Shutdown handler in an OMERO.script

[PaulVanSchayck]

Hey Josh,

Thanks for the suggestion of storing something in the session directly. That's something I hadn't thought about yet. I think much effort is made in rejoining an existing session for an user when one exists, right? So, even though this is not persistent, it would still be retrievable when say, launching a script from Insight and then logging into to the webclient?

Also, I ran into this problem when running "updateService.saveObject(jobObj)" as non admin user:

Code: Select all

serverExceptionClass = ome.conditions.SecurityViolation
message = Updating ome.model.jobs.ScriptJob:Id_10192 not allowed.

Is this a bug? The job is assigned to the user performing the update.

Thank you,

Paul

[jmoore]

Morning, Paul

I think much effort is made in rejoining an existing session for an user when one exists, right? So, even though this is not persistent, it would still be retrievable when say, launching a script from Insight and then logging into to the webclient?

I don't think this would be the case. Each client (insight, web, script) will be in its own session. One session can access the contents of another session, but there's nothing in the clients to just know which session to grab.

Also, I ran into this problem when running "updateService.saveObject(jobObj)" as non admin user:

Code: Select all

serverExceptionClass = ome.conditions.SecurityViolation
message = Updating ome.model.jobs.ScriptJob:Id_10192 not allowed.

Is this a bug? The job is assigned to the user performing the update.

Did this fail in one case but not another? If so, perhaps the group for the session was changed? Otherwise, could you send me the full exception as well as where it occurred?

Thanks,
~Josh

[PaulVanSchayck]

Morning Josh,

I don't think this would be the case. Each client (insight, web, script) will be in its own session. One session can access the contents of another session, but there's nothing in the clients to just know which session to grab.

Hmm.. that would cause too much hacking around to make this workable for our purposes.

Did this fail in one case but not another? If so, perhaps the group for the session was changed? Otherwise, could you send me the full exception as well as where it occurred?

Hmm.. no so far I had only been testing this with my own user (admin), and not a normal user. Changing a normal user to admin fixes the problem consistently. The full exception is:

Code: Select all

WARNING:omero.gateway:SecurityViolation on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <e451b544-0b37-4524-b2e8-06dee47d9c64omero.api.IUpdate> saveObject((object #0 (::omero::model::ScriptJob)
{
    _id = object #1 (::omero::RLong)
    {
        _val = 10195
    }
    _details = object #2 (::omero::model::Details)
    {
        _owner = object #3 (::omero::model::Experimenter)
        {
            _id = object #4 (::omero::RLong)
            {
                _val = 152
            }
            _details = <nil>
            _loaded = False
            _version = <nil>
            _groupExperimenterMapSeq =
            {
            }
            _groupExperimenterMapLoaded = False
            _omeName = <nil>
            _firstName = <nil>
            _middleName = <nil>
            _lastName = <nil>
            _institution = <nil>
            _email = <nil>
            _annotationLinksSeq =
            {
            }
            _annotationLinksLoaded = False
            _annotationLinksCountPerOwner =
            {
            }
        }
        _group = object #5 (::omero::model::ExperimenterGroup)
        {
            _id = object #6 (::omero::RLong)
            {
                _val = 53
            }
            _details = object #7 (::omero::model::Details)
            {
                _owner = <nil>
                _group = <nil>
                _creationEvent = <nil>
                _updateEvent = <nil>
                _permissions = object #8 (::omero::model::Permissions)
                {
                    _restrictions =
                    {
                        [0] = False
                        [1] = True
                        [2] = True
                        [3] = True
                    }
                    _perm1 = -40
                }
                _externalInfo = <nil>
                _call =
                {
                    key = omero.session.uuid
                    value = ec05a3fa-356c-432e-be7e-9305d019c4b6
                   
                    key = omero.client.uuid
                    value = e451b544-0b37-4524-b2e8-06dee47d9c64
                }
                _event = object #9 (::omero::sys::EventContext)
                {
                    shareId = -1
                    sessionId = 8219
                    sessionUuid = *********
                    userId = 152
                    userName = testing
                    groupId = 53
                    groupName = testing
                    isAdmin = False
                    eventId = -1
                    eventType = User
                    memberOfGroups =
                    {
                        [0] = 53
                        [1] = 1
                    }
                    leaderOfGroups =
                    {
                        [0] = 53
                    }
                    groupPermissions = object #10 (::omero::model::Permissions)
                    {
                        _restrictions =
                        {
                        }
                        _perm1 = -40
                    }
                }
            }
            _loaded = True
            _version = object #11 (::omero::RInt)
            {
                _val = 0
            }
            _name = object #12 (::omero::RString)
            {
                _val = testing
            }
            _groupExperimenterMapSeq =
            {
            }
            _groupExperimenterMapLoaded = False
            _annotationLinksSeq =
            {
            }
            _annotationLinksLoaded = False
            _annotationLinksCountPerOwner =
            {
            }
            _description = object #13 (::omero::RString)
            {
                _val = A group containing all testing users and data
            }
        }
        _creationEvent = object #14 (::omero::model::Event)
        {
            _id = object #15 (::omero::RLong)
            {
                _val = 125429
            }
            _details = <nil>
            _loaded = False
            _status = <nil>
            _time = <nil>
            _experimenter = <nil>
            _experimenterGroup = <nil>
            _type = <nil>
            _containingEvent = <nil>
            _logsSeq =
            {
            }
            _logsLoaded = False
            _session = <nil>
        }
        _updateEvent = object #16 (::omero::model::Event)
        {
            _id = object #17 (::omero::RLong)
            {
                _val = 125433
            }
            _details = <nil>
            _loaded = False
            _status = <nil>
            _time = <nil>
            _experimenter = <nil>
            _experimenterGroup = <nil>
            _type = <nil>
            _containingEvent = <nil>
            _logsSeq =
            {
            }
            _logsLoaded = False
            _session = <nil>
        }
        _permissions = object #18 (::omero::model::Permissions)
        {
            _restrictions =
            {
                [0] = True
                [1] = True
                [2] = True
                [3] = True
            }
            _perm1 = -40
        }
        _externalInfo = <nil>
        _call =
        {
            key = omero.session.uuid
            value = ec05a3fa-356c-432e-be7e-9305d019c4b6
           
