OMERO / Python 3 - 5.6 milestone for upgrade testing

There have still been no major objections to the rollout plan above, so we’re moving forward – :trumpet: :drum: – a first public milestone of OMERO (5.6.0-m4) is now available for downloading and upgrade testing:

https://downloads.openmicroscopy.org/omero/5.6/artifacts/

We encourage those of you who will be testing the migration to start with the migration page:

https://docs.openmicroscopy.org/omero/5.6/sysadmins/python3-migration.html

As a reminder, support for Python 2 will be dropped with the final release of 5.6.0 early in 2020. We’d very much liked to hear if anything is unclear or doesn’t work on your particular setup. We plan to push out documentation updates as frequently as necessary.

All the best,
The @OMETeam

3 Likes

(Migrated from OMERO / Python 3 Rollout Plan since I got feedback that it was hard to find.)

Hi,

I installed OMERO 5.6 in a test environment and here are some remarks/questions:

  • I followed https://docs.openmicroscopy.org/omero/5.6.0-m4/sysadmins/unix/server-ubuntu1804-ice36.html and found that I had to pip install wheel before pip install omero-py>=5.6.dev4". Same is actually true for the OMERO.web installation (https://docs.openmicroscopy.org/omero/5.6.0-m4/sysadmins/unix/install-web/walkthrough/omeroweb-install-ubuntu1804-ice3.6.html)
  • I found that setting OMERO_HOME would somehow interfere with the installation, at least OMERO.web, I got a ‘lib folder does not exist’ (or similar). Not setting OMERO_HOME solved it.
  • What is whitenoise good for, do I need it? I haven’t installed it and everything still seems to work fine
  • Directly after installing, I imported our institute’s database from a backup using pg_restore (PostgreSQL 11). (The backup was created with PostgreSQL 9.5, OMERO.server 5.4.10). During the import I got an error message could not execute query: ERROR: schema "public" already exists. This doesn’t happen if I run pg_restore using PostgreSQL 10). Nevertheless, everything still seems to work.
  • And finally: We will replace our old production server (not only software and OMERO, but also hardware) with a new one in the 2nd week of January, and I was briefly considering to ship it directly with OMERO 5.6.0. Would you discourage this? And will there be an OMERO.insight for OMERO.server 5.6? Are there any plans when?

Thanks a lot, I really value your work,
Bene

Hi Bene

Thanks for the feedback

  • We will update the doc for ubuntu18.04. The doc is prepared using installation steps tested using docker container. We will integrate the dependencies so it can used when not using docker
  • We will indicate to unset OMERO_HOME to avoid issues. Probably good to add to our troubleshooting page. It serves compressed content for example
  • Whitenoise is a library offering a way to serve static files for web apps so you do not rely on external services like nginx
  • We will add the pg workaround to our troubleshooting page.
  • if you do not notice any issue with the current pre-release of OMERO 5.6.0, we should probably go for 5.6.0. We certainly do not discourage it. We aim to have a release candidate first part of January. The current insight version should still be compatible with 5.6. Sorry, the versions start to be difficult to follow…

Cheers
Jmarie

Thanks Jmarie,

Two more comments regarding OMERO.figure:

  • I had to manually install numpy on the server for OMERO.figure to enable export to PDF (would maybe be good to mention this in the docs for the server installation)
  • In OMERO.figure, when trying to export to PDF, I get the error message below (I tried pip install markdown reportlab as well as apt-get install python-reportlab python-markdown, without success.
Markdown not installed. See https://pypi.python.org/pypi/Markdown
Reportlab not installed.
Traceback (most recent call last):
  File "./script", line 2326, in <module>
    run_script()
  File "./script", line 2312, in run_script
    file_annotation = export_figure(conn, script_params)
  File "./script", line 2268, in export_figure
    return fig_export.build_figure()
  File "./script", line 942, in build_figure
    self.create_figure()
  File "./script", line 1789, in create_figure
    "Need to install https://bitbucket.org/rptlab/reportlab")
ImportError: Need to install https://bitbucket.org/rptlab/reportlab`

Best wishes,
Bene

Regarding OMERO.insight:
I downloaded the newest version from https://www.openmicroscopy.org/omero/downloads/ (on the website it says 5.5.6). When starting it, it also shows ‘5.5.6’ in the login window (below the buttons). When I enter username & password and click on ‘Login’, it says:

Failed to log onto OMERO.
OMERO.insight version 5.5.4 is not compatible with the server
version.
Please download the latest 5.6 OMERO.insight.

Best wishes

Hi Bene,
Thanks for the feedback.
Did you install reportlab (and markdown) on the server (same place as you installed numpy)?

Will

Clarification
Actually python3-wheel was installed in the container, the line was missed when copied into our doc

Thanks again

Jmarie

For insight we need to review the version check, technically it should work
Cheers

Jmarie

numpy is a dependency of ``omero-py`
so it should be installed.

Hi Will,
no, I installed it for OMERO.web.
Just tried to install it on the server and it works nicely.

Thanks for the hint

I tested OMERO.java from https://downloads.openmicroscopy.org/omero/5.6.0-m4/artifacts/OMERO.java-5.6.0-m4-ice36-b128.zip and I get a version mismatch error:

Caused by: omero.gateway.exception.DSOutOfServiceException: Client version 5.5.3 is not compatible with server version 5.6.0

Best wishes

Hi Bene,
thanks for the extensive testing! You’re right, the current Insight version still does the strict version checking and refuses to connect to a 5.6 server. It as actually already fixed, but we have to release a new version of Insight.
The error message is indeed quite confusing. The reason for this is that since we split up the repositories, the different components can have different versions. So current Insight 5.5.6 uses the omero-gateway-java 5.5.4, where the version check actually takes place. I’ll fix the error message which is presented in these cases.
Cheers,
Dominik

Hi Dominik,
ok, that makes sense. The same is probably true for OMERO.java? Or is OMERO.insight using OMERO.java?
Cheers

Yes, OMERO.java is basically the same as OMERO.insight but without the UI bits. Both use the java gateway version 5.5.4 at the moment which is the issue.

Hi @bene.schmid,

An OMERO.insight 5.5 build which can connect to a 5.6.0-X server is now available at https://github.com/ome/omero-insight/releases/latest if you’d like to try that out. (The Windows build is still in-progress).

~Josh

Update: URL modified to point to /latest rather than a specific version since new releases are being pushed out.

Thanks,

I tested OMERO.insight-5.5.8.zip and it works, I can open it, log in to the 5.6.0-m4 server, browse the data and import new images.
Do you think the Windows build will be available soon? I don’t want to be pushy, I’ve just still not decided whether to ship our new server with the current 5.5.1 release or use the new 5.6 version right from the beginning. We will do the transition from January 7th to 10th, and I am happy to stay with 5.5.1 for now if you say it needs more time for a new insight release.

Thanks and best wishes

Hi Bene,
sorry, took a bit longer. I just attached the Windows builds to the Github release page.
Regards,
Dominik

Hi Dominik,

thanks a lot, I didn’t expect it so fast. Very cool

See Release of OMERO 5.6.0 with Python 3 for the official release.