From 807a0539db4433533300266519cf2e220ed41b90 Mon Sep 17 00:00:00 2001
From: minghangli-uni <minghang.li1@anu.edu.au>
Date: Mon, 9 Sep 2024 09:30:20 +1000
Subject: [PATCH] Add standardise_mom6_filenames.sh script (#32)

---
 payu_config/archive.sh                        |  1 +
 .../standardise_mom6_filenames.sh             | 53 +++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100755 payu_config/archive_scripts/standardise_mom6_filenames.sh

diff --git a/payu_config/archive.sh b/payu_config/archive.sh
index b5d3ff4..f098f15 100644
--- a/payu_config/archive.sh
+++ b/payu_config/archive.sh
@@ -2,4 +2,5 @@
 
 source $(dirname "$0")/archive_scripts/archive_cice_restarts.sh
 source $(dirname "$0")/archive_scripts/concat_ice_daily.sh
+source $(dirname "$0")/archive_scripts/standardise_mom6_filenames.sh
 python3 $(dirname "$0")/archive_scripts/build_intake_ds.py
diff --git a/payu_config/archive_scripts/standardise_mom6_filenames.sh b/payu_config/archive_scripts/standardise_mom6_filenames.sh
new file mode 100755
index 0000000..8c1e0bf
--- /dev/null
+++ b/payu_config/archive_scripts/standardise_mom6_filenames.sh
@@ -0,0 +1,53 @@
+#!/usr/bin/bash
+# Copyright 2024 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
+# SPDX-License-Identifier: Apache-2.0.
+#
+# Standardise file naming for MOM6 output files from access-om3.
+# This was written assuming it would be used as a payu "userscript" at the "archive" stage, but alternatively a path to an "archive" directory can be provided.
+# For more details, see https://github.com/COSIMA/om3-scripts/issues/32
+
+Help()
+{
+    # Display help
+    echo -e "Standardise file naming for MOM6 output files.\n"
+    echo "Syntax: scriptTemplate [-h|d DIRECTORY]"
+    echo "options:"
+    echo "h    Print this help message."
+    echo -e "d    Process files in the specified 'DIRECTORY'."
+}
+
+while getopts ":hd:" option; do
+    case $option in
+        h) # display help
+           Help
+           exit;;
+        d) # Enter a directory
+            out_dir=$OPTARG
+            if [ ! -d $out_dir ]; then
+                echo $out_dir Does not exist
+                exit
+            fi;;
+        \?) # Invalid option
+            echo "Error: Invalid option"
+            exit;;
+    esac
+done
+
+# if no directory was specified, collect all directories from 'archive'
+if [ -z $out_dir ]; then
+    out_dirs=$(ls -rd archive/output*[0-9] 2>/dev/null)
+else
+    out_dirs=$out_dir
+fi
+
+# process each output directory
+for dir in ${out_dirs[@]}; do
+    # process each mom6 file
+    for current_file in $dir/access-om3.mom6.*.nc; do
+       if [ -f $current_file ]; then
+            new_filename=$(echo $current_file | sed -E 's/_([0-9]{4})\./\1./')
+                # rename the file without overwriting exisiting files
+                mv -n $current_file $new_filename
+        fi
+    done
+done