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Fix bug where the checksum of zipfiles is wrong #930

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Merged
merged 3 commits into from
Jan 6, 2022
Merged

Fix bug where the checksum of zipfiles is wrong #930

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317de6f
Fix bug where the checksum of zipfiles is wrong
orenwatson Jan 5, 2022
6dee888
add test and use a view instead of a copy
orenwatson Jan 5, 2022
a68f7c9
Merge branch 'master' into orenwatson-patch-zipfile-bug
jakirkham Jan 6, 2022
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2 changes: 1 addition & 1 deletion zarr/storage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1551,7 +1551,7 @@ def __getitem__(self, key):
def __setitem__(self, key, value):
if self.mode == 'r':
raise ReadOnlyError()
value = ensure_contiguous_ndarray(value)
value = ensure_contiguous_ndarray(value).view("u1")
with self.mutex:
# writestr(key, value) writes with default permissions from
# zipfile (600) that are too restrictive, build ZipInfo for
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7 changes: 7 additions & 0 deletions zarr/tests/test_storage.py
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Expand Up @@ -1549,6 +1549,13 @@ def test_permissions(self):
assert perm == '0o40775'
z.close()

def test_store_and_retrieve_ndarray(self):
store = ZipStore('data/store.zip')
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@joshmoore joshmoore Jan 6, 2022

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I'm not actually sure why some of these tests use data/store.zip explicitly here, but I think for your test, @orenwatson, it would be best to use the self.create_store() method so that you are testing a fresh zip, independently of other tests.

I can confirm though that this test fails without this PR and passes with it. 👍

NB: A second run with this PR raises the warning:

/usr/local/anaconda3/envs/z/lib/python3.9/zipfile.py:1505: UserWarning: Duplicate name: 'foo'
  return self._open_to_write(zinfo, force_zip64=force_zip64)

which is what makes me think that create_store would be safer.

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@jakirkham jakirkham Jan 6, 2022 •
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Good point Josh 👍

I think with test_permissions this is needed because the file needs to be flushed/closed and then reopened for the test (so it doesn't follow the norm). Though agree we should be able to use create_store here

Edit: As an aside I think this all precedes moving to pytest. So we can probably do some maintenance on this kind of thing to improve the ergonomics

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@joshmoore joshmoore Jan 6, 2022

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Makes sense. If the test is passing, I say we release @orenwatson (and add a grand "Huzzah!" in thanks 🎉) and we can handle the cleanup separately.

x = np.array([[1, 2], [3, 4]])
store['foo'] = x
y = np.frombuffer(store['foo'], dtype=x.dtype).reshape(x.shape)
assert np.array_equiv(y, x)


class TestDBMStore(StoreTests):

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