Open Microscopy Environment

Hey, we've got another one for you...

We've had the server up and running for three weeks successfully when we had the webserver freeze on us. It was when I changed the name of one particular group (permission private). I had changed the name of two others previously and had no problems with it. I repeated it and every time that one group had its name changed, the server came up with the error :

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request....

The Dropbox log changed:-

Code: Select all

[s2686739@omero log]$ tail -c 555 DropBox.log
2011-11-11 08:32:34,304 WARNI [                omero.util.ServerContext] (Thread-2  ) Connection failure: exception ::Ice::ObjectNotExistException
{
    id =
    {
        name = babc87f6-4739-4c71-9d85-00000000000
        category = session-52762680-77da-4e97-a057-00000000000
    }
    facet =
    operation = keepAlive
}
2011-11-11 08:32:34,418 INFO  [                omero.util.ServerContext] (Thread-2  ) Established connection: session-52762680-77da-4e97-a057-0000000c4f/af6ed926-e868-0000-0000-0618c52c2ef5 -t:tcp -h our.ip.000.000 -p 0000



To get OMERO working again, I need to restart the OMERO server. All the admin diagnostics are coming up as normal. And once its started up again, images in that particular dataset are missing but the number next to dataset is saying that there is the correct number of images in there. Also they have padlocks on them (like the Read Only ones)


The OMEROweb.log came up with :

Code: Select all

ValidationException: exception ::omero::ValidationException
{
    serverStackTrace = ome.conditions.ValidationException: could not insert: [ome.model.containers.DatasetImageLink]; SQL [insert into datasetimagelink (child, creation_id, external_id, group_id, owner_id, permissions, update_id, parent, version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; constraint [datasetimagelink_pkey]; nested exception is org.hibernate.exception.ConstraintViolationException: could not insert: [ome.model.containers.DatasetImageLink]
        at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:637)
        at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
        at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at $Proxy78.saveObject(Unknown Source)
        at sun.reflect.GeneratedMethodAccessor1005.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        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 ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
        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 $Proxy78.saveObject(Unknown Source)
        at sun.reflect.GeneratedMethodAccessor1010.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        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:136)
        at ome.services.blitz.impl.UpdateI.saveObject_async(UpdateI.java:85)
        at omero.api._IUpdateTie.saveObject_async(_IUpdateTie.java:113)
        at omero.api._IUpdateDisp.___saveObject(_IUpdateDisp.java:141)
        at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:377)
        at IceInternal.Incoming.invoke(Incoming.java:159)
        at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
        at Ice.ConnectionI.message(ConnectionI.java:972)
        at IceInternal.ThreadPool.run(ThreadPool.java:577)
        at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)

    serverExceptionClass = ome.conditions.ValidationException
    message = could not insert: [ome.model.containers.DatasetImageLink]; SQL [insert into datasetimagelink (child, creation_id, external_id, group_id, owner_id, permissions, update_id, parent, version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; constraint [datasetimagelink_pkey]; nested exception is org.hibernate.exception.ConstraintViolationException: could not insert: [ome.model.containers.DatasetImageLink]
}



I noticed there was a similar bug here http://trac.openmicroscopy.org.uk/ome/ticket/6663

Would you be able to point us to a possible area to investigate?

Thanks,
Manda

Hi Manda,

what's the name of the group in question? Is there a difference between that group and the other one in terms of who might have been logged in while you were trying it out?

~Josh

There was no other people logged in. I've changed the names of the group numerous times (after it crashes abin/omero nd the server has rebooted, the group name has changed) and tried names with and without special characters. The group name currently is

Adrian Meedeniyas private group Private (rw----)

And I am logged in as the owner when changing it.

Manz wrote:There was no other people logged in. ...And I am logged in as the owner when changing it.

Have you tried when you are not logged into the group in question? Also, could you send us your log files zipped up so that we have the full stack traces?

Thanks!
~Josh

I found that if you were logged in as an admin who was not an owner of that group, it worked with no problems. The bug only replicated when I was logged in as an owner. However I have other groups that were owned by the same owner that I tested while logged in that worked without problems. I will PM you the logs

problem sovled? the info is also useful for me

viewtopic.php?f=6&t=1028

Not solved, but reproduced in the following (we were playing with the next version up)

Hi Manda,

can you turn on web debugging (bin/omero config set omero.web.debug true) and reproduce? And when you say you had to restart the server did you mean the whole stack (bin/omero admin restart) or the web server?

Cheers,
~Josh.