Question about postgres database during upgrade from 5.4.9 to 5.5.1

Hello OME team,

I am in the process of upgrading OMERO.server from 5.4.9 to 5.5.1 and am stuck on the database upgrade part. I am following instructions at https://docs.openmicroscopy.org/omero/5.5.1/sysadmins/server-upgrade.html. First, the section looks a little fishy to me

It says

Warning: This section only concerns users upgrading from a 5.4 or earlier server. If upgrading from a 5.5 server, you do not need to upgrade the database.

So it seems that I should be doing this.

Then in the instructions, I see:

$ cd OMERO.server
$ psql -h localhost -U db_user omero_database < sql/psql/OMERO5.4__0/OMERO5.3__1.sql

And that sure doesn’t look right. That would seem to be a script for upgrading from 5.3 to 5.4. In fact, below I see the following warning:

Warning: The sql/psql/OMERO5.4__0/OMERO5.3__1.sql script referenced by the above psql command assumes upgrade from OMERO 5.3.4. If you are instead currently running OMERO 5.3.3 or an earlier 5.3.x version then you upgrade the database directly to OMERO 5.4.0 by using the above command with sql/psql/OMERO5.4__0/OMERO5.3__0.sql .

And that doesn’t look right at all. So I think, okay I will just try to find an sql/psql/OMERO5.5__0 directory and fill in the blanks, but the highest version directory I see is OMERO5.4DEV__3. So that is no good. So I tried following the instructions anyway (i.e., psql -h localhost -U db_user omero_database < sql/psql/OMERO5.4__0/OMERO5.3__1.sql), and that produces a very impressive string of error messages:

BEGIN
CREATE FUNCTION
ERROR:  wrong OMERO database version for this upgrade script
CONTEXT:  PL/pgSQL function omero_assert_db_version(character varying,integer) line 12 at RAISE
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ERROR:  current transaction is aborted, commands ignored until end of transaction block
...
ERROR:  current transaction is aborted, commands ignored until end of transaction block

So what am I doing wrong here? Or is this an issue with OMERO.server-5.5.1-ice36-b122.zip or its documentation?

That’s a documentation error. There is no upgrade of the database needed when you go from 5.4.x to 5.5.x so you can/should skip that section.

  • Damir
2 Likes

Indeed. The source for that page looks like this:

    .. warning::
        This section only concerns users upgrading from a |previousversion| or
        earlier server. If upgrading from a |version| server, you do not need
        to upgrade the database.

but starting with 5.5, the database has its own version. I’ll hardcode the page for the moment and we’ll get the docs updated.
~Josh

1 Like