Open Microscopy Environment

Hi,

This question has probably been asked before but I feel that the results I got from searching over might be missing about our particular case... We have a very old OMERO app (5.1.2) running on a similarly old Debian install (Wheezy). I want to move it to latest Ubuntu LTS with OMERO 5.4.9 so my question: what is the best way of doing this? I am afraid of having to move forward piecemeal on this...

Thanks in advance

S. Foisy
Project manager
Bioinformatics
Inflammgen Lab
Montreal Heart Institute

Hi Sylvain,

In theory, this should work fine. The process would be to perform each of the upgrade steps:

• 5.1 to 5.2: https://docs.openmicroscopy.org/omero/5 ... grade.html
• 5.2 to 5.3: https://docs.openmicroscopy.org/omero/5 ... grade.html
• and 5.3 to 5.4: https://docs.openmicroscopy.org/omero/5 ... grade.html

I'd suggest reading each of those pages just to make sure there are no particular warnings that apply to your situation (It's been a while since we've done this, too!)

The most critical parts of the process are:

• Take a backup of your database (or perhaps even better, work on a copy)
• Apply each of the upgrade scripts in term:
  
  • sql/psql/OMERO5.2__0/OMERO5.1__1.sql
  • sql/psql/OMERO5.3__0/OMERO5.2__0.sql
  • sql/psql/OMERO5.4__0/OMERO5.3__1.sql

It's probably in your best interest to start the server after each of those steps to know whether or not things are working before you move on.

And if course, if you run into any issues, let us know.

Good luck!
~Josh

Hi,

Thanks for the inputs, pretty much what I was expecting/planning Another possibility that I am playing with is to move to a VM with latest version and migrating the data from the old version toward the new server. Would it be just a simple as backing up DB and data and re-uploading everything on the new virtualized server?

Best regards

S

Would it be just a simple as backing up DB and data and re-uploading everything on the new virtualized server?

We think skipping the intermediate server startups up will work, but obviously, there's a lot of history here (3.5 years to the day ) You may run into issues during some of the SQL upgrades, but the necessary corrective steps will be outlined on the related upgrade page.

Regardless, we're interested to hear how it goes.

All the best,
~Josh

Hi,

It has been a while...

Ok, I succeeded in upgrading from Debian 7 to 8 not without some difficulties: I discovered that the sysadmin created way too small partitions for /var and /usr so I had to be creative... I d/l the 5.2.8 app, did an upgrade on the Postgresql database and reloaded the config file. When I restart the server, it tells me that it starts OK. On the web front, I recreated the server file for nginx, setup the nginx server (I think, I am more an Apache user), set omero.web.application_server to wsgi-tcp and restarted the web server but I get stuck at the Maintenance page...

How do I go troubleshooting this?

Best regards

S

Hi

Since the webclient isn't necessary for running OMERO I think it's best to continue upgrading OMERO.server to the latest release (5.4.9) before fixing OMERO.web.

The only version of Debian that's currently tested by us is Debian 9, are you able to upgrade to that? If you need to stick with Debian 8 we'll try and help with any problems but you'll have to do some investigation and problem solving yourself.

Note that some of the installation instructions have changed significantly since 5.1, especially for OMERO.web, so I'd recommended checking the latest docs https://docs.openmicroscopy.org/omero/5 ... index.html

The walkthroughs for Ubuntu should be helpful.

Hi,

Not touching OMERO.web was also on my list I can confirm that Omero.Insight 5.2 sees the new server a-ok, so my migration path works. I will move on to 5.4.9 ASAP.

I don't intend to stay with Debian 8 and I am planning to move toward Debian 9; I started with Debian 7 to 8 because looking at dependencies, I saw that the migration would need specific versions of libraries in a given version. Using Debian was not my choice, I am more of an Ubuntu guy but the very junior sysadmin that build our server used Debian instructions at the time and just could not figure out how to migrate...

I'll let you know how it is working.

Best regards

S

Dear Sylvain,

While not officially supported by OME there are plenty of sites that run OMERO on Debian. Watch out for the last couple of items on https://docs.openmicroscopy.org/omero/5 ... oting.html but neither is a showstopper.

Cheers,
Mark

Hi,

Ok, migration to Debian 9 successful I installed latest ZeroC 3.6 from repo and modified my environment accordingly for ICE_HOME but I get this after trying to start the server :

Code: Select all

Traceback (most recent call last):
  File "./omero", line 97, in <module>
    import omero.cli
  File "/home/OMS/apps/OMERO/OMERO.server-5.3.5-ice36-b73/lib/python/omero/__init__.py", line 43, in <module>
    raise Exception(msg)
Exception:

        ERROR: Ice version mismatch!

        Your OMERO code has been compiled using Ice version 3.6.3
        but you seem to have Ice version 3.5.1 installed. If you need
        help understanding this issue, please send this error message
        to the OME community:

        http://www.openmicroscopy.org/site/community

        Debugging Info:
        --------------
        VERSION=5.3.5-ice36-b73
        PYTHONPATH=/home/OMS/apps/OMERO/OMERO.server-5.3.5-ice36-b73/lib/python:/home/OMS/apps/OMERO/OMERO.server-5.3.5-ice36-b73/var/lib:/home/OMS/apps/OMERO/OMERO.server-5.3.5-ice36-b73/bin:/usr/lib/pymodules/python2.7:/home/OMS/apps/OMERO/OMERO.server-5.3.5-ice36-b73/bin:/usr/lib/python2.7:/usr/lib/python2.7/plat-x86_64-linux-gnu:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload:/usr/local/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/PILcompat:/usr/lib/python2.7/dist-packages/gtk-2.0:/home/OMS/apps/OMERO/OMERO.server-5.3.5-ice36-b73/lib/fallback

A leftover from previous Debian 8? Surely a simple thing that I am overlooking

Best regards

S

Hi,

Ok, I can answer that myself: the migration to Debian 9 did not updated the python-zeroc-ice package. I erased it and used the instructions for regular installation to reinstall using pip and the server starts now w/o errors. However... I can't logged on the server using the 5.3.5 client: I get a message Error: System failure.

My 5.1 to 5.2 migration worked but both were still using ICE 3.5; am I missing something in the new ICE 3.6?

How do I go troubleshooting this?

Best regards

S