Open pwalczysko opened 6 months ago
cc @jburel @sbesson @will-moore
The corresponding error from the Blitz-0.log is
...
2024-01-23 15:38:24,725 INFO [ ome.security.basic.EventHandler] (.Server-10) Auth: user=0,group=0,event=null(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,731 INFO [ org.perf4j.TimingLogger] (.Server-10) start[1706024304723] time[7] tag[omero.call.success.ome.logic.MetadataImpl.loadLogFiles]
2024-01-23 15:38:24,731 INFO [ ome.services.util.ServiceHandler] (.Server-10) Rslt: {52=(ome.model.core.OriginalFile:Id_343)}
2024-01-23 15:38:24,737 DEBUG [ loci.formats.Memoizer] (2-thread-4) saved to temp file: /OMERO/BioFormatsCache/OMERO/ManagedRepository/root_0/2024-01/23/15-38-23.609/18188.zarr/0/0/.0.bfmemo3665809805424360812
2024-01-23 15:38:24,737 DEBUG [ loci.formats.Memoizer] (2-thread-4) start[1706024304716] time[20] tag[loci.formats.Memoizer.saveMemo]
2024-01-23 15:38:24,737 DEBUG [ loci.formats.Memoizer] (2-thread-4) saved memo file: /OMERO/BioFormatsCache/OMERO/ManagedRepository/root_0/2024-01/23/15-38-23.609/18188.zarr/0/0/.0.bfmemo (35545 bytes)
2024-01-23 15:38:24,737 DEBUG [ loci.formats.Memoizer] (2-thread-4) start[1706024304663] time[73] tag[loci.formats.Memoizer.setId]
2024-01-23 15:38:24,738 INFO [ o.s.blitz.repo.ManagedImportRequestI] (2-thread-4) File format: Zarr
2024-01-23 15:38:24,738 INFO [ o.s.blitz.repo.ManagedImportRequestI] (2-thread-4) Base reader: loci.formats.in.ZarrReader
2024-01-23 15:38:24,738 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304606] time[131] tag[omero.import.request.init]
2024-01-23 15:38:24,738 INFO [ ome.formats.OMEROMetadataStoreClient] (2-thread-4) Handling # of containers: 5
2024-01-23 15:38:24,739 INFO [ ome.services.util.ServiceHandler] (.Server-11) Executor.doWork -- ome.services.blitz.impl.MetadataStoreI.updateObjects[]
2024-01-23 15:38:24,739 INFO [ ome.services.util.ServiceHandler] (.Server-11) Args: [null, InternalSF@1761040949]
2024-01-23 15:38:24,740 INFO [ ome.security.basic.BasicEventContext] (.Server-11) cctx: group=0
2024-01-23 15:38:24,741 INFO [ ome.security.basic.EventHandler] (.Server-11) Auth: user=0,group=0,event=null(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,742 INFO [ org.perf4j.TimingLogger] (.Server-11) start[1706024304739] time[3] tag[omero.call.success.ome.services.blitz.impl.MetadataStoreI$4.doWork]
2024-01-23 15:38:24,742 INFO [ ome.services.util.ServiceHandler] (.Server-11) Rslt: null
2024-01-23 15:38:24,742 INFO [ ome.formats.OMEROMetadataStoreClient] (2-thread-4) Handling # of references: 0
2024-01-23 15:38:24,744 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Executor.doWork -- ome.services.blitz.impl.MetadataStoreI.saveToDb[]
2024-01-23 15:38:24,744 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Args: [null, InternalSF@1761040949]
2024-01-23 15:38:24,744 INFO [ ome.security.basic.BasicEventContext] (l.Server-7) cctx: group=0
2024-01-23 15:38:24,758 INFO [ ome.security.basic.EventHandler] (l.Server-7) Auth: user=0,group=0,event=2606(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,768 INFO [ ome.security.basic.CurrentDetails] (l.Server-7) Adding log:INSERT,class ome.model.core.Image,52
2024-01-23 15:38:24,770 INFO [ ome.security.basic.CurrentDetails] (l.Server-7) Adding log:INSERT,class ome.model.core.Pixels,52
2024-01-23 15:38:24,771 INFO [ ome.security.basic.CurrentDetails] (l.Server-7) Adding log:INSERT,class ome.model.core.LogicalChannel,52
2024-01-23 15:38:24,773 INFO [ ome.security.basic.CurrentDetails] (l.Server-7) Adding log:INSERT,class ome.model.core.Channel,52
