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Fix download separator
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@dstansby
dstansby committed Dec 28, 2024
1 parent 9ac61ea commit 073d009
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Showing 2 changed files with 18 additions and 199 deletions.
4 changes: 3 additions & 1 deletion ome_zarr/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,9 @@ def download(input_path: str, output_dir: str = ".") -> None:
for dataset, data in reversed(list(zip(datasets, resolutions))):
LOGGER.info("resolution %s...", dataset)
with pbar:
data.to_zarr(str(target_path / dataset))
data.to_zarr(
str(target_path / dataset), dimension_separator="/"
)
else:
# Assume a group that needs metadata, like labels
zarr.group(str(target_path))
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213 changes: 15 additions & 198 deletions tests/test_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,16 @@
from ome_zarr.utils import strip_common_prefix


def directory_items(directory: Path):
"""
Get all items (files and folders) in a directory, relative to that directory.
"""
if not directory.is_dir():
raise ValueError(f"{p} is not a directory")

return sorted([p.relative_to(directory) for p in directory.glob("*")])


class TestCli:
@pytest.fixture(autouse=True)
def initdir(self, tmpdir):
Expand Down Expand Up @@ -40,9 +50,7 @@ def test_astronaut_download(self, tmpdir):
main(["download", filename, f"--output={out}"])
main(["info", f"{out}/{basename}"])

out_path = Path(out) / "data-3"
paths = [p.relative_to(out_path) for p in out_path.glob("*")]
assert sorted(paths) == [
assert directory_items(Path(out) / "data-3") == [
Path(".zattrs"),
Path(".zgroup"),
Path("0"),
Expand All @@ -53,202 +61,11 @@ def test_astronaut_download(self, tmpdir):
Path("labels"),
]

data_path = Path(out) / "data-3" / "1"
paths = [p.relative_to(data_path) for p in data_path.glob("*")]
assert sorted(paths) == [
assert directory_items(Path(out) / "data-3" / "1") == [
Path(".zarray"),
Path("0.0.0"),
Path("0.0.1"),
Path("0.0.2"),
Path("0.0.3"),
Path("0.0.4"),
Path("0.0.5"),
Path("0.0.6"),
Path("0.0.7"),
Path("0.1.0"),
Path("0.1.1"),
Path("0.1.2"),
Path("0.1.3"),
Path("0.1.4"),
Path("0.1.5"),
Path("0.1.6"),
Path("0.1.7"),
Path("0.2.0"),
Path("0.2.1"),
Path("0.2.2"),
Path("0.2.3"),
Path("0.2.4"),
Path("0.2.5"),
Path("0.2.6"),
Path("0.2.7"),
Path("0.3.0"),
Path("0.3.1"),
Path("0.3.2"),
Path("0.3.3"),
Path("0.3.4"),
Path("0.3.5"),
Path("0.3.6"),
Path("0.3.7"),
Path("0.4.0"),
Path("0.4.1"),
Path("0.4.2"),
Path("0.4.3"),
Path("0.4.4"),
Path("0.4.5"),
Path("0.4.6"),
Path("0.4.7"),
Path("0.5.0"),
Path("0.5.1"),
Path("0.5.2"),
Path("0.5.3"),
Path("0.5.4"),
Path("0.5.5"),
Path("0.5.6"),
Path("0.5.7"),
Path("0.6.0"),
Path("0.6.1"),
Path("0.6.2"),
Path("0.6.3"),
Path("0.6.4"),
Path("0.6.5"),
Path("0.6.6"),
Path("0.6.7"),
Path("0.7.0"),
Path("0.7.1"),
Path("0.7.2"),
Path("0.7.3"),
Path("0.7.4"),
Path("0.7.5"),
Path("0.7.6"),
Path("0.7.7"),
Path("1.0.0"),
Path("1.0.1"),
Path("1.0.2"),
Path("1.0.3"),
Path("1.0.4"),
Path("1.0.5"),
Path("1.0.6"),
Path("1.0.7"),
Path("1.1.0"),
Path("1.1.1"),
Path("1.1.2"),
Path("1.1.3"),
Path("1.1.4"),
Path("1.1.5"),
Path("1.1.6"),
Path("1.1.7"),
Path("1.2.0"),
Path("1.2.1"),
Path("1.2.2"),
Path("1.2.3"),
Path("1.2.4"),
Path("1.2.5"),
Path("1.2.6"),
Path("1.2.7"),
Path("1.3.0"),
Path("1.3.1"),
Path("1.3.2"),
Path("1.3.3"),
Path("1.3.4"),
Path("1.3.5"),
Path("1.3.6"),
Path("1.3.7"),
Path("1.4.0"),
Path("1.4.1"),
Path("1.4.2"),
Path("1.4.3"),
Path("1.4.4"),
Path("1.4.5"),
Path("1.4.6"),
Path("1.4.7"),
Path("1.5.0"),
Path("1.5.1"),
Path("1.5.2"),
Path("1.5.3"),
Path("1.5.4"),
Path("1.5.5"),
Path("1.5.6"),
Path("1.5.7"),
Path("1.6.0"),
Path("1.6.1"),
Path("1.6.2"),
Path("1.6.3"),
Path("1.6.4"),
Path("1.6.5"),
Path("1.6.6"),
Path("1.6.7"),
Path("1.7.0"),
Path("1.7.1"),
Path("1.7.2"),
Path("1.7.3"),
Path("1.7.4"),
Path("1.7.5"),
Path("1.7.6"),
Path("1.7.7"),
Path("2.0.0"),
Path("2.0.1"),
Path("2.0.2"),
Path("2.0.3"),
Path("2.0.4"),
Path("2.0.5"),
Path("2.0.6"),
Path("2.0.7"),
Path("2.1.0"),
Path("2.1.1"),
Path("2.1.2"),
Path("2.1.3"),
Path("2.1.4"),
Path("2.1.5"),
Path("2.1.6"),
Path("2.1.7"),
Path("2.2.0"),
Path("2.2.1"),
Path("2.2.2"),
Path("2.2.3"),
Path("2.2.4"),
Path("2.2.5"),
Path("2.2.6"),
Path("2.2.7"),
Path("2.3.0"),
Path("2.3.1"),
Path("2.3.2"),
Path("2.3.3"),
Path("2.3.4"),
Path("2.3.5"),
Path("2.3.6"),
Path("2.3.7"),
Path("2.4.0"),
Path("2.4.1"),
Path("2.4.2"),
Path("2.4.3"),
Path("2.4.4"),
Path("2.4.5"),
Path("2.4.6"),
Path("2.4.7"),
Path("2.5.0"),
Path("2.5.1"),
Path("2.5.2"),
Path("2.5.3"),
Path("2.5.4"),
Path("2.5.5"),
Path("2.5.6"),
Path("2.5.7"),
Path("2.6.0"),
Path("2.6.1"),
Path("2.6.2"),
Path("2.6.3"),
Path("2.6.4"),
Path("2.6.5"),
Path("2.6.6"),
Path("2.6.7"),
Path("2.7.0"),
Path("2.7.1"),
Path("2.7.2"),
Path("2.7.3"),
Path("2.7.4"),
Path("2.7.5"),
Path("2.7.6"),
Path("2.7.7"),
Path("0"),
Path("1"),
Path("2"),
]

def test_s3_info(self, s3_address):
Expand Down

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