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change copy_file to ignore failing copy of file metadata by using shutil.copyfile + shutil.copystat rather than shutil.copy2 #3912

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change copy_file to ignore failing copy of file metadata by using shutil.copyfile + shutil.copystat rather than shutil.copy2 #3912

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26 changes: 23 additions & 3 deletions easybuild/tools/filetools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2382,10 +2382,30 @@ def copy_file(path, target_path, force_in_dry_run=False):
shutil.copyfile(path, target_path)
_log.info("Copied contents of file %s to %s", path, target_path)
else:
mkdir(os.path.dirname(target_path), parents=True)
if os.path.isdir(target_path):
target_path = os.path.join(target_path, os.path.basename(path))

target_parent_dir = os.path.dirname(target_path)
if not os.path.exists(target_parent_dir):
mkdir(target_parent_dir, parents=True)

if path_exists:
shutil.copy2(path, target_path)
_log.info("%s copied to %s", path, target_path)
# always try to copy file contents
shutil.copyfile(path, target_path)
_log.info("File contents of %s copied to %s", path, target_path)

# also try to copy metadata, but only log in case of failure;
# there could be various valid reasons that copying of metadata failed,
# like the target file being owned by someone else than the current user
# (since chown required file ownership),
# or the source filesystem having more attributes than the target filesystem
# (cfr. https://github.com/easybuilders/easybuild-framework/issues/3910)
try:
shutil.copystat(path, target_path)
_log.info("Metadata of %s copied to %s", path, target_path)
except Exception as err:
_log.info("Ignoring failure to copy metadata of %s to %s: %s", path, target_path, err)

elif os.path.islink(path):
if os.path.isdir(target_path):
target_path = os.path.join(target_path, os.path.basename(path))
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