2024-01-23 15:38:24,775 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1706024304759] time[16] tag[omero.saveImportGraph]
2024-01-23 15:38:24,785 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1706024304744] time[41] tag[omero.call.success.ome.services.blitz.impl.MetadataStoreI$3.doWork]
2024-01-23 15:38:24,785 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Rslt: {Image=(ome.model.core.Image:Id_52), Pixels=(ome.model.core.Pixels:Id_52), Plate=null}
2024-01-23 15:38:24,787 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304738] time[48] tag[omero.import.request.metadata]
2024-01-23 15:38:24,787 INFO [ ome.services.util.ServiceHandler] (.Server-10) Meth: interface ome.api.IQuery.get
2024-01-23 15:38:24,788 INFO [ ome.services.util.ServiceHandler] (.Server-10) Args: [class ome.model.core.OriginalFile, 343]
2024-01-23 15:38:24,789 INFO [ ome.security.basic.BasicEventContext] (.Server-10) cctx: group=0
2024-01-23 15:38:24,791 INFO [ ome.security.basic.EventHandler] (.Server-10) Auth: user=0,group=0,event=null(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,793 INFO [ org.perf4j.TimingLogger] (.Server-10) start[1706024304788] time[5] tag[omero.call.success.ome.logic.QueryImpl.get]
2024-01-23 15:38:24,793 INFO [ ome.services.util.ServiceHandler] (.Server-10) Rslt: ome.model.core.OriginalFile:Id_343
2024-01-23 15:38:24,794 INFO [ ome.services.util.ServiceHandler] (.Server-11) Meth: interface ome.api.IUpdate.saveObject
2024-01-23 15:38:24,794 INFO [ ome.services.util.ServiceHandler] (.Server-11) Args: [ome.model.core.OriginalFile:Id_343]
2024-01-23 15:38:24,795 INFO [ ome.security.basic.BasicEventContext] (.Server-11) cctx: group=0
2024-01-23 15:38:24,802 INFO [ ome.security.basic.EventHandler] (.Server-11) Auth: user=0,group=0,event=2607(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,805 INFO [ ome.security.basic.CurrentDetails] (.Server-11) Adding log:UPDATE,class ome.model.core.OriginalFile,343
2024-01-23 15:38:24,808 INFO [ org.perf4j.TimingLogger] (.Server-11) start[1706024304794] time[13] tag[omero.call.success.ome.logic.UpdateImpl.saveObject]
2024-01-23 15:38:24,808 INFO [ ome.services.util.ServiceHandler] (.Server-11) Rslt: null
2024-01-23 15:38:24,809 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304738] time[70] tag[omero.import.request.step]
2024-01-23 15:38:24,809 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304738] time[70] tag[omero.request.step.0]
2024-01-23 15:38:24,809 INFO [ o.s.b.r.ManagedImportRequestI.@603ef8f9] (2-thread-4) notify step 1 of 5
2024-01-23 15:38:24,810 INFO [ o.s.b.r.ManagedImportRequestI.@603ef8f9] (2-thread-4) Cancelled
2024-01-23 15:38:24,811 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Meth: interface ome.api.IQuery.get
2024-01-23 15:38:24,811 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Args: [class ome.model.core.OriginalFile, 343]
2024-01-23 15:38:24,812 INFO [ ome.security.basic.BasicEventContext] (l.Server-7) cctx: group=0
2024-01-23 15:38:24,813 INFO [ ome.security.basic.EventHandler] (l.Server-7) Auth: user=0,group=0,event=null(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,815 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1706024304811] time[3] tag[omero.call.success.ome.logic.QueryImpl.get]
2024-01-23 15:38:24,815 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Rslt: ome.model.core.OriginalFile:Id_343
2024-01-23 15:38:24,816 INFO [ ome.services.util.ServiceHandler] (.Server-10) Meth: interface ome.api.IUpdate.saveObject
2024-01-23 15:38:24,816 INFO [ ome.services.util.ServiceHandler] (.Server-10) Args: [ome.model.core.OriginalFile:Id_343]
