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fix: clean up target path upon storage in order to avoid merges of directories #25

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merged 3 commits into from
Aug 16, 2024
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fix: clean up target path upon storage in order to avoid merges of directories #25

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fix: clean up target path upon storage in order to avoid merges of di…
johanneskoester Aug 16, 2024
84e1133
fix
johanneskoester Aug 16, 2024
cd09e08
fix
johanneskoester Aug 16, 2024
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11 changes: 9 additions & 2 deletions snakemake_storage_plugin_fs/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,8 +206,15 @@ def retrieve_object(self):

def store_object(self):
# Ensure that the object is stored at the location specified by
# self.local_path().
self.query_path.parent.mkdir(exist_ok=True, parents=True)
# self.query_path.
if self.query_path.exists():
# Clean up the target path
if self.query_path.is_dir():
shutil.rmtree(self.query_path, ignore_errors=True)
else:
self.query_path.unlink(missing_ok=True)
else:
self.query_path.parent.mkdir(exist_ok=True, parents=True)
# We want to respect the permissions in the target folder, in particular the
# setgid bit. Hence, we use --no-p to avoid preserving of permissions from the
# source to the target.
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