Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Bug #1315 (closed)

Opened 15 years ago

Closed 15 years ago

scripting Engine

Reported by: dzmacdonald Owned by: jamoore
Priority: blocker Cc: jos@…
Sprint: n.a.
Total Remaining Time: n.a.

Description (last modified by jmoore)

Scripting engine seems to be broken

when uploading script

Ice.UnknownException
    unknown = "ome.conditions.InternalException:  Wrapped Exception: (org.springframework.beans.factory.NoSuchBeanDefinitionException):
               No bean named 'processManager' is defined
               	at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeanDefinition(DefaultListableBeanFactory.java:387)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.getMergedLocalBeanDefinition(AbstractBeanFactory.java:968)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:246)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:168)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:238)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
               	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
               	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
               	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1245)
               	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1010)
               	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:472)
               	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
               	at java.security.AccessController.doPrivileged(Native Method)
               	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:283)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
               	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
               	at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:881)
               	at ome.system.ServiceFactory.getServiceByClass(ServiceFactory.java:339)
               	at ome.system.ServiceFactory.createJobHandle(ServiceFactory.java:247)
               	at ome.services.blitz.impl.ServiceFactoryI$1.doWork(ServiceFactoryI.java:444)
               	at ome.services.blitz.impl.ServiceFactoryI$1.doWork(ServiceFactoryI.java:439)
               	at sun.reflect.GeneratedMethodAccessor223.invoke(Unknown Source)
               	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
               	at java.lang.reflect.Method.invoke(Method.java:597)
               	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:310)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
               	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:377)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
               	at ome.security.basic.EventHandler.invoke(EventHandler.java:132)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
               	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
               	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
               	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:169)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
               	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:97)
               	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
               	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
               	at $Proxy55.doWork(Unknown Source)
               	at ome.services.util.Executor$Impl.execute(Executor.java:307)
               	at ome.services.blitz.impl.ServiceFactoryI.acquireProcessor(ServiceFactoryI.java:438)
               	at ome.services.blitz.impl.ScriptI.getScriptParams(ScriptI.java:488)
               	at ome.services.blitz.impl.ScriptI.access$400(ScriptI.java:61)
               	at ome.services.blitz.impl.ScriptI$2.run(ScriptI.java:134)
               	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:51)
               	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:128)
               	at ome.services.blitz.impl.ScriptI.uploadScript_async(ScriptI.java:121)
               	at omero.api._IScriptTie.uploadScript_async(_IScriptTie.java:113)
               	at omero.api._IScriptDisp.___uploadScript(_IScriptDisp.java:178)
               	at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:368)
               	at IceInternal.Incoming.invoke(Incoming.java:166)
               	at Ice.ConnectionI.invokeAll(ConnectionI.java:2045)
               	at Ice.ConnectionI.message(ConnectionI.java:977)
               	at IceInternal.ThreadPool.run(ThreadPool.java:575)
               	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
               	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:951)
               "
	at IceInternal.Outgoing.invoke(Outgoing.java:147)
	at omero.api._IScriptDelM.uploadScript(_IScriptDelM.java:397)
	at omero.api.IScriptPrxHelper.uploadScript(IScriptPrxHelper.java:525)
	at omero.api.IScriptPrxHelper.uploadScript(IScriptPrxHelper.java:497)
	at OmeroGateway.uploadScript(OmeroGateway.java:78)
	at Main.main(Main.java:97)

Change History (4)

comment:1 Changed 15 years ago by jmoore

  • Description modified (diff)
  • Owner changed from jmoore to dzmacdonald

r4307 (untested). Passing off to Donald.

comment:2 Changed 15 years ago by jmoore

  • Owner changed from dzmacdonald to jmoore

Other issues: (first one fixed locally - caused by local changes to processor.py but shouldn't be a NPE)

======================================================================
ERROR: testPingViaISCript (test.integration.ping.TestPing)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/josh/code/git/components/tools/OmeroPy/test/integration/ping.py", line 102, in testPingViaISCript
    p = self._getProcessor()
  File "/Users/josh/code/git/components/tools/OmeroPy/test/integration/ping.py", line 95, in _getProcessor
    id = scripts.uploadScript(PINGFILE)
  File "/Users/josh/GlencoeSoftware.git/git/omero.git/components/tools/OmeroPy/target/omero_api_IScript_ice.py", line 112, in uploadScript
    return _M_omero.api.IScript._op_uploadScript.invoke(self, ((script, ), _ctx))
UnknownException: exception ::Ice::UnknownException
{
    unknown = java.lang.NullPointerException
        at ome.services.blitz.impl.ScriptI.getScriptParams(ScriptI.java:490)
        at ome.services.blitz.impl.ScriptI.access$400(ScriptI.java:61)
        at ome.services.blitz.impl.ScriptI$2.run(ScriptI.java:134)
        at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:51)
        at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:128)
        at ome.services.blitz.impl.ScriptI.

ERROR: testUploadAndPing (test.integration.ping.TestPing)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/josh/code/git/components/tools/OmeroPy/test/integration/ping.py", line 77, in testUploadAndPing
    p = self.client.sf.acquireProcessor(j, 100)
  File "/Users/josh/GlencoeSoftware.git/git/omero.git/components/tools/OmeroPy/target/omero_API_ice.py", line 4419, in acquireProcessor
    return _M_omero.api.ServiceFactory._op_acquireProcessor.invoke(self, ((job, seconds), _ctx))
UnknownException: exception ::Ice::UnknownException
{
    unknown = ome.conditions.SecurityViolation: Cannot read ome.model.core.OriginalFile
        at ome.security.basic.BasicACLVoter.throwLoadViolation(BasicACLVoter.java:97)
        at ome.security.CompositeACLVoter.throwLoadViolation(CompositeACLVoter.java:86)
        at ome.security.ACLEventListener.onPostLoad(ACLEventListener.java:104)
        at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:204)
        at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:854)
        at org.hibernate.loader.Loader.doQuery(Loader.java:729)
        at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
        at org.hibernate.loader.Loader.loadEntity(Loader.java:1860)
        at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48)
        at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42)
        at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.ja

comment:3 Changed 15 years ago by jmoore

The SecurityViolation comes from the reduced permissions in 4.x. Uploads will have to be careful about giving the proper permissions.

comment:4 Changed 15 years ago by jmoore

  • Resolution set to fixed
  • Status changed from new to closed

r4333 should have the basic issues fixed. #1322 et al. still remain.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.65836 sec.)

© 2000-2014 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 3.0 Unported License
OME source code is available under the GNU General public license or through commercial license from Glencoe Software

We're Hiring!