[ome-users] [OMERO.server] #1108: DB Upgrade fails on Postgres 8.1

[josh.moore at gmx.de]

Hi Paulo,

Good to hear that the upgrade worked. The server is not getting stuck
but has different logging settings, a change that we should have made
more apparent. The console will now only show warnings and similar
error messages, since often this is somewhere in the background or
even piped to /dev/null.

The primary log is available under:

  jboss-4.2.3.GA/server/default/log/server.log

and is significantly cleaned up so that you shouldn't have untold
gigabytes flying around in there after a few hours of hard OMERO
work. But since WebAdmin and the clients are functioning, I'm assuming
that your server is otherwise healthy.

I'm unsure what the LDAP issue may be and so will leave that up to the
guys and gals in Dundee. You might zip and email the logs under
server/default/log to help us track down the problem, or alternatively
open up a ticket if you'd rather not email them.

Best wishes,
~Josh.


Paulo Almeida writes:
 > Hi,
 > 
 > Now the DB upgrade works, but when I run the server the output gets stuck on 
 > this part:
 > 
 > 11:29:35,853 INFO  [WebService] Using RMI server codebase: 
 > http://omero.igc.gulbenkian.pt:8083/
 > 11:29:35,856 INFO  [Log4jService$URLWatchTimerTask] Configuring from URL: 
 > resource:jboss-log4j.xml
 > 2008-10-15 11:30:05,760 ERROR [                                  STDERR] (      
 > main) Oct 15, 2008 11:30:05 AM java.util.prefs.FileSystemPreferences$7 run
 > WARNING: Prefs file removed in 
 > background /home/palmeida/.java/.userPrefs/prefs.xml
 > 2008-10-15 11:30:05,762 ERROR [                                  STDERR] (      
 > main) Oct 15, 2008 11:30:05 AM java.util.prefs.FileSystemPreferences$7 run
 > WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
 > 
 > ----------
 > 
 > Nothing else shows on the console after that, but the server is running and I 
 > can connect to it with root (both the WebAdmin interface and Omero clients 
 > work), but not with my LDAP users. I tried reverting to the old database, 
 > using Beta 3.0.1, and I can login with LDAP then, so that is not the problem.
 > 
 > By the way, as my data directory is not /OMERO and I am using LDAP 
 > authentication, I had to make those changes in omero.properties when I 
 > upgraded. Unless I missed it, the upgrade instructions only mention 
 > local.properties, so maybe you could add a note telling users to edit 
 > omero.properties if necessary (or even better, if possible, rearrange the 
 > configuration files so you only need to copy local.properties, because that 
 > would make mistakes less likely).
 > 
 > Best regards,
 > -Paulo
 > 
 > 
 > On Tuesday 14 October 2008 20:24, OMERO.server wrote:
 > > #1108: DB Upgrade fails on Postgres 8.1
 > > ----------------------+----------------------------------------------------
 > >- Reporter:  jmoore   |       Owner:  jmoore
 > >       Type:  defect   |      Status:  closed
 > >   Priority:  blocker  |   Milestone:  3.0-Beta4
 > >  Component:  General  |     Version:
 > > Resolution:  fixed    |    Keywords:  postgres
 > > ----------------------+----------------------------------------------------
 > >- Changes (by jmoore):
 > >
 > >   * status:  new => closed
 > >   * resolution:  => fixed
 > >
 > >
 > > Comment:
 > >
 > >  r2934 (trunk) and r2935 (Beta3.1) have a fix for this. The file can be
 > >  downloaded directly via:
 > >
 > > 
 > > https://trac.openmicroscopy.org.uk/omero/browser/trunk/sql/psql/OMERO3A__11
 > >/OMERO3A__5.sql?format=txt
 > >
 > >  and executed as per OmeroUpgrade:
 > >
 > >  {{{
 > >  $ psql -h localhost -U omero omero3 < OMERO3A__5.sql
 > >  }}}
 > >
 > >  from wherever you downloaded it to.