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CZI : Processing on server failed

https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8723

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CZI : Processing on server failed

PostPosted: Thu Apr 04, 2019 11:47 am
by sukunis
Hello,

i have problems with the import of our CZI file format on Zeiss Axio Observer.Z1 (ZEN 2012-blue edition v1.1.2.0) .
For some files the import processing step is terminated with the following error:
Code: Select all
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: error-on-init
Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index: 3, Size: 2
   at java.util.ArrayList.rangeCheck(ArrayList.java:657)
   at java.util.ArrayList.get(ArrayList.java:433)
   at ome.xml.model.Instrument.getLightSource(Instrument.java:353)
   at ome.xml.meta.OMEXMLMetadataImpl.setLaserID(OMEXMLMetadataImpl.java:9512)
   at ome.xml.meta.FilterMetadata.setLaserID(FilterMetadata.java:1557)
   at loci.formats.in.ZeissCZIReader.translateInformation(ZeissCZIReader.java:2233)
   at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1915)
   at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:1131)
   at loci.formats.FormatReader.setId(FormatReader.java:1397)
   at loci.formats.ImageReader.setId(ImageReader.java:842)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at loci.formats.Memoizer.setId(Memoizer.java:690)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)
   at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:762)
   at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:244)
   at omero.cmd.HandleI.steps(HandleI.java:438)
   at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)
   at omero.cmd.HandleI$2.doWork(HandleI.java:383)
   at omero.cmd.HandleI$2.doWork(HandleI.java:380)
   at sun.reflect.GeneratedMethodAccessor320.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:498)
   at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
   at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:573)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at com.sun.proxy.$Proxy72.doWork(Unknown Source)
   at ome.services.util.Executor$Impl.execute(Executor.java:452)
   at omero.cmd.HandleI.run(HandleI.java:379)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
   at ome.services.util.Executor$Impl$1.call(Executor.java:493)
   at java.util.concurrent.FutureTask.run(FutureTask.java:266)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
   at java.lang.Thread.run(Thread.java:748)
, message=Index: 3, Size: 2}

   at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:756)
   at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)
   at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
   at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
   at IceInternal.Incoming.invoke(Incoming.java:221)
   at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
   at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
   at Ice.ConnectionI.message(ConnectionI.java:1056)
   at IceInternal.ThreadPool.run(ThreadPool.java:395)
   at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
   at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
   at java.lang.Thread.run(Thread.java:748)

   at org.openmicroscopy.shoola.env.data.util.Status.update(Status.java:601)
   at ome.formats.importer.ImportLibrary.notifyObservers(ImportLibrary.java:254)
   at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:762)
   at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)
   at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
   at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
   at IceInternal.Incoming.invoke(Incoming.java:221)
   at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
   at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
   at Ice.ConnectionI.message(ConnectionI.java:1056)
   at IceInternal.ThreadPool.run(ThreadPool.java:395)
   at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
   at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
   at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: error-on-init
Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index: 3, Size: 2
   at java.util.ArrayList.rangeCheck(ArrayList.java:657)
   at java.util.ArrayList.get(ArrayList.java:433)
   at ome.xml.model.Instrument.getLightSource(Instrument.java:353)
   at ome.xml.meta.OMEXMLMetadataImpl.setLaserID(OMEXMLMetadataImpl.java:9512)
   at ome.xml.meta.FilterMetadata.setLaserID(FilterMetadata.java:1557)
   at loci.formats.in.ZeissCZIReader.translateInformation(ZeissCZIReader.java:2233)
   at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1915)
   at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:1131)
   at loci.formats.FormatReader.setId(FormatReader.java:1397)
   at loci.formats.ImageReader.setId(ImageReader.java:842)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at loci.formats.Memoizer.setId(Memoizer.java:690)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
   at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)
   at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:762)
   at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:244)
   at omero.cmd.HandleI.steps(HandleI.java:438)
   at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)
   at omero.cmd.HandleI$2.doWork(HandleI.java:383)
   at omero.cmd.HandleI$2.doWork(HandleI.java:380)
   at sun.reflect.GeneratedMethodAccessor320.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:498)
   at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
   at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:573)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at com.sun.proxy.$Proxy72.doWork(Unknown Source)
   at ome.services.util.Executor$Impl.execute(Executor.java:452)
   at omero.cmd.HandleI.run(HandleI.java:379)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
   at ome.services.util.Executor$Impl$1.call(Executor.java:493)
   at java.util.concurrent.FutureTask.run(FutureTask.java:266)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
   at java.lang.Thread.run(Thread.java:748)
, message=Index: 3, Size: 2}

   at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:756)
   ... 11 more



Open the file with bftools/showinf produced no error.

Sorry, I can't use the QA System to upload a sample file.
Should i pass it to Josh?

Best,
Susanne

Re: CZI : Processing on server failed

PostPosted: Fri Apr 05, 2019 10:55 am
by jmoore
Thanks for sending the file `Experiment-369.czi`, Susanne. I've placed it in the inbox for further investigation. Do you have any feeling for how many of the files? and is it only newer ones?

~Josh.

Re: CZI : Processing on server failed

PostPosted: Mon Apr 08, 2019 9:44 am
by mtbc
Dear Susanne,

Thank you for the report and sample image. Experiment-369.czi imports and looks fine to me with OMERO 5.4.10. I expect that the bug you are seeing is already fixed so that you will be able to import your images just fine when you are using a current OMERO. I'd be happy to create you an account on our demo server should you wish to try with any other images, if so then just ask.

Cheers,
Mark

Re: CZI : Processing on server failed

PostPosted: Tue Apr 16, 2019 11:22 am
by sukunis
Hello,

i'm sorry - the exception is due my reader implementation.
Excuses the circumstances!

Regards,
Susanne

Re: CZI : Processing on server failed

PostPosted: Tue Apr 16, 2019 11:52 am
by mtbc
I'm glad you figured it out Susanne. :) Thank you for letting us know!

Cheers,
Mark
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