Add standardise_mom6_filenames.sh script (#32)

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

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 existing files
+                mv -n $current_file $new_filename
+        fi
+    done
+done

test/test_payu_conf/test_mom6_filenames.py

@@ -0,0 +1,147 @@
+import pytest
+import xarray as xr
+import numpy as np
+import pandas as pd
+
+from os import makedirs, chdir
+from subprocess import run
+from pathlib import Path
+
+scripts_base = Path(__file__).parents[2]
+run_str = f"{scripts_base}/payu_config/archive_scripts/standardise_mom6_filenames.sh"
+
+DIAG_BASE = "access-om3.mom6.h.test"
+
+
+def assert_file_exists(p):
+    if not Path(p).resolve().is_file():
+        raise AssertionError("File does not exist: %s" % str(p))
+
+
+def assert_f_not_exists(p):
+    if Path(p).resolve().is_file():
+        raise AssertionError("File exists and should not: %s" % str(p))
+
+
+def monthly_files(dir_name, nmonths, tmp_path):
+    """
+    Make 12 months of empty data files data, and then write it into 12 files
+
+    request = (path, ndays)
+    e.g. request = ("archive/output000", "365")
+
+    """
+
+    times = pd.date_range("2010-01-01", freq="ME", periods=nmonths)
+
+    out_dir = str(tmp_path) + "/" + dir_name + "/"
+    paths = [f"{out_dir}{DIAG_BASE}_{str(t)[0:4]}_{str(t)[5:7]}.nc" for t in times]
+
+    makedirs(out_dir)
+
+    for p in paths:
+        with open(p, "w") as f:
+            # f.write("blank")
+            f.close()
+
+    for p in paths:
+        assert_file_exists(p)
+
+    return paths
+
+
+@pytest.mark.parametrize(
+    "hist_dir, use_dir, nmonths",
+    [
+        ("Default", False, 12),
+        ("archive/output999", False, 1),
+        ("archive/output9999", False, 1),
+        ("archive/output574", True, 12),
+    ],
+)  # run this test with a several folder names and lengths, provide the directory as an argument sometimes
+def test_true_case(hist_dir, use_dir, nmonths, tmp_path):
+
+    monthly_paths = monthly_files(hist_dir, nmonths, tmp_path)
+    chdir(tmp_path)
+    output_dir = Path(monthly_paths[0]).parents[0]
+
+    if not use_dir:  # default path
+        run([run_str])
+        expected_months = pd.date_range("2010-01-01", freq="ME", periods=nmonths + 1)
+    else:  # provide path
+        run(
+            [
+                run_str,
+                "-d",
+                output_dir,
+            ],
+        )
+        expected_months = pd.date_range("2010-01-01", freq="ME", periods=nmonths + 1)
+
+    # valid output filenames
+    expected_paths = [
+        f"{output_dir}/{DIAG_BASE}_{str(t)[0:4]}-{str(t)[5:7]}.nc"
+        for t in expected_months
+    ]
+
+    for p in expected_paths[0:nmonths]:
+        assert_file_exists(p)
+
+    for p in expected_paths[nmonths]:
+        assert_f_not_exists(p)
+
+    for p in monthly_paths:
+        assert_f_not_exists(p)
+
+
+# @pytest.mark.parametrize("hist_dir, ndays", [("Default", 1), ("Default", 30)])
+# def test_incomplete_month(hist_dir, ndays, hist_base, tmp_path):
+#     """
+#     Run the script to convert the daily data into monthly files, with less than 28 days data, and check no things happen.
+#     """
+
+#     daily_paths = daily_files(hist_dir, hist_base, ndays, tmp_path)
+
+#     chdir(tmp_path)
+#     output_dir = Path(daily_paths[0]).parents[0]
+
+#     run([run_str])
+#     expected_months = pd.date_range("2010-01-01", freq="ME", periods=1)
+
+#     monthly_paths = [
+#         f"{output_dir}/{hist_base}.{str(t)[0:7]}.nc" for t in expected_months
+#     ]
+
+#     for p in daily_paths:
+#         assert_file_exists(p)
+
+#     for p in monthly_paths:
+#         assert_f_not_exists(p)
+
+
+# @pytest.mark.parametrize("hist_dir, ndays", [("Default", 31), ("Default", 27)])
+# def test_no_override(hist_dir, ndays, hist_base, tmp_path):
+#     """
+#     Run the script to convert the daily data into monthly files, but the output filename already exists, and check nothing happens.
+#     """
+
+#     daily_paths = daily_files(hist_dir, hist_base, ndays, tmp_path)
+
+#     chdir(tmp_path)
+#     output_dir = Path(daily_paths[0]).parents[0]
+
+#     expected_months = pd.date_range("2010-01-01", freq="ME", periods=1)
+
+#     monthly_paths = [
+#         f"{output_dir}/{hist_base}.{str(t)[0:7]}.nc" for t in expected_months
+#     ]
+#     for p in monthly_paths:
+#         Path(p).touch()
+
+#     run([run_str])
+
+#     for p in daily_paths:
+#         assert_file_exists(p)
+
+#     for p in monthly_paths:
+#         assert_file_exists(p)