Feature/cdo post ocean format

parm/post/mom6_update.csv

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+SST coordinates geolon,geolat,time
+SSS coordinates geolon,geolat,time
+SSH coordinates geolon,geolat,time
+speed coordinates geolon,geolat,time
+MLD_003 coordinates geolon,geolat,time
+so coordinates geolon,geolat,time
+temp coordinates geolon,geolat,time
+latent coordinates geolon,geolat,time
+sensible coordinates geolon,geolat,time
+SW coordinates geolon,geolat,time
+LW coordinates geolon,geolat,time
+evap coordinates geolon,geolat,time
+lprec coordinates geolon,geolat,time
+LwLatSens coordinates geolon,geolat,time
+Heat_PmE coordinates geolon,geolat,time
+SSU coordinates geolon_u,geolat_u,time
+uo coordinates geolon_u,geolat_u,time
+taux coordinates geolon_u,geolat_u,time
+SSV coordinates geolon_v,geolat_v,time
+vo coordinates geolon_v,geolat_v,time
+tauy coordinates geolon_v,geolat_v,time

ush/cdo_post_ocean_format.sh

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+#! /usr/bin/env bash
+
+#######
+# Script for updating/adding specified netCDF variable metadata
+#   attribute values.
+#
+# Syntax:
+#   cdo_post_prep.sh variable_file input_netcdf output_netcdf
+#
+#   Arguments:
+#
+#     variable_file: ASCII formatted file containing netCDF variables
+#                      and the respective metadata attributes to be
+#                      updated/added; the supported format is as
+#                      follows.
+#
+#     <netCDF variable name> <netCDF metadata attribute name>
+#       <netCDF metadata values>
+#
+#       An example using the format described above is as follows.
+#
+#     SST coordinates geolon,geolat,time
+#     uo coordinates geolon_u,geolon_u,time
+#     vo coordinates geolon_v,geolon_v,time
+#
+#       The example above will perform the following task using this
+#       script.
+#
+#       * Assign the netCDF metadata attribute `coordinates` for
+#         variable `SST` the values `geolon,geolat,time` and update
+#         the `output_netcdf` file path.
+#
+#       * Assign the netCDF metadata attribute `coordinates` for
+#         variable `uo` the values `geolon_u,geolat_u,time` and update
+#         the `output_netcdf` file path.
+#
+#       * Assign the netCDF metadata attribute `coordinates` for
+#         variable `vo` the values `geolon_v,geolat_v,time` and update
+#         the `output_netcdf` file path.
+#
+#     input_netcdf: The netCDF-formatted file path containing the
+#                     variables defined in `variable_file`.
+#
+#     output_netcdf: A netCDF-formatted file path to contain the
+#                      specified variables remapped to the destination
+#                      grid projection.
+#######
+
+# Collect the command line arguments and check the validity.
+variable_file="${1}"
+input_path="${2}"
+output_path="${3}"
+
+#######
+
+if [[ "$#" -ne 3 ]]; then
+    echo "Usage: $0 <variable_file> <input_path> <output_path>"
+    exit 100
+fi
+
+#######
+
+# _comma_split_string - Split a comma-delimited string into an array.
+#
+# Description:
+#   This function takes a comma-delimited string as input and splits
+#     it into an array. Each element in the resulting array is
+#     obtained by splitting the input string at commas and then
+#     removing leading and trailing spaces.
+#
+# Parameters:
+#   $1 - The comma-delimited string to split.
+#
+# Global Variables:
+#   global_array - An array containing the split elements.
+#
+# Example usage:
+#   _comma_split_string "item1,item2 item3,item4"
+#   for element in "${global_array[@]}"; do
+#       echo "$element"
+#   done
+#
+# This example will split the input string into individual elements
+#   and print each element on a separate line.
+function _comma_split_string() {
