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Update zenodo dataset for tests (ref #420) #454

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Merged
merged 2 commits into from
Jun 29, 2023
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Update zenodo dataset for tests (ref #420) #454

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2105fbd
Update zenodo dataset for tests (ref #420)
tcompa Jun 29, 2023
afb44a9
Update CHANGELOG
tcompa Jun 29, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
* Update Zenodo datasets used in tests (\#454).

# 0.10.0

* Restructure the package and repository:
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29 changes: 2 additions & 27 deletions tests/conftest.py
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@@ -1,5 +1,4 @@
import json
import logging
import os
import shutil
from pathlib import Path
Expand Down Expand Up @@ -70,7 +69,7 @@ def zenodo_images_multiplex(testdata_path, zenodo_images):
@pytest.fixture(scope="session")
def zenodo_zarr(testdata_path, tmpdir_factory):

doi = "10.5281/zenodo.7674545"
doi = "10.5281/zenodo.8091756"
rootfolder = testdata_path / (doi.replace(".", "_").replace("/", "_"))
platenames = ["plate.zarr", "plate_mip.zarr"]
folders = [rootfolder / plate for plate in platenames]
Expand All @@ -86,37 +85,13 @@ def zenodo_zarr(testdata_path, tmpdir_factory):
]
for zarrname, folder in zip(zarrnames, folders):
zipname = f"{zarrname}.zip"
url = f"https://zenodo.org/record/7674545/files/{zipname}"
url = f"https://zenodo.org/record/8091756/files/{zipname}"
wget.download(url, out=str(tmp_path / zipname), bar=None)
shutil.unpack_archive(
str(tmp_path / zipname), extract_dir=rootfolder, format="zip"
)
shutil.move(str(rootfolder / zarrname), str(folder))

# Fix a wrong piece of metadata
zattrs_path = folder / "B/03/0/.zattrs"
logging.warning(
f"Update coordinateTransformations in {str(zattrs_path)}, "
"see https://github.com/fractal-analytics-platform/"
"fractal-tasks-core/issues/420."
)
with zattrs_path.open("r") as f:
zattrs = json.load(f)
for ind, ds in enumerate(zattrs["multiscales"][0]["datasets"]):
new_ds = ds.copy()
old_transf = ds["coordinateTransformations"][0]
new_transf = old_transf.copy()
assert old_transf["type"] == "scale"
assert len(old_transf["scale"]) == 3
new_transf["scale"] = [1.0, *old_transf["scale"]]
new_ds["coordinateTransformations"][0] = new_transf
assert len(new_transf["scale"]) == len(
zattrs["multiscales"][0]["axes"]
)
zattrs["multiscales"][0]["datasets"][ind] = new_ds
with zattrs_path.open("w") as f:
json.dump(zattrs, f, indent=2)

folders = [str(f) for f in folders]

return folders
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