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Fix dataset pickling #1218

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merged 5 commits into from
Nov 25, 2024
Merged

Fix dataset pickling #1218

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ee8b0ec
Add regression test for dataset picklability
daniel-wer Nov 21, 2024
397b350
try just string?
normanrz Nov 25, 2024
9fa7b32
try copyreg
normanrz Nov 25, 2024
fd121c6
Merge branch 'master' into fix-ssl-context-pickling
normanrz Nov 25, 2024
ebdace9
changelog
normanrz Nov 25, 2024
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3 changes: 2 additions & 1 deletion webknossos/Changelog.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
### Changed

### Fixed
- Fixed pickling issue that has been introduced in 0.15.9. [#1218](https://github.com/scalableminds/webknossos-libs/pull/1218)


## [0.15.9](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.9) - 2024-11-25
Expand All @@ -32,7 +33,7 @@ Removed the CZI installation extra from `pip install webknossos[all]` by default
[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.7...v0.15.8)

### Changed
- Fixes SSL certificate verification for remote datasets by adding CA certificates using `certifi`. [#1211](https://github.com/scalableminds/webknossos-libs/pull/1211)
- Fixed SSL certificate verification for remote datasets by adding CA certificates using `certifi`. [#1211](https://github.com/scalableminds/webknossos-libs/pull/1211)


## [0.15.7](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.7) - 2024-10-25
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5 changes: 5 additions & 0 deletions webknossos/tests/dataset/test_dataset_download_upload_remote.py
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@@ -1,3 +1,4 @@
import pickle
from pathlib import Path
from tempfile import TemporaryDirectory
from time import gmtime, strftime
Expand Down Expand Up @@ -73,6 +74,10 @@ def test_url_open_remote(
data,
sample_dataset.get_color_layers()[0].get_finest_mag().read(),
)
assert set(pickle.loads(pickle.dumps(ds)).layers.keys()) == {
"color",
"segmentation",
}, "Dataset instances should be picklable."


def test_remote_dataset(sample_dataset: wk.Dataset) -> None:
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10 changes: 10 additions & 0 deletions webknossos/webknossos/dataset/defaults.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import copyreg
import os
import ssl

Expand All @@ -6,6 +7,15 @@
from ..geometry import Vec3Int
from .data_format import DataFormat


def _save_sslcontext(
obj: ssl.SSLContext,
) -> tuple[type[ssl.SSLContext], tuple[ssl._SSLMethod]]:
return obj.__class__, (obj.protocol,)


copyreg.pickle(ssl.SSLContext, _save_sslcontext)

DEFAULT_WKW_FILE_LEN = 32
DEFAULT_CHUNK_SHAPE = Vec3Int.full(32)
DEFAULT_DATA_FORMAT = (
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