[ome-users] OMERO b2.2 problems

Tue Nov 13 15:50:51 GMT 2007

Hi Mike-

Thanks for all this.  Very helpful.

We will address these.

Cheers,

Jason

On 13 Nov 2007, at 15:37, McCaughey, Michael J wrote:

> Sorry for the ridiculous inability to do inline quoting on this (I  
> *hate* MS LookOut).
>
> I have figured out the problem with the client access to the server  
> upgraded from b2 to b2.2.  The server did not have a DNS entry, so  
> when accessing the b2 server with b2.1 clients, I used the server  
> IP address.  That worked fine for the pre-b2.2 server and clients,  
> but does not work with the b2.2 server/clients. Getting a proper  
> DNS entry for the server cured the access problem.  Note that my / 
> etc/hosts file has not been changed, and has always mapped the  
> server name to it's IP. Just FYI for anyone else using non- 
> resolvable addresses.
>
> As for the laptop, I used a stock pre-built binary install. Killing  
> and restarting yields this:
> 09:19:06,051 INFO  [HbmBinder] Mapping collection:  
> ome.model.containers.Dataset.annotations -> datasetannotation
> 09:19:06,203 INFO  [ConnectionProviderFactory] Initializing  
> connection provider:  
> org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider
> 09:19:06,247 WARN  [JBossManagedConnectionPool] Throwable while  
> attempting to get a new connection: null
> org.jboss.resource.JBossResourceException: Could not create  
> connection; - nested throwable: (org.postgresql.util.PSQLException:  
> FATAL: database "omero3" does not exist)
>        at  
> org.jboss.resource.adapter.jdbc.local.LocalManagedConnectionFactory.cr 
> eateManagedConnection(LocalManagedConnectionFactory.java:179)
>        at  
> org.jboss.resource.connectionmanager.InternalManagedConnectionPool.cre 
> ateConnectionEventListener(InternalManagedConnectionPool.java:57
>
>
> The omero3 db is gone?  Yep:
> postgres$ psql -l
>        List of databases
>   Name    |  Owner   | Encoding -----------+----------+-----------
> postgres  | postgres | SQL_ASCII
> template0 | postgres | SQL_ASCII
> template1 | postgres | SQL_ASCII
> (3 rows)
>
> Yep, gone.  Weird. And I'd created users, uploaded images, etc.
>
> I don't think I'm going to reinstall given the frequency of sleep  
> events.  It's not worth doing a laptop edition; it's just handy for  
> demos where network connectivity is not available.  If I can help  
> with debugging, let me know.
>
> Mike
>
> Michael J. McCaughey, PhD
> Molecular Physiology and Biophysics
> U9203 MRBIII
> 6-6175
>
>
>
> -----Original Message-----
> From: ome-users-bounces at lists.openmicroscopy.org.uk on behalf of  
> Jason Swedlow
> Sent: Mon 11/12/2007 4:36 PM
> To: McCaughey, Michael J
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] OMERO b2.2 problems
>
> Hi Mike-
>
> Thanks for this.
>
> On 12 Nov 2007, at 22:12, McCaughey, Michael J wrote:
>
> > I've run into a couple of problems with the beta 2.2 release that I
> > could use some help with...
> >
> > First, I upgraded a 2 server to 2.2. The upgrade went smoothly, and
> > process matched those on the upgrade wiki page.  I deleted the
> > existing 2.1 clients and installed 2.2 versions.  The WebAdmin tool
> > works as expected, the old users are there and new ones can be
> > added, but now clients cannot connect to the server. I've deleted
> > and reinstalled, etc., no luck.
> > The server hosts file is correct (I had to fix it for the 2.1
> > clients).  Brian is looking into this, but I thought I'd put it out
> > there and see if anyone else had a suggestion.
> >
> That sounds strange- I'll let the systems guys take that. To confirm,
> webadmin connects and works (so server is up) but insight and
> importer do not connect?
> > Second, I installed 2.2 on a MacBook Pro (core duo), and installed
> > the 2.2 clients on the same machine.  This worked great, I used it
> > for several hours setting up test users and the updated importer
> > (thanks Brian & Mellisa for fixing the LSM large-file problem). No
> > problems.  I then let the machine hibernate a few minutes while I
> > walked to a conference room to demo it for a group of interested
> > parties. When I tried the clients (which I had left running), they
> > bombed.  WebAdmin did too. I rebooted, and now the clients won't
> > connect.  WebAdmin doesn't recognize any logins as valid, including
> > root.  Oops.  Good thing the rest of my talk was long.
> > So, does suspend/power save kill the server (the jboss process is
> > still running, tho). Could it corrupt the db?
> >
>
> The phenotype you describe is expected-- JBOSS does not like sleep.
> It doesn't like network changes (e.g., disconnecting network
> connection).  But no worries, the DB should be just fine.  I've made
> a similar mistake with my own machine-- and yes, things are then no
> good at all.  We've built OMERO assuming your server will stay up.
> Try to kill the JBOSS process, and then restart it.  I've done this
> previously, and never had a problem.
>
> You obviously want to run the whole system on your laptop.  We have
> talked about building a specific version for this, but haven't done
> it yet.  From a developer's point of view, your approach should "just
> work".  Let us know if this is a strong requirement and we will look
> into it.  We just didn't feel like competing with Aperture  ;-)!
>
> Hope that helps.
>
> Cheers,
>
> Jason
>
> **************************
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> phone (01382) 385819
> Intl phone:  44 1382 385819
> FAX   (01382) 388072
> email: jason at lifesci.dundee.ac.uk
>
> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>
>
>
>
>

**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

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