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(fix): ensure zip directory store compares key to prefix correctly #2758

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Merged
merged 9 commits into from
Feb 10, 2025
Merged

(fix): ensure zip directory store compares key to prefix correctly #2758

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d80fb2c
(fix): ensure zip directory store compares key to prefix correctly
ilan-gold Jan 24, 2025
16792ab
Merge branch 'main' into ig/fix_zip_store
ilan-gold Jan 24, 2025
f507fac
Merge branch 'main' into ig/fix_zip_store
ilan-gold Jan 27, 2025
d730dd2
(chore): add test for externally zipped zarr store
ilan-gold Jan 28, 2025
0cd3733
Merge branch 'main' into ig/fix_zip_store
ilan-gold Jan 28, 2025
b69b3f0
(fix): no need for async test
ilan-gold Jan 28, 2025
b6fbf8e
(chore): rel note
ilan-gold Feb 3, 2025
069d599
Merge branch 'main' into ig/fix_zip_store
ilan-gold Feb 3, 2025
c453bdf
Merge branch 'main' into ig/fix_zip_store
dcherian Feb 10, 2025
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1 change: 1 addition & 0 deletions changes/2758.bugfix.rst
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Fix zip-store path checking for stores with directories listed as files.
2 changes: 1 addition & 1 deletion src/zarr/storage/_zip.py
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Expand Up @@ -283,7 +283,7 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]:
yield key
else:
for key in keys:
if key.startswith(prefix + "/") and key != prefix:
if key.startswith(prefix + "/") and key.strip("/") != prefix:
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There is a TON of this kind of thing already in this codebase. We need these things defined in the IO layer generally, not in individual implementations, as they all face similar problems.

Similarly, do we actually need a ZIP implementation when fsspec can do this for you?

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there have been a LOT of these string parsing bugs. it's a weak point in the codebase, and we definitely need something more solid!

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fsspec knows how you feel.

We can come up with a small number of string normalising functions that live on the Store baseclass, something like os.path, and normalise all user-passed strings at the first opportunity. This is what fsspec's _strip_protocol attempts, but also has problems.

def norm_path(s):
    # this probably adds not insignificant runtime cost
    return re.sub("/+", "/", s.lstrip("/").rstrip("/"))

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@ilan-gold ilan-gold Jan 24, 2025 •
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it's a weak point in the codebase

I did wonder how widespread this could be. I noticed this sort of thing in other stores but wasn't sure if there was knowledge that they were kosher (for whatever reason) within the maintainers (and therefore didn't need this sort of fix).

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The integration with backend IO libraries (fsspec and probably objstore) is particularly thorny, since they do their own path munging!

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What if we didn't represent prefixes as strings, but as tuples of strings instead? e.g. instead of /foo/bar/baz we would just have ('', 'foo', 'bar','baz'), which would be very easy to distinguish from ('foo', 'bar', 'baz'). Lets ignore for a second the profound disruption this would have on our store APIs.

k = key.removeprefix(prefix + "/").split("/")[0]
if k not in seen:
seen.add(k)
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14 changes: 14 additions & 0 deletions tests/test_store/test_zip.py
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@@ -1,6 +1,7 @@
from __future__ import annotations

import os
import shutil
import tempfile
import zipfile
from typing import TYPE_CHECKING
Expand All @@ -14,6 +15,7 @@
from zarr.testing.store import StoreTests

if TYPE_CHECKING:
from pathlib import Path
from typing import Any


Expand Down Expand Up @@ -111,3 +113,15 @@ async def test_zip_open_mode_translation(
kws = {**store_kwargs, "mode": zip_mode}
store = await self.store_cls.open(**kws)
assert store.read_only == read_only

def test_externally_zipped_store(self, tmp_path: Path) -> None:
# See: https://github.com/zarr-developers/zarr-python/issues/2757
zarr_path = tmp_path / "foo.zarr"
root = zarr.open_group(store=zarr_path, mode="w")
root.require_group("foo")
root["foo"]["bar"] = np.array([1])
shutil.make_archive(zarr_path, "zip", zarr_path)
zip_path = tmp_path / "foo.zarr.zip"
zipped = zarr.open_group(ZipStore(zip_path, mode="r"), mode="r")
assert list(zipped.keys()) == list(root.keys())
assert list(zipped["foo"].keys()) == list(root["foo"].keys())