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

[josh.moore at gmx.de]

Forwarding this to the list.
Thanks for the feedback, Paulo.

~Josh.

Paulo Almeida writes:
 > Hi Josh,
 > 
 > Thanks for the information. It's certainly good to have less output from the 
 > server.
 > 
 > I am happy to say LDAP is functional again. I'm not sure what I did, but after 
 > you said the console output was normal I poked around a bit and got it to 
 > work. Maybe I had forgotten a "java omero deploy" after altering 
 > omero.properties.
 > 
 > Thanks,
 > Paulo
 > 
 > 
 > On Wednesday 15 October 2008 13:25, you wrote:
 > > 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/OMERO3
 > >  > >A__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.