[ome-users] Omero 4.4.9 to 5.0.0 RC1 upgrade - Error connecting to database table dbpatch

[Paulo Almeida]

Hello,

I finally figured it out... The variable name is omero.db.pass and in
5.0.0 I wrote omero.db.password. I corrected it and the server started.

Sorry for the waste of time, and thanks for pointing me in the right
direction.

Cheers,
Paulo

On Thu, 2014-01-09 at 17:14 +0000, Paulo Almeida wrote:
> Hi Ola,
> 
> Apparently you're right, because now I also saw lines like this in the
> log:
> 
> Caused by: org.postgresql.util.PSQLException: FATAL: password
> authentication failed for user "omero"
> 
> I'm a bit puzzled by that, because it was working before the upgrade.
> Initially I had thought it might be something with the settings, because
> when I first ran omero, after the upgrade, it complained about a missing
> "/OMERO" folder. But I set that up, along with DB name, user and
> password, so the output of "omero config get" is this:
> 
> omero.data.dir=/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/OMERO/binary-repository
> omero.db.name=omero
> omero.db.password=secret
> omero.db.user=omero
> 
> "secret" is the password that I successfully use to check the database
> using:
> 
> psql -h localhost -U omero
> 
> And this is the beginning of \l inside psql:
> 
>    Name    |  Owner   | Encoding |   Collate   |    Ctype    |   Access
> privileges   
> -----------+----------+----------+-------------+-------------+-----------------------
>  omero     | omero    | UTF8     | en_US.UTF-8 | en_US.UTF-8 | 
> 
> 
> Is there anything else I can do to check what credentials omero is
> using, if not those in etc/grid/config.xml? I even tried setting the
> password in etc/omero.properties, with no success (I guess I'm not
> supposed to do that anyway).
> 
> Thanks,
> Paulo
> 
> 
> On Thu, 2014-01-09 at 16:04 +0000, Aleksandra Tarkowska wrote:
> > Dear Paulo
> > 
> > 2014-01-09 13:55:05,796 ERROR [ome.services.db.SelfCorrectingDataSource] (
> >      main) Failed to acquire connection after retries=3
> > java.sql.SQLException: unable to get a connection from pool of a
> > PoolingDataSource containing an XAPool of resource
> > 99566f22-65bf-46b2-803e-835dad8ad75f with 0 connection(s) (0 still
> > available)
> > 
> > Sounds like wrong db username and/or password.
> > 
> > 
> > Could you check your omero properties?
> > Is your sql server running?
> > 
> > 
> > Kind regards
> > Ola
> > 
> > 
> > 
> > 
> > 
> > On 09/01/2014 15:58, "Paulo Almeida" <palmeida at igc.gulbenkian.pt> wrote:
> > 
> > >Hi,
> > >
> > >I just upgraded to Omero 5.0.0 and apparently it went well, but the
> > >server failed to restart, with exceptions in Blitz-0.log and the
> > >following message:
> > >
> > >Error connecting to database table dbpatch. You may need to bootstrap.
> > >
> > >I did run the database script and the dbpatch table exists, with this as
> > >the second and last entry (result of "SELECT * from db_patch"):
> > >
> > >  2 |            0 | OMERO5.0       |         -52 | 2014-01-09
> > >13:51:28.813421 | Database updated. |             0 | OMERO4.4        |
> > >
> > >I was using Java 6, but I saw an old Omero bug report mentioning a
> > >similar message with this version of Java, so I tried upgrading to 7.
> > >Nothing changed though. This is the bug report:
> > >
> > >http://trac.openmicroscopy.org.uk/ome/ticket/1269
> > >
> > >It's very old and the only thing in common is the message about not
> > >being able to connect to dbpatch, so I don't know if it's relevant.
> > >
> > >I'm attaching the output of bin/omero admin diagnostics, as well as
> > >Blitz-0.log and master.err , in case it helps diagnosing.
> > >
> > >Thanks,
> > >Paulo Almeida
> > >Instituto Gulbenkian de Ciência
> > >_______________________________________________
> > >ome-users mailing list
> > >ome-users at lists.openmicroscopy.org.uk
> > >http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> > 
> > 
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> 
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