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Add omero-zarr-pixel-buffer - #6478

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sbesson merged 15 commits into
ome:developfrom
dominikl:ozpb_2
Oct 6, 2026
Merged

sbesson merged 15 commits into
ome:developfrom
dominikl:ozpb_2

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@dominikl

@dominikl dominikl commented Aug 21, 2026 •

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This PR adds the omero-zarr-pixel-buffer to the OMERO.server build.

In order for that to work it also:

  • Removes ZarrReader and jzarr, because of incompatible dependencies (jzarr vs zarr-java, AWS S3 libraries, etc.)
  • Rewrites various integration tests to use ome.tiff mock images instead of ome.xml (because ome.xml will get picked up by the omero-zarr-pixel-buffer and fail, see LockTimeout Exception glencoesoftware/omero-zarr-pixel-buffer#43 ).

Note: Replaces #6450: Had to close the other one, because it seemed to have some kind of hidden "failed" flag which prevented scc from merging it, even after several all successful rebuilds.

@dominikl

dominikl commented Aug 21, 2026 •

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This now breaks the OMERO-build on merge-ci with:

14:16:41 copy-server:
14:16:41 :: problems summary ::
14:16:41 :::: WARNINGS
14:16:41 		[NOT FOUND  ] com.google.guava#failureaccess;1.0.3!failureaccess.jar (1ms)
14:16:41 	==== user-maven: tried
14:16:41 	  /home/omero/.m2/repository/com/google/guava/failureaccess/1.0.3/failureaccess-1.0.3.jar
14:16:41 		[NOT FOUND  ] org.jspecify#jspecify;1.0.0!jspecify.jar (1ms)
14:16:41 	==== user-maven: tried
14:16:41 	  /home/omero/.m2/repository/org/jspecify/jspecify/1.0.0/jspecify-1.0.0.jar
14:16:41 		::::::::::::::::::::::::::::::::::::::::::::::
14:16:41 		::              FAILED DOWNLOADS            ::
14:16:41 		:: ^ see resolution messages for details  ^ ::
14:16:41 		::::::::::::::::::::::::::::::::::::::::::::::
14:16:41 		:: com.google.guava#failureaccess;1.0.3!failureaccess.jar
14:16:41 		:: org.jspecify#jspecify;1.0.0!jspecify.jar
14:16:41 		::::::::::::::::::::::::::::::::::::::::::::::

I have absolutely no clue why and how to fix it.

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A few additional cleanup/organization suggestions but overall the proposed changes are consistent with the way Glencoe has been building OMERO.server with omero-zarr-pixel-buffer and all its dependencies included.

Comment thread etc/ivysettings.xml Outdated
@@ -85,6 +85,10 @@
usepoms="true" useMavenMetadata="true"
m2compatible="true"
root="https://nexus.senbox.net/nexus/content/groups/public/"/>

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We should be able to clean up the bc.releases resolver and the associated chain resolver below

Comment thread etc/omero.properties Outdated
Moved the 'versions.omero-zarr-pixel-buffer' property to the appended values section.

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Can you clean the references to bc.releases from etc/ivysettings.xml as well. As the latest state of this PR has been successfully tested in the nightly integration tests on OME CI, I think we should be in a place to get it merged soon.

@sbesson sbesson linked an issue Oct 2, 2026 that may be closed by this pull request

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The nightly CI tests have been passing with the last commit. Before merging, could you update the body of the PR to briefly summarize its content?

@sbesson
sbesson merged commit 7b02e17 into ome:develop Oct 6, 2026
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Importing ome metadata to omero server fails with ".zarr.ome.xml" files

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