Deploy OMERO.server 5.6.9 on pilot IDR instance

[sbesson]

Not intended for production usage yet (this will require a wider discussion and planning aroudn the upgrade of the OMERO.server as well as Bio-Formats)

[sbesson]

This should now be deployed onto pilot-idr0125 in addition to pilot-idr0138 /cc @will-moore

[sbesson]

The last commit has been deployed on pilot-idr0125 and pilot-idr0138 (as per the discussion in #389 (comment)). /cc @francesw @pwalczysko @dominikl @will-moore @khaledk2 @jburel

Looking into recreating pilot-idr0000 next

[sbesson]

This is now deployed on pilot-idr-testing as well /cc @dominikl

[dominikl]

Thanks @sbesson . I wonder, is there actually a reliable way to check it, e.g. omero admin diagnostics says: Jar: lib/server/omero-server.jar jar 5.6.5 but shouldn't it be 5.6.6?

[sbesson]

From OMERO.py 5.13 moving forward, omero admin diagnostics should display the OMERO.server version. Can you try upgrading omero-py if it's too old and see if that works?

[dominikl]

👍
The latest omero-py has an entry for omero server component:
Component: OMERO.server 5.6.6-ice36

The omero-server-jar apparently still is 5.6.5, but maybe that's fine:
Jar: lib/server/omero-server.jar jar 5.6.5

[sbesson]

This should contain the minimal set of changes to deploy the recently released OMERO.server 5.6.7 alongside OMEZarrReader 0.3.1.
@pwalczysko @dominikl @will-moore @dgault which pilots should this be deployed to?

[pwalczysko]

@pwalczysko @dominikl @will-moore @dgault which pilots should this be deployed to?

Definitely pilot-idrtesting please.

[sbesson]

Definitely pilot-idrtesting please.

Upgraded, if you want to give it a try

[sbesson]

Definitely pilot-idrtesting please.

Upgraded, if you want to give it a try

[pwalczysko]

Definitely pilot-idrtesting please.

Upgraded, if you want to give it a try

Thank you, I have idr0011 re-import in progress now.

[pwalczysko]

Thank you, I have idr0011 re-import in progress now.

this was a success, I would say that @dgault 's fix is working on idr0011, thanks

[sbesson]

Now deployed on pilot-idr0125 - see IDR/idr-metadata#652 (comment) for the rationale /cc @will-moore

[will-moore]

@sbesson Just discussed with @dgault the possibility of including ome/ZarrReader#41, which hopefully will allow us to import NGFF without chunks?

[sbesson]

The Ansible infrastructure downloads the JAR from a public location like the OME Artifactory. This is not straightforward to adapt as this work is currently at the Pull Request level.

If you are interested in testing the artifact, it should be more direct and more efficient to deploy it manually on the pilot of your choice. Simply replace the JARs under lib/server and lib/client in the standard OMERO.server location on the pilot server and restart the omero-server service.

[sbesson]

The last state of this PR was deployed on test120

[sbesson]

As discussed earlier today, merging this for the initial deployment of prod120. A follow-up PR will be required to bump ZarrReader.