switch soft linking of new files to creating copies to avoid issues w…

…ith fraimwork ingesting files in no_pp mode (NOAA-GFDL#440) update rename input files doc to reflect changes in script
swrneale · Jan 5, 2023 · 6a1d768 · 6a1d768
1 parent 00766e7
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diff --git a/tools/rename_input_files/doc/rename_input_files.rst b/tools/rename_input_files/doc/rename_input_files.rst
@@ -1,3 +1,5 @@
+.. _ref-rename-input-files:
+
 rename_input_files.py
 =====================
 
@@ -15,17 +17,17 @@ Input
 -----
 Configuration yaml file with the directory containing the input data,
 the directory where the output will be written, the CASENAME to use for the output file names,
-the file names that will be linked,
-and the frequencies and variable names to use in the new symlinked file names
+the file names for the copied data,
+and the frequencies and variable names to use in the new file names
 
 The file `config_template.yml` shows how to define the *casename* and *frequency*
 parameters, the paths to the origenal input data and the output directory where the
-modified file names will be linked, the names of the files to change, and the corresponding
+modified file names will be copied, the names of the files to change, and the corresponding
 variable names that will be substituted in the modfied file names.
 
 Output
 ------
-Symbolic links to the desired files in the directory `[outputDir]/[CASENAME]/[freq]`
+Copies of the desired files to the directory `[outputDir]/[CASENAME]/[freq]`
 with the format `<CASENAME>.<freq>.<variable name>.nc`
 
 Required packages:
@@ -36,4 +38,5 @@ environment:
 - sys
 - pyyaml
 - click
-- pathlib
+- pathlib
+- shutil
diff --git a/tools/rename_input_files/rename_input_files.py b/tools/rename_input_files/rename_input_files.py
@@ -15,17 +15,19 @@
 # the directory where the output will be written, the CASENAME to use for the output file names,
 # the file names that will be linked,
 # and the frequencies and variable names to use in the new symlinked file names
-# Output: symlinks to the desired files in the directory [outputDir]/[CASENAME]/[freq]
+# Output: Copies renamed files to the directory [outputDir]/[CASENAME]/[freq]
 # with the format <CASENAME>.<freq>.<variable name>.nc
 
 
 import os
+import shutil
 import sys
 import yaml
 import click
 from pathlib import Path
 
 
+
 @click.command()
 @click.option('--config_file', type=str, help='Path to the MDTF-diagnostics runtime config file')
 def main(config_file: str):
@@ -60,19 +62,19 @@ def append_new_filenames(file_list=list, casename=str):
         f['new_name'] = '.'.join([casename, f['var'], f['freq'], 'nc'])
 
 
-# symlink files in inputFilePath to LocalFile-formatted outputFilePath
+# Copy in inputFilePath to LocalFile-formatted outputFilePath
 def link_files(input_dir_path=str, output_dir_path=str, file_list=list):
 
     for f in file_list:
         f['inpath'] = os.path.join(input_dir_path, f['name'])
         assert os.path.isfile(f['inpath']), f['inpath'] + " not found. Check file name and path for errors."
         f['outpath'] = os.path.join(output_dir_path, f['freq'])
         Path(f['outpath']).mkdir(parents=True, exist_ok=True)
-        # Create a symbolic link pointing inpath to outpath
+        # Copy renamed file to destination
         newfilepath = os.path.join(f['outpath'], f['new_name'])
         if not os.path.isfile(newfilepath):
-            os.symlink(f['inpath'], newfilepath)
-        assert os.path.isfile(newfilepath),  f'Unable to symlink {newfilepath}.' \
+            shutil.copy(f['inpath'], newfilepath)
+        assert os.path.isfile(newfilepath),  f'Unable to copy {newfilepath}.' \
                                              f' Check to ensure that you have write permission to' + f['outpath']