[ome-users] Making Omero work with Ice
Paulo Almeida
palmeida at igc.gulbenkian.pt
Thu Mar 26 20:00:33 GMT 2009
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/001184.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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: server.log
Type: text/x-log
Size: 525011 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20090326/c9f211f9/attachment.bin>
More information about the ome-users
mailing list