[ome-users] Making Omero work with Ice
Paulo Almeida
palmeida at igc.gulbenkian.pt
Fri Mar 27 14:13:50 GMT 2009
Hi Josh,
It's working now! The problem was indeed the password in omero.properties
being set to a different thing when I cleaned and rebuilt. I had changed it
after building, but I didn't know it was pointless. Now the server starts and
I can create sessions in python, so I think everything is good.
Thanks a lot Josh and Chris,
Paulo
On Friday 27 March 2009 11:54:33 josh.moore at gmx.de wrote:
> Paulo Almeida writes:
> > Hi Chris,
> >
> > Thanks, that was the problem. I forgot I had to rebuild after 'svn up'.
> >
> > That log was from an omero3.2 server I set up just for tests, but
> > it's not important now that I built omero4. Now bin/omero db script
> > worked and I created the database with
> >
> > psql omero4 -U omero -h localhost < OMERO4__0.sql
> >
> > but when I run
> >
> > bin/omero admin start
> >
> > it still fails. I am attaching the logs, but this bit doesn't seem
> > good:
> >
> > Caused by: org.postgresql.util.PSQLException: FATAL: password
> > authentication failed for user "omero"
> >
> > Is it getting the database user and password from
> > etc/omero.properties? I think that is correctly set, and
>
> etc/omero.properties is compiled into the jar and so changes you made
> after building will not take effect. Try:
>
> $ bin/omero config set omero.db.name omero4
>
> > psql -U omero -h localhost omero4
> >
> > works, with password omero, which is what I put in
> > etc/local.properties and etc/omero.properties .
> >
> > Thank you,
> > Paulo
>
> Best wishes,
> ~Josh.
>
> > On Thursday 26 March 2009 20:42:06 Chris Allan wrote:
> > > Hi Paulo,
> > >
> > > Something seems very wonky here. r4134 is OMERO Trunk and "db script"
> > > has been present for a while. Also, the Beta4 series does not use
> > > JBoss so is that server.log from your production installation?
> > >
> > > I'd start from "scratch" on your test OMERO checkout by running:
> > >
> > > * ./build.py clean ; ./build.py
> > > * cd dist
> > > * bin/omero db script
> > >
> > > and then see where we are.
> > >
> > > Ciao.
> > >
> > > -Chris
> > >
> > > On 26 Mar 2009, at 20:00, Paulo Almeida wrote:
> > > > Hi Josh,
> > > >
> > > > Thank you very much for the instructions. Regarding your
> > > > questions, I saw the adduser option when I ran /bin/omero admin
> > > > with no argument. That returns usage instructions that include
> > > > 'adduser' as an option. Command line addition is not important
> > > > to us, I was trying that because I thought it was the only way.
> > > >
> > > > But now I'm not sure I'm using the right version. I have been
> > > > using svn and just did 'svn up' (at revision 4134), but when I
> > > > tried:
> > > >
> > > > bin/omero db script
> > > >
> > > > I got:
> > > >
> > > > Unknown command: db script
> > > >
> > > > Running bin/omero without arguments and typing '?' gives me this
> > > > list of
> > > > commands:
> > > >
> > > > admin
> > > > config
> > > > download
> > > > help
> > > > load
> > > > node
> > > > quit
> > > > script
> > > > server
> > > > setup
> > > > submit
> > > > upload
> > > > version
> > > >
> > > > The version is "OmeroCli client, version 1.0".
> > > >
> > > > I also tried installing omero3.2 and I get the same error when
> > > > creating the
> > > > session within an omero script:
> > > >
> > > > Traceback (most recent call last):
> > > > File "<stdin>", line 1, in <module>
> > > > File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
> > > > line 334,
> > > > in createSession
> > > > prx = self.getRouter(self.__ic).createSession(username, password)
> > > > File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
> > > > line 104,
> > > > in createSession
> > > > return _M_Glacier2.Router._op_createSession.invoke(self,
> > > > ((userId, password), _ctx))
> > > > Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
> > > > Connection refused
> > > >
> > > > I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/
> > > > server.log in
> > > > case it may help understand that error.
> > > >
> > > > Thanks again,
> > > > Paulo
> > > >
> > > > On Thursday 26 March 2009 18:07:44 you wrote:
> > > >> Paulo Almeida writes:
> > > >>> Hello,
> > > >>
> > > >> Hi Paulo.
> > > >>
> > > >>> Unfortunately I got stuck again... After running 'bin/omero admin
> > > >>> start'
> > > >>> and 'bin/omero admin deploy', when I run 'bin/omero admin status'
> > > >>> I get:
> > > >>>
> > > >>> palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin
> > > >>> status node is up
> > > >>> Server not reachable
> > > >>
> > > >> Hmmmm.....ok. That could be various things. Could you send us the
> > > >> var/log/* files?
