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Add path check to 7-Zip symlink as a safety window against stale links (caused by mergerfs?)

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RichardG867
2022-04-05 21:59:00 -03:00
parent 1318b7e713
commit aca84baada
1 changed files with 8 additions and 10 deletions
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18
biostools/extractors.py
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@@ -159,13 +159,11 @@ class ArchiveExtractor(Extractor):
# Test symlink creation.
link_path = os.path.join(dir_path, temp_file_name)
try:
# Create symlink.
# Create symlink and check if it was actually created.
os.symlink(my_file_path, link_path)
if not os.path.islink(link_path):
raise Exception()
# Test passed, add to temporary path list.
self._temp_paths.append(link_path)
if os.readlink(link_path) == my_file_path:
# Test passed, add to temporary path list.
self._temp_paths.append(link_path)
except:
pass
@@ -193,17 +191,17 @@ class ArchiveExtractor(Extractor):
# Try creating temporary symlink with the archive's extension.
file_path_abs = os.path.abspath(file_path)
basename, ext = os.path.splitext(file_path_abs)
_, ext = os.path.splitext(file_path_abs)
link_path = file_path_abs
for temp_path in self._temp_paths:
temp_path_ext = temp_path + ext
try:
os.symlink(file_path_abs, temp_path_ext)
if os.readlink(temp_path_ext) == file_path_abs:
link_path = temp_path_ext
break
except:
pass
if os.path.islink(temp_path_ext):
link_path = temp_path_ext
break
# Run 7z command to extract the archive.
# The dummy password prevents any password prompts from stalling 7z.