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feat: on demand retrieval (via symlinking) in case input is annotated as on-demand eligible by Snakemake (e.g. because of sequential access being annotated by the developer #32

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Merged
merged 1 commit into from
Mar 20, 2025
Merged

feat: on demand retrieval (via symlinking) in case input is annotated as on-demand eligible by Snakemake (e.g. because of sequential access being annotated by the developer #32

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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ keywords = ["snakemake", "plugin", "storage", "filesystem", "rsync"]
[tool.poetry.dependencies]
python = "^3.11"
snakemake-interface-common = "^1.17.0"
snakemake-interface-storage-plugins = "^4.0.1"
snakemake-interface-storage-plugins = "^4.1.0"
sysrsync = "^1.1.1"
reretry = "^0.11.8"

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18 changes: 14 additions & 4 deletions snakemake_storage_plugin_fs/__init__.py
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Expand Up @@ -199,10 +199,20 @@ def size(self) -> int:

def retrieve_object(self):
# Ensure that the object is accessible locally under self.local_path()
cmd = sysrsync.get_rsync_command(
str(self.query_path), str(self.local_path()), options=["-av"]
)
self._run_cmd(cmd)
if self.is_ondemand_eligible:
self.provider.logger.info(
f"Creating symlink for on-demand retrieval of {self.query_path}."
)
os.symlink(
self.query_path,
self.local_path(),
target_is_directory=self.query_path.is_dir(),
)
else:
cmd = sysrsync.get_rsync_command(
str(self.query_path), str(self.local_path()), options=["-av"]
)
self._run_cmd(cmd)

def store_object(self):
# Ensure that the object is stored at the location specified by
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