Open Microscopy Environment

Hello everyone. I am relatively new to OMERO and have some questions about its use. I currently have an OMERO virtual appliance deployed within a virtual box machine. If i needed to access data files, or if I wanted to move a database would that be possible? For instance, if I wanted to move a database or a series of data files from the OMERO virtual appliance to somewhere else would that be possible? Is it even possible to access the database itself?

Thanks so much.

Hello.

If I wanted to move the database and data files to a new server, I'd follow the "OMERO.server backup and restore" documentation at https://www.openmicroscopy.org/site/sup ... store.html

In short, the process would be:

On the source:
* stop the OMERO server
* use pg_dump to take a 'dump' of the database
* rsync the binary data store to the destination server
* rsync the config file to the destination server

On the destination:
* use pg_restore to restore from the database dump
* 'install' OMERO in the usual fashion (same version as you previously had, you can upgrade later)
* restore your old OMERO config
* configure your new OMERO instance to use the binary data store from the previous server (if path is different)
* configure your new OMERO instance to use the database you've restored (again, if db name or db server is different)
* confirm all your Memory allocation, postgres connection pool size etc is as you'd like it

This is a process we do regularly and should be all you need. I may have misunderstood your question though.

Hope that's of some use?

Kenny

Thank you so much! I will try it out.

shaneklumpp wrote:Thank you so much! I will try it out.

You're welcome.

shaneklumpp wrote:a database or a series of data files

It's worth noting, that's an "all or nothing" approach - i.e. migrating your virtual appliance OMERO to a different server.

If you're after access to just individual files, other options should be explored.

Best of luck, and please be in touch if we can help.

Best,

Kenny

If I am trying to access individual files, is there a way to do that as well?

Hi,

shaneklumpp wrote:If I am trying to access individual files, is there a way to do that as well?

So I'd suggest a new forum thread - rather than this one titled "Moving datafiles/database if possible".

Perhaps someone may pick this one up, but one way or the other you'd be likely better off describing more about what you want to achieve or end up with. It's certainly possible to provide access to files in the OMERO binary repository, there are many different ways to achieve this, so a good description of what you would like to end up with would help the community steer you in the right direction.

All the best,

Kenny