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Migrating OMERO from Windows Server 2012 to CentOS 7

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Migrating OMERO from Windows Server 2012 to CentOS 7

Postby labriedion » Fri Apr 22, 2016 3:44 pm

Hi all,

Following the sad news that Windows support would be dropped starting from 5.3, I decided to switch my OMERO installation from Windows Server 2012 R2 to CentOS 7. I decided to do it ASAP since I had yet to do the official roll out of OMERO in my facility.

I didn't have access to an extra computer for the migration and I did it all on the same machine. I don't recommend that. I partitioned my OS drive and the data drive for the linux instance. Then I installed CentOS 7. You will need to update the grub file otherwise you won't be able to boot back into windows (http://unix.stackexchange.com/questions ... -boot-menu). Then, I made a copy of the repository into the new data drive in Linux and followed the online intructions to install OMERO in CentOS 7.

Issues related to the migration I encountered:

- Restoring the Postgres database from the pg_dump, I was getting the error "invalid byte sequence for encoding "UTF8": 0xff": I think this is because I switched from a french localized Windows installation to an english CentOS installation. The fix was to force the export of my database in UTF-8 (pg_dump --encoding utf8). Also make sure the postgres versions are the same (I migrated from 9.5.1 to 9.5.2 and it worked but I think it's best to use the exact same).

- Images could not be opened with the Insight Image Viewer although they could still be downloaded. New uploaded images were fine. Fix: I had to go in the postgres database and switch the backslashes to forward slashes in the path column of the tables pixels and originalfile [example: UPDATE path SET pixels = regexp_replace(path,"\\","/","g");]. As a precaution, I replaced the double escaped backslashes first using "\\\\", then I replaced the single backslashes. I'm not sure this is necessary.

I'm still trying to get the web instance to work but that is unrelated to the migration.

Let me know if you have any questions related to the migration. I have very little experience with Linux in general but my experience could be helpful.

Good luck,
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Joined: Wed Jan 06, 2016 9:26 pm

Re: Migrating OMERO from Windows Server 2012 to CentOS 7

Postby mtbc » Mon Apr 25, 2016 8:59 am

Dear Étienne,

Your detailed report is really helpful, thank you. Congratulations on navigating a tricky process. I've noted that we should come back and look at your findings when we work on documenting the migration process for others. It's great that you are already thinking ahead.


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