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CZI : Processing on server failed

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CZI : Processing on server failed

Postby sukunis » Thu Apr 04, 2019 11:47 am

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
sukunis
 
Posts: 16
Joined: Fri Sep 18, 2015 8:12 am
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Re: CZI : Processing on server failed

Postby jmoore » Fri Apr 05, 2019 10:55 am

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.
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jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany
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Re: CZI : Processing on server failed

Postby mtbc » Mon Apr 08, 2019 9:44 am

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
User avatar
mtbc
Team Member
 
Posts: 282
Joined: Tue Oct 23, 2012 10:59 am
Location: Dundee, Scotland
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Re: CZI : Processing on server failed

Postby sukunis » Tue Apr 16, 2019 11:22 am

Hello,

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

Regards,
Susanne
sukunis
 
Posts: 16
Joined: Fri Sep 18, 2015 8:12 am
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Re: CZI : Processing on server failed

Postby mtbc » Tue Apr 16, 2019 11:52 am

I'm glad you figured it out Susanne. :) Thank you for letting us know!

Cheers,
Mark
User avatar
mtbc
Team Member
 
Posts: 282
Joined: Tue Oct 23, 2012 10:59 am
Location: Dundee, Scotland
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