+    local string="${1}"
+
+    local local_array=()
+    global_array=()
+    IFS="," read -ra items <<< "${string}"
+    for item in "${items[@]}"; do
+        local_array+=("${item} ")
+    done
+    for item in "${local_array[@]}"; do
+        IFS=" " read -ra items <<< "${item}"
+        for element in "${items[@]}"; do
+            global_array+=("${element} ")
+        done
+    done
+}
+
+#######
+
+# _strip_whitespace - Remove whitespace from a string.
+#
+# Description:
+#   This function takes an input string and removes all whitespace
+#   characters (spaces, tabs, and newline characters) to produce a
+#   cleaned output string.
+#
+# Parameters:
+#   $1 - The input string from which whitespace will be removed.
+#
+# Return:
+#   The cleaned string with no whitespace.
+#
+# Example usage:
+#   cleaned_string=$(_strip_whitespace "   This is a string   with spaces  ")
+#   echo "Cleaned string: \"$cleaned_string\""
+#
+# This example will remove all leading, trailing, and internal
+# whitespace from the input string and display the cleaned result.
+function _strip_whitespace(){
+    local in_string="${1}"
+
+    out_string=$(echo "${in_string}" | $(command -v sed) "s/ //g")
+}
+
+#######
+
+# ncattr_update - Update/add attributes for a variable in a netCDF file.
+#
+# Description:
+#   This function updates the specified attribute for a specified
+#     variable in a netCDF file using the `ncatted` command.
+#
+# Parameters:
+#   $1 - The variable name to update.
+#   $2 - netCDF variable metadata attribute name.
+#   $3 - The coordinates as a comma-separated string.
+#
+# Global Variables:
+#   global_array - An array containing the split coordinates.
+#   output_path - The path to the output netCDF file.
+#
+# Example usage:
+#   ncupdate "variable_name" "coords" "lon,lat,time"
+#
+# This example updates the `coords` attributes for the specified
+#   variable and writes the updates to the output netCDF file.
+function ncattr_update(){
+    local varname="${1}"
+    local ncattr="${2}"
+    local coords="${3}"
+
+    _comma_split_string "${coords}"
+    coords="${global_array[@]}"
+    coords_str="$(echo "${coords}" | $(command -v tr) -s ' ')"
+    ncattr_str="$(echo "${ncattr}" | $(command -v tr) -s ' ')"
+    echo "Adding netCDF attribute ${ncattr_str} values ${coords_str} to variable ${varname} metadata and writing to file ${output_path}"
+    ($(command -v ncatted) -O -a "${ncattr_str}","${varname}",c,c," ${coords_str}" "${output_path}" "${output_path}")
+}
+
+#######
+
+start_time=$(gdate +%s) # TODO: For local debugging.
+_calling_script=$(basename "${BASH_SOURCE[0]}")
+start_time_human=$(gdate -d"@${start_time}" -u) # TODO: For local debugging.
+echo "Begin ${_calling_script} at ${start_time_human}."
+
+# Copy the input file path to the output file path.
+echo "Copying file ${input_path} to ${output_path} and preparing for variable updates."
+$(command -v cp) "${input_path}" "${output_path}"
+
+# Read the configuration file for the the variables to be updated and
+# proceed accordingly.
+while IFS= read -r line; do
+
+    # Get the attributes for the respective variable.
+    varname=$(echo "${line}" | $(command -v awk) '{print $1}')
+    ncattr=$(echo "${line}" | $(command -v awk) '{print $2}')
+    coords=$(echo "${line}" | $(command -v awk) '{print $3}')
+
+    # Update the variable attributes and write the updates to the
+    # specified output file (see `output_path`).
+    ncattr_update "${varname}" "${ncattr}" "${coords}"
+
+done < "${variable_file}"
+
+stop_time=$(gdate +%s) # TODO: For local debugging.
+_calling_script=$(basename "${BASH_SOURCE[0]}")
+stop_time_human=$(gdate -d"@${stop_time}" -u) # TODO: For local debugging.
+echo "End ${_calling_script} at ${stop_time_human}."