Under 5.2 Omero importer fails to transfer nd files.
Import log
2015-11-17 11:25:05,721 INFO [ ome.formats.OMEROMetadataStoreClient] (2-thread-4) Call context: {omero.logfilename:root_0/2015-11/17/11-25-03.603.log}
2015-11-17 11:25:05,729 INFO [ ome.security.basic.EventHandler] (erver-1101) Auth: user=0,group=3,event=null(User),sess=2f9551bf-e3f1-411c-886b-25dcbf19200b
2015-11-17 11:25:05,838 INFO [ loci.formats.ImageReader] (2-thread-4) MetamorphReader initializing /OMERO/ManagedRepository/root_0/2015-11/17/11-25-03.603/1_w1Single SPI 405.TIF
2015-11-17 11:25:05,838 INFO [ loci.formats.in.MinimalTiffReader] (2-thread-4) Reading IFDs
2015-11-17 11:25:05,839 INFO [ loci.formats.in.MinimalTiffReader] (2-thread-4) Populating metadata
2015-11-17 11:25:05,842 INFO [ loci.formats.in.BaseTiffReader] (2-thread-4) Populating OME metadata
2015-11-17 11:25:05,863 DEBUG [ loci.formats.Memoizer] (2-thread-4) start[1447755905763] time[99] tag[loci.formats.Memoizer.setId]
2015-11-17 11:25:05,863 INFO [ o.s.b.r.ManagedImportRequestI.@7019d5f1] (2-thread-4) Cancelled
2015-11-17 11:25:05,879 INFO [ ome.security.basic.EventHandler] (erver-1087) Auth: user=0,group=3,event=1491688(User),sess=2f9551bf-e3f1-411c-886b-25dcbf19200b
2015-11-17 11:25:05,881 DEBUG [ omero.util.ServantHolder] (erver-1087) Removed omero.api._RawFileStoreTie@737ba81c from omero.util.ServantHolder@4345926 as 4016a300-41e4-4d5a-8c2f-64f5eec39a01omero.api.RawFileStore
2015-11-17 11:25:05,881 INFO [ omero.cmd.SessionI] (erver-1087) Unregistered servant:2f9551bf-e3f1-411c-886b-25dcbf19200b/4016a300-41e4-4d5a-8c2f-64f5eec39a01omero.api.RawFileStore(omero.api._RawFileStoreTie@737ba81c)
2015-11-17 11:25:05,899 INFO [ ome.security.basic.EventHandler] (erver-1101) Auth: user=0,group=3,event=1491689(User),sess=2f9551bf-e3f1-411c-886b-25dcbf19200b
2015-11-17 11:25:05,900 DEBUG [ omero.util.ServantHolder] (erver-1101) Removed omero.api._RawPixelsStoreTie@a902ae05 from omero.util.ServantHolder@4345926 as a36e0a63-8609-47c5-a6a2-4c95166a549eomero.api.RawPixelsStore
2015-11-17 11:25:05,900 INFO [ omero.cmd.SessionI] (erver-1101) Unregistered servant:2f9551bf-e3f1-411c-886b-25dcbf19200b/a36e0a63-8609-47c5-a6a2-4c95166a549eomero.api.RawPixelsStore(omero.api._RawPixelsStoreTie@a902ae05)
2015-11-17 11:25:05,902 INFO [ ome.security.basic.EventHandler] (erver-1101) Auth: user=0,group=3,event=null(User),sess=2f9551bf-e3f1-411c-886b-25dcbf19200b
2015-11-17 11:25:05,903 DEBUG [ omero.util.ServantHolder] (erver-1101) Removed omero.api._ThumbnailStoreTie@82705048 from omero.util.ServantHolder@4345926 as 4ec6d522-bb1e-420f-bd5a-01196ac07456omero.api.ThumbnailStore
2015-11-17 11:25:05,904 INFO [ omero.cmd.SessionI] (erver-1101) Unregistered servant:2f9551bf-e3f1-411c-886b-25dcbf19200b/4ec6d522-bb1e-420f-bd5a-01196ac07456omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie@82705048)
2015-11-17 11:25:05,904 DEBUG [ omero.util.ServantHolder] (erver-1102) Removed omero.api._MetadataStoreTie@9171c4ca from omero.util.ServantHolder@4345926 as 36520035-4d70-4566-be6a-97bfa665fa0bomero.api.MetadataStore
2015-11-17 11:25:05,904 INFO [ omero.cmd.SessionI] (erver-1102) Unregistered servant:2f9551bf-e3f1-411c-886b-25dcbf19200b/36520035-4d70-4566-be6a-97bfa665fa0bomero.api.MetadataStore(omero.api._MetadataStoreTie@9171c4ca)
2015-11-17 11:25:05,904 INFO [ o.s.blitz.repo.ManagedImportRequestI] (2-thread-4) Finalizing log file.
Exception
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: error-on-init
Parameters: {message=Non-terminating decimal expansion; no exact representable decimal result., stacktrace=java.lang.ArithmeticException: Non-terminating decimal expansion; no exact representable decimal result.
at java.math.BigDecimal.divide(BigDecimal.java:1616)
at loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:810)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.Memoizer.setId(Memoizer.java:678)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:404)
at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:634)
at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:227)
at omero.cmd.HandleI.steps(HandleI.java:428)
at omero.cmd.HandleI$1.doWork(HandleI.java:366)
at omero.cmd.HandleI$1.doWork(HandleI.java:362)
at sun.reflect.GeneratedMethodAccessor295.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$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.$Proxy70.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:443)
at omero.cmd.HandleI.run(HandleI.java:360)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at ome.services.util.Executor$Impl$1.call(Executor.java:484)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
}
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:663)
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: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:745)
at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:678)
at ome.formats.importer.ImportLibrary.notifyObservers(ImportLibrary.java:251)
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:669)
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: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:745)
Caused by: java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: error-on-init
Parameters: {message=Non-terminating decimal expansion; no exact representable decimal result., stacktrace=java.lang.ArithmeticException: Non-terminating decimal expansion; no exact representable decimal result.
at java.math.BigDecimal.divide(BigDecimal.java:1616)
at loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:810)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.Memoizer.setId(Memoizer.java:678)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:404)
at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:634)
at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:227)
at omero.cmd.HandleI.steps(HandleI.java:428)
at omero.cmd.HandleI$1.doWork(HandleI.java:366)
at omero.cmd.HandleI$1.doWork(HandleI.java:362)
at sun.reflect.GeneratedMethodAccessor295.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$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.$Proxy70.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:443)
at omero.cmd.HandleI.run(HandleI.java:360)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at ome.services.util.Executor$Impl$1.call(Executor.java:484)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
}
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:663)
... 11 more
In fact it's a bioformat problem, I got the same exception when I try to open the nd files in Fiji.
Philippe