            key = omero.client.uuid
            value = e451b544-0b37-4524-b2e8-06dee47d9c64
        }
        _event = object #19 (::omero::sys::EventContext)
        {
            shareId = -1
            sessionId = 8219
            sessionUuid = *********
            userId = 152
            userName = testing
            groupId = 53
            groupName = testing
            isAdmin = False
            eventId = -1
            eventType = User
            memberOfGroups =
            {
                [0] = 53
                [1] = 1
            }
            leaderOfGroups =
            {
                [0] = 53
            }
            groupPermissions = object #20 (::omero::model::Permissions)
            {
                _restrictions =
                {
                }
                _perm1 = -40
            }
        }
    }
    _loaded = True
    _version = <nil>
    _username = object #21 (::omero::RString)
    {
        _val = testing
    }
    _groupname = object #22 (::omero::RString)
    {
        _val = testing
    }
    _type = object #23 (::omero::RString)
    {
        _val = User
    }
    _message = object #24 (::omero::RString)
    {
        _val = |PID:18263 |Progress:0.00 |Message:Initializing...
    }
    _status = object #25 (::omero::model::JobStatus)
    {
        _id = object #26 (::omero::RLong)
        {
            _val = 5
        }
        _details = object #27 (::omero::model::Details)
        {
            _owner = <nil>
            _group = <nil>
            _creationEvent = <nil>
            _updateEvent = <nil>
            _permissions = object #28 (::omero::model::Permissions)
            {
                _restrictions =
                {
                    [0] = True
                    [1] = True
                    [2] = True
                    [3] = True
                }
                _perm1 = -40
            }
            _externalInfo = <nil>
            _call =
            {
                key = omero.session.uuid
                value = ec05a3fa-356c-432e-be7e-9305d019c4b6
               
                key = omero.client.uuid
                value = e451b544-0b37-4524-b2e8-06dee47d9c64
            }
            _event = object #29 (::omero::sys::EventContext)
            {
                shareId = -1
                sessionId = 8219
                sessionUuid = *********
                userId = 152
                userName = testing
                groupId = 53
                groupName = testing
                isAdmin = False
                eventId = -1
                eventType = User
                memberOfGroups =
                {
                    [0] = 53
                    [1] = 1
                }
                leaderOfGroups =
                {
                    [0] = 53
                }
                groupPermissions = object #30 (::omero::model::Permissions)
                {
                    _restrictions =
                    {
                    }
                    _perm1 = -40
                }
            }
        }
        _loaded = True
        _value = object #31 (::omero::RString)
        {
            _val = Running
        }
    }
    _submitted = object #32 (::omero::RTime)
    {
        _val = 1404199963829
    }
    _scheduledFor = object #33 (::omero::RTime)
    {
        _val = 1404199963829
    }
    _started = object #34 (::omero::RTime)
    {
        _val = 1404199963982
    }
    _finished = <nil>
    _originalFileLinksSeq =
    {
    }
    _originalFileLinksLoaded = False
    _originalFileLinksCountPerOwner =
    {
    }
    _description = <nil>
},), {})
Traceback (most recent call last):
  File "/home/service-unix-img/OMERO.server/lib/python/omero/gateway/__init__.py", line 3533, in __call__
    return self.f(*args, **kwargs)
  File "/home/service-unix-img/OMERO.server/lib/python/omero_api_IUpdate_ice.py", line 107, in saveObject
    return _M_omero.api.IUpdate._op_saveObject.invoke(self, ((obj, ), _ctx))
SecurityViolation: exception ::omero::SecurityViolation
{
    serverStackTrace = ome.conditions.SecurityViolation: Updating ome.model.jobs.ScriptJob:Id_10195 not allowed.
   at ome.security.basic.BasicACLVoter.throwUpdateViolation(BasicACLVoter.java:228)
   at ome.security.CompositeACLVoter.throwUpdateViolation(CompositeACLVoter.java:96)
   at ome.security.ACLEventListener.onPreUpdate(ACLEventListener.java:129)
   at org.hibernate.action.EntityUpdateAction.preUpdate(EntityUpdateAction.java:236)
   at org.hibernate.action.EntityUpdateAction.execute(EntityUpdateAction.java:87)
   at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:267)
   at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:259)
   at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:179)
   at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
   at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
   at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1208)
   at ome.logic.UpdateImpl.afterUpdate(UpdateImpl.java:294)
   at ome.logic.UpdateImpl.doAction(UpdateImpl.java:312)
   at ome.logic.UpdateImpl.doAction(UpdateImpl.java:302)
   at ome.logic.UpdateImpl.saveObject(UpdateImpl.java:108)
   at sun.reflect.GeneratedMethodAccessor829.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:606)
   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.EventHandler.invoke(EventHandler.java:154)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
   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$Interceptor.invoke(ProxyCleanupFilter.java:241)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at com.sun.proxy.$Proxy98.saveObject(Unknown Source)
   at sun.reflect.GeneratedMethodAccessor829.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:606)
   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:98)
   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 com.sun.proxy.$Proxy98.saveObject(Unknown Source)
   at sun.reflect.GeneratedMethodAccessor848.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:606)
   at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
   at ome.services.throttling.Callback.run(Callback.java:56)
   at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
   at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
   at ome.services.blitz.impl.UpdateI.saveObject_async(UpdateI.java:81)
   at sun.reflect.GeneratedMethodAccessor847.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:606)
   at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
   at omero.cmd.CallContext.invoke(CallContext.java:78)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at com.sun.proxy.$Proxy99.saveObject_async(Unknown Source)
   at omero.api._IUpdateTie.saveObject_async(_IUpdateTie.java:108)
   at omero.api._IUpdateDisp.___saveObject(_IUpdateDisp.java:136)
   at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:357)
   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:745)

