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Task #12603 (closed)

Opened 10 years ago

Closed 9 years ago

Last modified 9 years ago

Bug: Import (Fake) Screen Failure

Reported by: drussell-x Owned by: mlinkert
Priority: major Milestone: 5.1.0-m4
Component: Bio-Formats Version: 5.1.0-m1
Keywords: n.a. Cc: jburel, mlinkert, mtbc
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

I made the fake screen like this:

where ${i} ==  in this case

$OMERO_PREFIX/../components/bioformats/tools/mkfake /tmp/fakes/plates${i}_runs${i}_rows${i}_columns${i}_fields${i} -plates ${i} -runs ${i} -rows ${i} -columns ${i} -fields ${i}

Result on import snippet

serverExceptionClass = "ome.conditions.ValidationException"
    message = "not-null property references a null or transient value: ome.model.acquisition.LightSettings.lightSource; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.acquisition.LightSettings.lightSource"
        at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:1912)
        at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(ManagedImportRequestI.java:513)
        at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:383)
        at omero.cmd.HandleI.steps(HandleI.java:436)
        at omero.cmd.HandleI$1.doWork(HandleI.java:365)
        at omero.cmd.HandleI$1.doWork(HandleI.java:361)
        at sun.reflect.GeneratedMethodAccessor259.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at ome.tools.hibernate.ProxyCleanupFilter$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 $Proxy65.doWork(Unknown Source)
        at ome.services.util.Executor$Impl.execute(Executor.java:457)
        at omero.cmd.HandleI.run(HandleI.java:359)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
        at ome.services.util.Executor$Impl$1.call(Executor.java:498)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
Caused by: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.acquisition.LightSettings.lightSource; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.acquisition.LightSettings.lightSource
                                at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648)
                                at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
                                at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
                                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 $Proxy65.doWork(Unknown Source)
                                at ome.services.util.Executor$Impl.execute(Executor.java:457)
                                at ome.services.util.Executor$Impl.execute(Executor.java:401)
                                at ome.services.throttling.Adapter.run(Adapter.java:51)
                                at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
                                at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:163)
                                at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218)
                                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 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 $Proxy102.saveToDB_async(Unknown Source)
                                at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:84)
                                at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:246)
                                at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:388)
                                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:662)
                        "
    serverExceptionClass = "ome.conditions.ValidationException"
    message = "not-null property references a null or transient value: ome.model.acquisition.LightSettings.lightSource; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.acquisition.LightSettings.lightSource"
        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.createUserException(BasicStream.java:2615)
        at IceInternal.BasicStream.access$300(BasicStream.java:12)
        at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3406)
        at IceInternal.BasicStream.throwException(BasicStream.java:2077)
        at IceInternal.Outgoing.throwUserException(Outgoing.java:538)
        at omero.api._MetadataStoreDelM.saveToDB(_MetadataStoreDelM.java:184)
        at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:573)
        at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:545)
        at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:1896)
        ... 34 more
}

        at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:627) ~[blitz.jar:na]
        at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:301) [blitz.jar:na]
        at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) [blitz.jar:na]
        at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) [blitz.jar:na]
        at IceInternal.Incoming.invoke(Incoming.java:222) [ice.jar:na]
        at Ice.ConnectionI.invokeAll(ConnectionI.java:2482) [ice.jar:na]
        at Ice.ConnectionI.dispatch(ConnectionI.java:1258) [ice.jar:na]
        at Ice.ConnectionI.message(ConnectionI.java:1213) [ice.jar:na]
        at IceInternal.ThreadPool.run(ThreadPool.java:321) [ice.jar:na]
        at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693) [ice.jar:na]
        at java.lang.Thread.run(Thread.java:662) [na:1.6.0_35]
2014-10-17 14:18:27,914 245688     [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import
java.lang.Exception: Import failure
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:526) ~[blitz.jar:na]
        at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) ~[blitz.jar:na]
        at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]
        at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:737) [blitz.jar:na]
2014-10-17 14:18:27,914 245688     [      main] INFO         ome.formats.importer.ImportLibrary - Exiting on error

==> Summary
1024 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:03:22.699

Change History (6)

comment:1 Changed 9 years ago by jamoore

  • Cc jburel mlinkert added
  • Component changed from General to Import
  • Milestone changed from Unscheduled to 5.1.0-m4
  • Priority changed from minor to major

Bumping.

comment:2 Changed 9 years ago by jamoore

  • Cc mtbc added

If I can get Hibernate 3.6 in, I'll retry this.

comment:3 Changed 9 years ago by jamoore

  • Owner changed from jmoore to jamoore

comment:4 Changed 9 years ago by mlinkert

  • Component changed from Import to Bio-Formats
  • Owner changed from jamoore to mlinkert

Nearly have this working; expecting to have a PR by the weekend.

comment:5 Changed 9 years ago by mlinkert

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

PR opened: ​https://github.com/openmicroscopy/openmicroscopy/pull/3486

comment:6 Changed 9 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [e7fbff5bb4b545c077b4cbb485ae4b09033d705c/ome.git] on branch develop) Make LightSettings? indexing work with Channel and MicrobeamManipulation?

A LightSettings? object can be attached to either a Channel (with 2
indexes) or a MicrobeamManipulation? (with 3 indexes). This removes the
hard-coded index counts and updates ReferenceProcessor? to fill in the
index map appropriately for both cases. This should prevent
OMEXMLModelComparator from incorrectly detecting the LSID equality when
there are many of both types of LightSettings? linkages.

Fixes #12603.

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