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WIP: Allow link_only for posix file sources #19125

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WIP: Allow link_only for posix file sources #19125

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b8b5160
Add link only option to posix file source
guerler Nov 9, 2024
503e69b
Add symlink operation to posix file source
guerler Nov 9, 2024
5052b21
Add link_only to serializer
guerler Nov 9, 2024
e105703
Naive attempt to force symlink
guerler Nov 9, 2024
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21 changes: 17 additions & 4 deletions lib/galaxy/files/sources/posix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,15 @@
DEFAULT_ENFORCE_SYMLINK_SECURITY = True
DEFAULT_DELETE_ON_REALIZE = False
DEFAULT_ALLOW_SUBDIR_CREATION = True
DEFAULT_LINK_ONLY = False


class PosixFilesSourceProperties(FilesSourceProperties, total=False):
root: str
enforce_symlink_security: bool
delete_on_realize: bool
allow_subdir_creation: bool
link_only: bool


class PosixFilesSource(BaseFilesSource):
Expand All @@ -50,6 +52,7 @@ def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
self.root = props.get("root")
if not self.root:
self.writable = False
self.link_only = props.get("link_only", DEFAULT_LINK_ONLY)
self.enforce_symlink_security = props.get("enforce_symlink_security", DEFAULT_ENFORCE_SYMLINK_SECURITY)
self.delete_on_realize = props.get("delete_on_realize", DEFAULT_DELETE_ON_REALIZE)
self.allow_subdir_creation = props.get("allow_subdir_creation", DEFAULT_ALLOW_SUBDIR_CREATION)
Expand Down Expand Up @@ -103,7 +106,11 @@ def _realize_to(
source_native_path = os.path.normpath(source_native_path)
assert source_native_path.startswith(os.path.normpath(effective_root))

if not self.delete_on_realize:
if self.link_only:
if os.path.exists(native_path) or os.path.islink(native_path):
os.remove(native_path)
os.symlink(source_native_path, native_path)
elif not self.delete_on_realize:
shutil.copyfile(source_native_path, native_path)
else:
shutil.move(source_native_path, native_path)
Expand Down Expand Up @@ -133,9 +140,14 @@ def _write_from(

# Use a temporary name while writing so anything that consumes written files can detect when they've completed,
# and identify interrupted writes
target_native_path_part = os.path.join(target_native_path_parent, f"_{target_native_path_name}.part")
shutil.copyfile(native_path, target_native_path_part)
os.rename(target_native_path_part, target_native_path)
if self.link_only:
if os.path.exists(native_path) or os.path.islink(native_path):
os.remove(native_path)
os.symlink(target_native_path, native_path)
else:
target_native_path_part = os.path.join(target_native_path_parent, f"_{target_native_path_name}.part")
shutil.copyfile(native_path, target_native_path_part)
os.rename(target_native_path_part, target_native_path)

def _to_native_path(self, source_path: str, user_context: OptionalUserContext = None):
source_path = os.path.normpath(source_path)
Expand Down Expand Up @@ -182,6 +194,7 @@ def _serialization_props(self, user_context: OptionalUserContext = None) -> Posi
"enforce_symlink_security": self.enforce_symlink_security,
"delete_on_realize": self.delete_on_realize,
"allow_subdir_creation": self.allow_subdir_creation,
"link_only": self.link_only,
}

@property
Expand Down
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