    serverExceptionClass = ome.conditions.SecurityViolation
    message = Updating ome.model.jobs.ScriptJob:Id_10195 not allowed.
}

Thanks,

Paul

[jmoore]

Ah, I think I see. Did you try to move to `iUpdate.saveObject()` on the job as opposed to the job service? If so, that won't work, since those objects are protected from tampering. That method would only work with the annotation strategy I mentioned.

Cheers,
~Josh

[PaulVanSchayck]

Hmm.. that's unfortunate. Yes, I'm was always using updateService.saveObject(jobObj).

So moving to the job service. This also doesn't seem to actually set the message (regardless of being admin or not)

Code: Select all

handle = conn.c.sf.createJobHandle()
handle.attach(long(jobid))
handle.setMessage(msg)

Am I missing something here?

Thanks,

Paul

[jmoore]

That `setMesage()` doesn't work, certainly surprises me. But now I'm a bit confused. I read your previous forum posts as if this were already working for you. But that's not the case? ~J.

[PaulVanSchayck]

Oh! I'm sorry for the confusion. I was using this before:

Code: Select all

jobid = conn.getProperty("omero.job")
jobObj = queryService.findByQuery("from Job where id = :jobid", p)
jobObj.setMessage(rstring(msg))
updateService.saveObject(jobObj)

Which doesn't work as non-admin

Now I was trying to use:

Code: Select all

jobid = c.getProperty("omero.job")
handle = c.sf.createJobHandle()
handle.attach(long(jobid))
status = handle.jobStatus()
handle.setMessage("Foo")

Now, ignore my previous message. There was an unrelated mistake in my code causing the setMessage() call not to be executed. However, this fixing this it gives the following error:

Code: Select all

File "/home/service-unix-img/OMERO.server/lib/python/omero_api_JobHandle_ice.py", line 236, in setMessage
   return _M_omero.api.JobHandle._op_setMessage.invoke(self, ((message, ), _ctx))
serverStackTrace = ome.conditions.ApiUsageException: An ome.model.jobs.JobStatus enum does not exist with the value: null
at ome.logic.TypesImpl.getEnumeration(TypesImpl.java:128)
at ome.services.JobBean.setStatusAndMessage(JobBean.java:304)
at ome.services.JobBean.setMessage(JobBean.java:297)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

Changing to

Code: Select all

handle.setMessage(rstring("foobar"))

Gives:

Code: Select all

return _M_omero.api.JobHandle._op_setMessage.invoke(self, ((message, ), _ctx))
ValueError: invalid value for argument 1 in operation `setMessage'

Changing to:

Code: Select all

handle.setStatusAndMessage("Running",rstring("foobar"))

Does work! And also as normal user! Solving the problem. However the API usage from here is bit unclear in all this.

[edit]I see now, that the API docs do explain the rstring() usage. And I suspect that first calling handle.setStatus() before handle.setMessage() will fix the rather. Only this is not documented.[/edit]

Thanks,

Paul

[jmoore]

Glad it's all worked out, Paul! I'll make a note to either fix the status/message logic, or make a note of the ordering requirement in the docs.

Thanks for the feedback.
~Josh.