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"

Task #11307 (closed)

Opened 11 years ago

Closed 10 years ago

BUG: Creating Projection from Other's Data - Cannot Access Data Error

Reported by: rkferguson Owned by: jburel
Priority: major Milestone: 5.1.0
Component: Insight Version: 4.4.8
Keywords: n.a. Cc: nikolaus.ehrenfeuchter@…,
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Feedback received from Basel:

9/7/2013 - Scott
4.4.5 - Insight
Group projection
We have a small group setup where one scientist is doing the majority of the image aquisition, a second scientist is looking at these images and would like to create a projection of these images yet this is not possible. Is this a feasible function that could be added to the projection workflow?

GF:
Checked and using 4.4.8 in a read-annotate group I can create projections on someone else's data.
Queried Scott: Were they using a read-only group?

Scott:
I have double checked what was being done with my own test setup with the client version 4.4.8. I was previously trying with 4.4.5 client. The group is definitely a read annotate group. I have tried today again to create a projected image on a image that was not my own in the read annotate group. This time though I have the message An error occurred while creating the projected image". I had not previously had this message when I first submitted the feedback.

GF Note:
It worked fine for me - no error. Error looks like it is a permissions issue.

Log file info:

Data Retrieval Failure: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot project the image.
    at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:902)
    at org.openmicroscopy.shoola.env.data.OMEROGateway.projectImage(OMEROGateway.java:5765)
    at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.projectImage(OmeroImageServiceImpl.java:973)
    at org.openmicroscopy.shoola.env.data.views.calls.ProjectionSaver$2.doCall(ProjectionSaver.java:110)
    at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
    at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
    at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
    at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
    at java.lang.Thread.run(Unknown Source)
Caused by: omero.SecurityViolation
    serverStackTrace = "ome.conditions.SecurityViolation: Group is rwra--. Cannot link to object: ome.model.core.Pixels:Id_1743
                            at ome.security.basic.OmeroInterceptor.throwIfNotGranted(OmeroInterceptor.java:1072)
                            at ome.security.basic.OmeroInterceptor.evaluateLinkages(OmeroInterceptor.java:476)
                            at ome.security.basic.OmeroInterceptor.onSave(OmeroInterceptor.java:154)
                            at org.hibernate.event.def.AbstractSaveEventListener.substituteValuesIfNecessary(AbstractSaveEventListener.java:414)
                            at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:293)
                            at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:204)
                            at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:144)
                            at org.hibernate.event.def.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:415)
                            at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:341)
                            at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303)
                            at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:59)
                            at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:161)
                            at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258)
                            at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:94)
                            at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:871)
                            at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:853)
                            at org.hibernate.engine.CascadingAction$6.cascade(CascadingAction.java:279)
                            at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392)
                            at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335)
                            at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204)
                            at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:425)
                            at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:362)
                            at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:338)
                            at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204)
                            at org.hibernate.engine.Cascade.cascade(Cascade.java:161)
                            at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:476)
                            at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:388)
                            at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303)
                            at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:59)
                            at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:161)
                            at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258)
                            at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:94)
                            at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:84)
                            at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:80)
                            at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:861)
                            at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:845)
                            at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:849)
                            at ome.logic.UpdateImpl.internalMerge(UpdateImpl.java:273)
                            at ome.logic.UpdateImpl$2.run(UpdateImpl.java:121)
                            at ome.logic.UpdateImpl$2.run(UpdateImpl.java:118)
                            at ome.logic.UpdateImpl.doAction(UpdateImpl.java:311)
                            at ome.logic.UpdateImpl.doAction(UpdateImpl.java:302)
                            at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:118)
                            at ome.logic.PixelsImpl.copyAndResizeImage(PixelsImpl.java:270)
                            at ome.services.projection.ProjectionBean.projectPixels(ProjectionBean.java:193)
                            at sun.reflect.GeneratedMethodAccessor3016.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 $Proxy116.projectPixels(Unknown Source)
                            at sun.reflect.GeneratedMethodAccessor3016.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 $Proxy116.projectPixels(Unknown Source)
                            at sun.reflect.GeneratedMethodAccessor3346.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.ProjectionI.projectPixels_async(ProjectionI.java:45)
                            at sun.reflect.GeneratedMethodAccessor3345.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 $Proxy117.projectPixels_async(Unknown Source)
                            at omero.api._IProjectionTie.projectPixels_async(_IProjectionTie.java:73)
                            at omero.api._IProjectionDisp.___projectPixels(_IProjectionDisp.java:165)
                            at omero.api._IProjectionDisp.__dispatch(_IProjectionDisp.java:213)
                            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 = "Group is rwra--. Cannot link to object: ome.model.core.Pixels:Id_1743"
    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:2243)
    at IceInternal.BasicStream.throwException(BasicStream.java:1632)
    at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
    at omero.api._IProjectionDelM.projectPixels(_IProjectionDelM.java:50)
    at omero.api.IProjectionPrxHelper.projectPixels(IProjectionPrxHelper.java:48)
    at omero.api.IProjectionPrxHelper.projectPixels(IProjectionPrxHelper.java:20)
    at org.openmicroscopy.shoola.env.data.OMEROGateway.projectImage(OMEROGateway.java:5760)
    ... 9 more

Exception in thread "AWT-EventQueue-0"

Change History (5)

comment:1 Changed 11 years ago by rkferguson

  • Cc s.loynton@… added

comment:2 Changed 11 years ago by jburel

This is probably due to the fact that when projecting an image, some elements are shared between the images i.e. acquisition data.

comment:3 Changed 11 years ago by jburel

  • Milestone changed from OMERO-4.4.x to 5.0.0-beta2
  • Sprint set to OMERO 5 Beta 2 (1)

comment:4 Changed 11 years ago by jburel

  • Cc nikolaus.ehrenfeuchter@… added; s.loynton@… removed
  • Milestone changed from 5.0.0-beta2 to 5.0.0-beta3
  • Sprint OMERO 5 Beta 2 (1) deleted

Graph issue to be addressed in Beta3

comment:5 Changed 10 years ago by jburel

  • Resolution set to duplicate
  • Status changed from new to closed
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: 0.68957 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!