> > > >>
> > > >>> Running 'bin/omero admin adduser' displays the usage help message
> > > >>> for
> > > >>> the omero command and trying the script in
> > > >>
> > > >> adduser got taken out of this release for lack of testing. Can you
> > > >> point me to where you found it listed in the documentation so I can
> > > >> quietly delete it? :)
> > > >>
> > > >>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
> > > >>>
> > > >>> returns an error after 'sf = c.createSession()'
> > > >>>
> > > >>>>>> sf = c.createSession()
> > > >>>
> > > >>> Traceback (most recent call last):
> > > >>> File "<stdin>", line 1, in <module>
> > > >>> File
> > > >>> "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py", line
> > > >>> 334, in createSession
> > > >>> prx = self.getRouter(self.__ic).createSession(username,
> > > >>> password) File
> > > >>> "/var/lib/python-support/python2.5/Glacier2_Router_ice.py", line
> > > >>> 104, in createSession
> > > >>> return _M_Glacier2.Router._op_createSession.invoke(self,
> > > >>> ((userId,
> > > >>> password), _ctx))
> > > >>> Glacier2.PermissionDeniedException:
> > > >>> exception ::Glacier2::PermissionDeniedException
> > > >>> {
> > > >>> reason = internal server error
> > > >>> }
> > > >>
> > > >> This is most likely that your database is not properly configured.
> > > >> But
> > > >> the logs would tell us.
> > > >>
> > > >>> But I guess that is expected if the server is unreachable and I
> > > >>> can't
> > > >>> add users. Do you have any idea why this would happen? I checked
> > > >>> that
> > > >>> postgre is running and the database omero4 exists and is owned by
> > > >>> omero,
> > > >>> but it is empty:
> > > >>>
> > > >>> omero4=> \d
> > > >>> No relations found.
> > > >>
> > > >> Aha. Cancel the logs, that would be the problem.
> > > >>
> > > >>> Shouldn't the deploy command create the tables?
> > > >>
> > > >> No. The deploy command -- which is no longer necessary by the way
> > > >> -- deploys the definition of your grid, i.e. etc/grid/default.xml.
> > > >> It defines which processes will be started and what properties they
> > > >> receive. It doesn't do anything with the database, since that
> > > >> persists
> > > >> longer than a single server start. (When I say deploy is no longer
> > > >> necessary, I mean that a deploy happens automatically every time
> > > >> you call "bin/omero admin start" so only if you want to change the
> > > >> configuration of a running grid do you need "deploy".)
> > > >>
> > > >> Now, we're hard at work on the release documentation and they're
> > > >> *almost*
> > > >> done, but for now you'll need to look at the RC1 email I sent:
> > > >>
> > > >>
> > > >> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/0
> > > >>01184 .ht ml
> > > >>
> > > >> for how to create your database. In summary, your next steps are:
> > > >>
> > > >> bin/omero db script
> > > >>
> > > >> which creates OMERO4__0.sql. If you haven't added the PLPGSQL
> > > >> language
> > > >> to your database, then you'll need to:
> > > >>
> > > >> createlang plpgsql omero4
> > > >>
> > > >> and finally:
> > > >>
> > > >> psql omero4 < OMERO4__0.sql
> > > >> bin/omero admin stop
> > > >> bin/omero admin start
> > > >>
> > > >> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin
> > > >> to
> > > >> add new users. If the command-line addition is of interest, we'll
> > > >> certainly have that re-scheduled for an upcoming release.
> > > >>
> > > >>> Thanks,
> > > >>> Paulo
> > > >>
> > > >> No problem and cheers,
> > > >> ~Josh
> > > >>
> > > >>> On Wednesday 25 March 2009 19:23:11 you wrote:
> > > >>>> Paulo Almeida writes:
> > > >>>>> Hi again...
> > > >>>>>
> > > >>>>> Ignore my last e-mail, it really was a simple permissions
> > > >>>>> problem. I didn't think it was because I tried running as root,
> > > >>>>> but the directory was mounted in NFS so root didn't have access
> > > >>>>> either. It seems to be running fine now.
> > > >>>>
> > > >>>> Whew. Good to hear! :) Thanks for letting us know, Paulo.
> > > >>>>
> > > >>>> ~J.
> > > >>>>
> > > >>>>> Best,
> > > >>>>> Paulo
> > > >>>>>
> > > >>>>> On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
> > > >>>>>> Hi,
> > > >>>>>>
> > > >>>>>> I had an OmeroGrid installation that was working, but I had to
> > > >>>>>> reinstall the OS and now I am getting an error. When I run:
> > > >>>>>>
> > > >>>>>> bin/omero admin start
> > > >>>>>>
> > > >>>>>> there is not output, but then I run:
> > > >>>>>>
> > > >>>>>> bin/omero admin deploy etc/grid/default.xml
> > > >>>>>>
> > > >>>>>> and I get this:
> > > >>>>>>
> > > >>>>>> error: IceGrid::DeploymentException:
> > > >>>>>> couldn't load `Blitz-0' on node `master':
> > > >>>>>> can't set permissions on directory
> > > >>>>>> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
> > > >>>>>>
> > > >>>>>> -----------
> > > >>>>>>
> > > >>>>>> When I reinstalled the OS I had to install Ice, PostgreSQL,
> > > >>>>>> etc, but I didn't touch the Omero folder. Do you have any idea
> > > >>>>>> about what I may have forgotten that would cause this error? I
> > > >>>>>> also tried compiling Omero.blitz, but I get this error when
> > > >>>>>> running 'bin/omero admin start':
> > > >>>>>>
> > > >>>>>> icegridnode: failure occurred in daemon:
> > > >>>>>> service caught unhandled Ice exception:
> > > >>>>>> ../../include/Ice/BasicStream.h:412:
> > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of
> > > >>>>>> bounds during unmarshaling
> > > >>>>>> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
> > > >>>>>> ../../include/Ice/BasicStream.h:412:
> > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of
> > > >>>>>> bounds during unmarshaling
> > > >
> > > > <server.log>_______________________________________________
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> > > > ome-users at lists.openmicroscopy.org.uk
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