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Task #10262 (closed)

Opened 12 years ago

Closed 10 years ago

Bug: Moving projected images between groups

Reported by: saloynton Owned by: jburel
Priority: critical Milestone: 5.1.0
Component: Services Version: 4.4.8
Keywords: BACKPORT-4.4 Cc: s.loynton@…, nikolaus.ehrenfeuchter@…, jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

The following error was found when opening a projected image that had been moved from the default group to the new IMCF group. The steps taken a new project was created in the data manager. A copy paste action was made and the dataset was moved into the new group.
When trying to view the projected image the exception below occurred. The original image the projection was created from has also been lost.

A screenshot is attached.

Working with OMERO 4.4.5

java.lang.Exception:org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.

Cannot retrieve the pixels set for 1953

                at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:860)

                at org.openmicroscopy.shoola.env.data.OMEROGateway.getPixels(OMEROGateway.java:3221)

                at org.openmicroscopy.shoola.env.data.OmeroDataServiceImpl.getChannelsMetadata(OmeroDataServiceImpl.java:500)

                at org.openmicroscopy.shoola.env.data.views.calls.ChannelMetadataLoader$1.doCall(ChannelMetadataLoader.java:85)

                at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)

                at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)

                at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)

                at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)

                at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)

                at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)

                at java.lang.Thread.run(Unknown Source)

Caused by: omero.SecurityViolation

    serverStackTrace = "ome.conditions.SecurityViolation: Cannot read ome.model.core.LogicalChannel:Id_4185

                                at ome.security.basic.BasicACLVoter.throwLoadViolation(BasicACLVoter.java:163)

                                at ome.security.CompositeACLVoter.throwLoadViolation(CompositeACLVoter.java:88)

                                at ome.security.ACLEventListener.onPostLoad(ACLEventListener.java:104)

                                at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:250)

                                at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898)

                                at org.hibernate.loader.Loader.doQuery(Loader.java:773)

                                at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270)

                                at org.hibernate.loader.Loader.doList(Loader.java:2449)

                                at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2192)

                                at org.hibernate.loader.Loader.list(Loader.java:2187)

                                at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:452)

                                at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)

                                at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)

                                at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1260)

                                at org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)

                                at org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:859)

                                at ome.services.query.Query.doInHibernate(Query.java:244)

                                at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:406)

                                at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339)

                                at ome.logic.QueryImpl.execute(QueryImpl.java:144)

                                at ome.logic.QueryImpl.findByQuery(QueryImpl.java:356)

                                at ome.logic.PixelsImpl.retrievePixDescription(PixelsImpl.java:75)

                                at sun.reflect.GeneratedMethodAccessor939.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 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 $Proxy94.retrievePixDescription(Unknown Source)

                                at sun.reflect.GeneratedMethodAccessor939.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 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 $Proxy94.retrievePixDescription(Unknown Source)

                                at sun.reflect.GeneratedMethodAccessor1038.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:150)

                                at ome.services.blitz.impl.PixelsI.retrievePixDescription_async(PixelsI.java:99)

                                at sun.reflect.GeneratedMethodAccessor1037.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:59)

                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                                at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                                at $Proxy95.retrievePixDescription_async(Unknown Source)

                                at omero.api._IPixelsTie.retrievePixDescription_async(_IPixelsTie.java:129)

                                at omero.api._IPixelsDisp.___retrievePixDescription(_IPixelsDisp.java:187)

                                at omero.api._IPixelsDisp.__dispatch(_IPixelsDisp.java:589)

                                at IceInternal.Incoming.invoke(Incoming.java:159)

                                at Ice.ConnectionI.invokeAll(ConnectionI.java:2357)

                                at Ice.ConnectionI.dispatch(ConnectionI.java:1208)

                                at Ice.ConnectionI.message(ConnectionI.java:1163)

                                at IceInternal.ThreadPool.run(ThreadPool.java:302)

                                at IceInternal.ThreadPool.access$300(ThreadPool.java:12)

                                at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643)

                                at java.lang.Thread.run(Thread.java:722)

                        "

    serverExceptionClass = "ome.conditions.SecurityViolation"

    message = "Cannot read ome.model.core.LogicalChannel:Id_4185"

                at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

                at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)

                at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)

                at java.lang.reflect.Constructor.newInstance(Unknown Source)

                at java.lang.Class.newInstance0(Unknown Source)

                at java.lang.Class.newInstance(Unknown Source)

                at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142)

                at IceInternal.BasicStream.throwException(BasicStream.java:1564)

                at IceInternal.Outgoing.throwUserException(Outgoing.java:443)

                at omero.api._IPixelsDelM.retrievePixDescription(_IPixelsDelM.java:507)

                at omero.api.IPixelsPrxHelper.retrievePixDescription(IPixelsPrxHelper.java:1341)

                at omero.api.IPixelsPrxHelper.retrievePixDescription(IPixelsPrxHelper.java:1314)

                at org.openmicroscopy.shoola.env.data.OMEROGateway.getPixels(OMEROGateway.java:3219)

                ... 9 more

 

                at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)

                at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:287)

                at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:257)

                at org.openmicroscopy.shoola.agents.metadata.EditorLoader.handleException(EditorLoader.java:160)

                at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)

                at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)

                at java.awt.event.InvocationEvent.dispatch(Unknown Source)

                at java.awt.EventQueue.dispatchEventImpl(Unknown Source)

                at java.awt.EventQueue.access$400(Unknown Source)

                at java.awt.EventQueue$2.run(Unknown Source)

                at java.awt.EventQueue$2.run(Unknown Source)

                at java.security.AccessController.doPrivileged(Native Method)

                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)

                at java.awt.EventQueue.dispatchEvent(Unknown Source)

                at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)

                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)

                at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

                at java.awt.EventDispatchThread.run(Unknown Source)

Attachments (1)

Moving projected images between groups.png​ (677.5 KB) - added by saloynton 12 years ago.

Download all attachments as: .zip

Change History (7)

Changed 12 years ago by saloynton

comment:1 Changed 12 years ago by jburel

  • Cc jburel added
  • Component changed from Insight to Services
  • Milestone changed from Unscheduled to OMERO-4.5
  • Owner changed from jburel to jmoore
  • Priority changed from minor to critical

comment:2 Changed 11 years ago by jburel

  • Owner changed from jamoore to jburel
  • Version set to 4.4.8

Writing tests, will pass it back when ready if required.

comment:3 Changed 11 years ago by jburel

comment:4 Changed 11 years ago by jburel

96 tests written so far.

comment:5 Changed 11 years ago by jamoore

  • Milestone changed from OMERO-4.4.9 to OMERO-4.4.10

Added to known limitations for 4.4.9. Pushing to 4.4.10 with other
security & graph issues.

comment:6 Changed 10 years ago by jburel

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

linked to ​https://trac.openmicroscopy.org.uk/ome/ticket/11532

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