[ome-users] Issues with import and subsequent issues with removing mistakenly imported images from OMERO server
Caterina Strambio De Castillia
strambc at mail.rockefeller.edu
Tue Oct 5 14:21:58 BST 2010
Dear JMarie and all
the OMERO server here at the Istituto Cantonale di Microbiologia in Bellinzona, Switzerland is up and running and we have started our usage tests.
During one of such tests, while I was importing a dataset of .lsm files I encountered problems with the import. Some of the files in the dataset failed to import while others (they were all .lsm files) appeared to proceed just fine, except they were imported repeatedly a number of times. At the end I found myself with >100 images in a dataset where I was expecting <10.
At this point I tried to delete the mistakenly imported images and repeatedly encountered the same error (see below) which I duly reported on the qa support page.
While I understand from JMarie' reply to my error message, that you are aware of a problem with deleting images and you are currently fixing it, I was wondering whether the problem I have had, has something to do with the failed import / repeated import issues described above and whether there would be something I could do to fix the problem before the next 4.2.1 release.
Please let me know if I can be of further help to clarify and help fix the error.
Have a nice day
Caterina
_________
java.lang.Exception: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot delete the image: omero.rtypes$RLongI at ba
at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:729)
at org.openmicroscopy.shoola.env.data.OMEROGateway.deleteImage(OMEROGateway.java:5369)
at org.openmicroscopy.shoola.env.data.OmeroDataServiceImpl.delete(OmeroDataServiceImpl.java:215)
at org.openmicroscopy.shoola.env.data.OmeroDataServiceImpl.delete(OmeroDataServiceImpl.java:236)
at org.openmicroscopy.shoola.env.data.OmeroDataServiceImpl.delete(OmeroDataServiceImpl.java:1239)
at org.openmicroscopy.shoola.env.data.views.calls.DataObjectRemover$1.doCall(DataObjectRemover.java:102)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:637)
Caused by: omero.ValidationException
serverStackTrace = "ome.conditions.ValidationException: could not delete: [ome.model.core.OriginalFile#398]; SQL [delete from originalfile where id=?]; constraint [fkfileannotation_file_originalfile]; nested exception is org.hibernate.exception.ConstraintViolationException: could not delete: [ome.model.core.OriginalFile#398]
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.HibernateTemplate.doExecute(HibernateTemplate.java:411)
at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339)
at ome.logic.QueryImpl.execute(QueryImpl.java:132)
at ome.security.basic.BasicSecuritySystem.runAsAdmin(BasicSecuritySystem.java:555)
at ome.services.delete.DeleteBean.deleteImage(DeleteBean.java:175)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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.EventHandler.invoke(EventHandler.java:144)
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:222)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy81.deleteImage(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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:40)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy81.deleteImage(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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:132)
at ome.services.blitz.impl.DeleteI.deleteImage_async(DeleteI.java:52)
at omero.api._IDeleteTie.deleteImage_async(_IDeleteTie.java:74)
at omero.api._IDeleteDisp.___deleteImage(_IDeleteDisp.java:190)
at omero.api._IDeleteDisp.__dispatch(_IDeleteDisp.java:319)
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 delete: [ome.model.core.OriginalFile#398]; SQL [delete from originalfile where id=?]; constraint [fkfileannotation_file_originalfile]; nested exception is org.hibernate.exception.ConstraintViolationException: could not delete: [ome.model.core.OriginalFile#398]"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at java.lang.Class.newInstance0(Class.java:355)
at java.lang.Class.newInstance(Class.java:308)
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._IDeleteDelM.deleteImage(_IDeleteDelM.java:99)
at omero.api.IDeletePrxHelper.deleteImage(IDeletePrxHelper.java:125)
at omero.api.IDeletePrxHelper.deleteImage(IDeletePrxHelper.java:91)
at org.openmicroscopy.shoola.env.data.OMEROGateway.deleteImage(OMEROGateway.java:5367)
... 11 more
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:158)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:245)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:217)
at org.openmicroscopy.shoola.agents.treeviewer.DataTreeViewerLoader.handleException(DataTreeViewerLoader.java:170)
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(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caterina Strambio De Castillia
Dottore in Scienze Biologiche, Ph.D.
Instructor of Anatomy and Physiology
Biologiste 2 - Senior Research Scientist
Laboratory of viral replication, pathogenesis, and immunity
http://www.mimo.unige.ch/luban_lab/
Department of Microbiology and Molecular Medicine
University of Geneva
1 Rue Michel Servet
CH-1211 Geneva 4
Switzerland
+41 22 3795720
+41 78 7367537
_________________
Visiting Fellow
Laboratory of Cellular and Structural Biology
http://www.rockefeller.edu/labheads/rout/research_project_3.php
The Rockefeller University
1230 York Avenue
New York NY 10065
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