate processed files
+  ncrcat "${ctmpdir}"/* "${fTempDir}/${fName}_cat.nc"
+
+  # Clean up
+  rm -rf "$ctmpdir"
 }