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[pull] dev from galaxyproject:dev #949

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@pull pull bot added the ⤵️ pull label Oct 10, 2024
):
if error:
error_code = self._ensure_valid_oauth_error_code(error)
return RedirectResponse(f"{trans.request.url_path}{ERROR_REDIRECT_PATH}?error={error_code}")

Check warning

Code scanning / CodeQL

URL redirection from remote source Medium

Untrusted URL redirection depends on a
user-provided value
.
davelopez and others added 27 commits November 5, 2024 09:57
- Rename generic to ZarrDirectory
- Detect Zarr version in metadata
- Add zarr.zip datatype
…file

Instead of the default behavior of downloading an empty file.
Should help when opening the Zarr ZipStore if there is compression involved
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
uv: Do not recalculate dependencies when exporting
`./run_tests.sh --skip-common-startup -api lib/galaxy_test/api -- -s -k
cache` would fail on sqlite with database locked.

Not using a separate connection means that we expire loaded attributes
in the sqlite case, but I don't think we need to be concerned about
performance if you're using sqlite.
Prevent purged users from logging in
bernt-matthias and others added 30 commits November 13, 2024 22:18
- it needs to be specified in the XML
- needs to refer to an existing parameter
Replace static Cytoscape plugin with npm package
Allow a posix file source to prefer linking.
otherwise `uv lock` will have no effect if the `uv.lock` file is
present and there are no changes to the project's dependencies in
`pyproject.toml` .
because it's a transitive dependency (from ase).
Fix word wrapping in invocation panel list items
Restore access to saved visualizations
Add Workflow Title and Annotation sections
Implement workflow parameter validators.
Assert that `data_column` parameters have a valid `data_ref`
Add Interactive Tool Ilastik
by running `make update-dependencies`.
Switch update annotate image to new script entry_point
Update tiff viewer to use script entry_point
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