[ome-users] Making Omero work with Ice

Chris Allan callan at blackcat.ca
Thu Mar 26 20:42:06 GMT 2009 

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/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
>
>
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