From 5a9bd27a40377b0cadfc51fd576ae98c9ee06668 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@uni-due.de>
Date: Fri, 16 Aug 2024 15:03:45 +0200
Subject: [PATCH] fix: clean up target path upon storage in order to avoid
 merges of directories (#25)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Enhanced the storage process with a cleanup procedure, ensuring a
clean state before storing new data.
- **Improvements**
- Improved robustness by effectively managing both directory and file
scenarios during cleanup, preventing conflicts from residual data.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---
 snakemake_storage_plugin_fs/__init__.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/snakemake_storage_plugin_fs/__init__.py b/snakemake_storage_plugin_fs/__init__.py
index 45a8a7e..00cdd60 100644
--- a/snakemake_storage_plugin_fs/__init__.py
+++ b/snakemake_storage_plugin_fs/__init__.py
@@ -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.