[ome-devel] Python SessionTimeoutException

Mon Mar 7 11:05:22 GMT 2016

Hi Niko,

On Fri, Mar 4, 2016 at 3:57 PM, Niko Ehrenfeuchter
<nikolaus.ehrenfeuchter at unibas.ch> wrote:
> Probably I should mention that I've read the forum post from 2010 about
> "Connection and Session timeouts" [1], but unfortunately this did not make
> me any smarter :-/
>
> ~Niko
>
> [1] https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=320
>
>
> On 04.03.2016 15:54, Niko Ehrenfeuchter wrote:
>>
>> we're constantly experiencing session timeouts in one of our Python
>> scripts (see the traceback below).

Just to be clear, here you mean a manually run script, not something you
intend to have OMERO run in the background, right?

>> I was very surprised to see the TTL
>> is reported as 60000 ms in the error trace, so I went and checked if
>> something is wrong with "omero.sessions.timeout". As this setting had
>> not been configured explicitly before, I did so by running
>>
>>> bin/omero config set omero.sessions.timeout 600000
>>> bin/omero admin restart

600000 (or 10 min) should be the default:
https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/config.html#omero-sessions-timeout

>> but the timeout persists. So apparently this is not about
>> "omero.sessions.timeout"...?
>>
>> Am I doing something wrong? Please note that this is on 5.1.2!

I'll see if I can find anything that's been fixed since then, though
it might also be worth upgrading (hint, hint). That being said, how
are the sessions for the script runs being created? In the script
itself? Or externally and passed via -k?

Cheers,
~Josh.

>> Cheers
>> Niko
>>
>>> Traceback (most recent call last):
>>>   File "/home/omeronas/misc/test.py", line 518, in <module>
>>>     sys.exit(main())
>>>   File "/home/omeronas/misc/test.py", line 514, in main
>>>     generate_tree(user)
>>>   File "/home/omeronas/misc/test.py", line 435, in get_orignames
>>>     for image in dset.listChildren():
>>>   File
>>> "/home/omeronas/OMERO.server/lib/python/omero/gateway/__init__.py",
>>> line 687, in listChildren
>>>     for child in self._listChildren(ns=ns, val=val, params=params):
>>>   File
>>> "/home/omeronas/OMERO.server/lib/python/omero/gateway/__init__.py",
>>> line 676, in _listChildren
>>>     ).findAllByQuery(query, params, self._conn.SERVICE_OPTS)):
>>>   File
>>> "/home/omeronas/OMERO.server/lib/python/omero/gateway/__init__.py",
>>> line 4126, in __call__
>>>     return self.handle_exception(e, *args, **kwargs)
>>>   File
>>> "/home/omeronas/OMERO.server/lib/python/omero/gateway/__init__.py",
>>> line 4123, in __call__
>>>     return self.f(*args, **kwargs)
>>>   File
>>> "/home/omeronas/OMERO.server/lib/python/omero_api_IQuery_ice.py", line
>>> 213, in findAllByQuery
>>>     return _M_omero.api.IQuery._op_findAllByQuery.invoke(self,
>>> ((query, params), _ctx))
>>> omero.SessionTimeoutException: exception ::omero::SessionTimeoutException
>>> {
>>>     serverStackTrace = ome.conditions.SessionTimeoutException: Session
>>> (started=2016-03-04 15:24:57.51, hits=1888, last access=2016-03-04
>>> 15:25:05.955) exceeded timeToLive (60000) by 653 ms
>>>         at
>>>
>>> ome.services.sessions.state.SessionCache.getDataNullOrThrowOnTimeout(SessionCache.java:465)
>>>
>>>         at
>>>
>>> ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:371)
>>>
>>>         at
>>>
>>> ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:356)
>>>
>>>         at
>>>
>>> ome.services.sessions.SessionManagerImpl.getUserRoles(SessionManagerImpl.java:652)
>>>
>>>         at
>>>
>>> ome.security.basic.BasicMethodSecurity.checkMethod(BasicMethodSecurity.java:112)
>>>
>>>         at
>>>
>>> ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:81)
>>>
>>>         at
>>>
>>> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>>
>>>         at
>>>
>>> ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
>>>
>>>         at
>>>
>>> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>>
>>>         at
>>>
>>> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>>>
>>>         at $Proxy80.findAllByQuery(Unknown Source)
>>>         at sun.reflect.GeneratedMethodAccessor675.invoke(Unknown Source)
>>>         at
>>>
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>
>>>         at java.lang.reflect.Method.invoke(Method.java:601)
>>>         at
>>>
>>> ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
>>>
>>>         at ome.services.throttling.Callback.run(Callback.java:56)
>>>         at
>>>
>>> ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
>>>
>>>         at
>>>
>>> ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
>>>
>>>         at
>>> ome.services.blitz.impl.QueryI.findAllByQuery_async(QueryI.java:66)
>>>         at sun.reflect.GeneratedMethodAccessor674.invoke(Unknown Source)
>>>         at
>>>
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>
>>>         at java.lang.reflect.Method.invoke(Method.java:601)
>>>         at
>>>
>>> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
>>>
>>>         at
>>>
>>> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>>>
>>>         at
>>>
>>> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
>>>
>>>         at omero.cmd.CallContext.invoke(CallContext.java:78)
>>>         at
>>>
>>> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>>
>>>         at
>>>
>>> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>>>
>>>         at $Proxy81.findAllByQuery_async(Unknown Source)
>>>         at omero.api._IQueryTie.findAllByQuery_async(_IQueryTie.java:90)
>>>         at omero.api._IQueryDisp.___findAllByQuery(_IQueryDisp.java:341)
>>>         at omero.api._IQueryDisp.__dispatch(_IQueryDisp.java:464)
>>>         at IceInternal.Incoming.invoke(Incoming.java:222)
>>>         at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
>>>         at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
>>>         at Ice.ConnectionI.message(ConnectionI.java:1213)
>>>         at IceInternal.ThreadPool.run(ThreadPool.java:321)
>>>         at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
>>>         at
>>> IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
>>>         at java.lang.Thread.run(Thread.java:722)
>>>
>>>     serverExceptionClass = ome.conditions.SessionTimeoutException
>>>     message = Session (started=2016-03-04 15:24:57.51, hits=1888, last
>>> access=2016-03-04 15:25:05.955) exceeded timeToLive (60000) by 653 ms
>>> }
>>
>> _________