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Question about fs repo and users.

PostPosted: Tue Apr 23, 2019 9:37 am
by rikardjo


We have a Omero-installation in production, it's fs repo is the default one:
%user%_%userId%//%year%-%month%/%day%/%time% )

We would like to keep track on folder sizes per group, so in a test environment I've change repo:

According to the documentation I've read, you need to move the files yourself when altering the fs repo.

So my question is, would it be enough to just move the folder of %user% to corresponding group on disk after altering the fs path, or would it break anything?


In our environment, guest scientist will access from time to time. Once their account isn't needed anymore, is it possible to remove those account (and not just mark them inactive).

Thanks in advance ~ Rikard

Re: Question about fs repo and users.

PostPosted: Tue Apr 23, 2019 11:04 am
by mtbc
Dear Rikard,

Things would break if you simply moved the files. The columns "path" and "name" in both the "originalfile" and "pixels" tables of the database record the file locations: those too would need to be somehow kept up to date. We had been working on an OMERO.cli utility to update existing images based on a new template path prefix but that does not yet work well enough for production use.

Also note that your new template path setting takes effect only at import time. If images are subsequently moved among groups then they do not automatically move on disk. Further, attachments on users' images are stored in the Files/ directory rather than the directory configured in omero.managed.dir.

With OMERO.cli,
Code: Select all
bin/omero fs usage ExperimenterGroup:123

provides an accurate and up-to-date report for the data usage of group ID 123 but its query takes some time and can be overly demanding for the server so if there is a lot of data in the group then the command is best avoided, though it will become a little safer to run that query with OMERO 5.5.

In short, files can be relocated but I am afraid that with OMERO 5.4 it is not for the faint-hearted. I would definitely recommend experimenting on a test system first and taking a backup before attempting anything in production. We can help you to make sense of what about the managed repository is stored in the database if you do still want to make the attempt.

If you do not relocate existing imports then it is still fine to change the configuration setting for the template path prefix: existing imports will remain readable from their old location and new imports will go into the new directories.

I am afraid that there is no provision for deleting user accounts. It is non-trivial for similar database reasons: so much is tied to the related user, such as the "eventlog" table, so it is the kind of work that probably awaits being agreed as high-enough priority by a funder. If it is of any help, the OMERO.cli "chown" command allows giving all a user's data to another so you can at least be sure that these dormant users have no data left on their account.