2024-01-23 15:38:24,816 INFO [ ome.security.basic.BasicEventContext] (.Server-10) cctx: group=0
2024-01-23 15:38:24,823 INFO [ ome.security.basic.EventHandler] (.Server-10) Auth: user=0,group=0,event=2608(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,825 INFO [ ome.security.basic.CurrentDetails] (.Server-10) Adding log:UPDATE,class ome.model.core.OriginalFile,343
2024-01-23 15:38:24,828 INFO [ org.perf4j.TimingLogger] (.Server-10) start[1706024304816] time[12] tag[omero.call.success.ome.logic.UpdateImpl.saveObject]
2024-01-23 15:38:24,829 INFO [ ome.services.util.ServiceHandler] (.Server-10) Rslt: null
2024-01-23 15:38:24,829 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304809] time[19] tag[omero.import.request.step]
2024-01-23 15:38:24,829 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304809] time[20] tag[omero.request.step.1]
2024-01-23 15:38:24,829 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304606] time[222] tag[omero.request]
2024-01-23 15:38:24,829 INFO [ org.perf4j.TimingLogger] (2-thread-4) start[1706024304598] time[230] tag[omero.call.exception]
2024-01-23 15:38:24,829 INFO [ ome.services.util.ServiceHandler] (2-thread-4) Excp: omero.cmd.HandleI$Cancel: import-request-failure
2024-01-23 15:38:24,829 DEBUG [ o.s.b.r.ManagedImportRequestI.@603ef8f9] (2-thread-4) Request cancelled by java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
2024-01-23 15:38:24,830 INFO [ ome.services.util.ServiceHandler] (.Server-11) Meth: interface ome.api.StatefulServiceInterface.close
2024-01-23 15:38:24,830 INFO [ ome.services.util.ServiceHandler] (.Server-11) Args: ()
2024-01-23 15:38:24,831 INFO [ ome.security.basic.BasicEventContext] (.Server-11) cctx: group=0
2024-01-23 15:38:24,837 INFO [ ome.security.basic.EventHandler] (.Server-11) Auth: user=0,group=0,event=2609(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,839 INFO [ org.perf4j.TimingLogger] (.Server-11) start[1706024304830] time[8] tag[omero.call.success.ome.services.RawFileBean.close]
2024-01-23 15:38:24,839 INFO [ ome.services.util.ServiceHandler] (.Server-11) Rslt: null
2024-01-23 15:38:24,839 INFO [ ome.services.util.ServiceHandler] (.Server-11) Cleanup: ome.services.RawFileBean@5231077b
2024-01-23 15:38:24,839 INFO [ omero.cmd.SessionI] (.Server-11) Unregistered servant:49050db0-d57a-43e3-b2e1-0f8439dc10ac/f61b464d-47d8-4a0f-90cb-e4167198170domero.api.RawFileStore(omero.api._RawFileStoreTie@1d74443)
2024-01-23 15:38:24,839 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Meth: interface ome.api.StatefulServiceInterface.close
2024-01-23 15:38:24,839 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Args: ()
2024-01-23 15:38:24,840 INFO [ ome.security.basic.BasicEventContext] (l.Server-7) cctx: group=0
2024-01-23 15:38:24,845 INFO [ ome.security.basic.EventHandler] (l.Server-7) Auth: user=0,group=0,event=2610(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,847 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1706024304839] time[7] tag[omero.call.success.ome.services.RawPixelsBean.close]
2024-01-23 15:38:24,847 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Rslt: null
2024-01-23 15:38:24,847 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Cleanup: ome.services.RawPixelsBean@32c62652
2024-01-23 15:38:24,847 INFO [ omero.cmd.SessionI] (l.Server-7) Unregistered servant:49050db0-d57a-43e3-b2e1-0f8439dc10ac/a66e0d04-4fdb-469f-a914-5fa9eed0103fomero.api.RawPixelsStore(omero.api._RawPixelsStoreTie@3e26b4fc)
2024-01-23 15:38:24,848 INFO [ ome.services.util.ServiceHandler] (.Server-10) Meth: interface ome.api.StatefulServiceInterface.close
2024-01-23 15:38:24,848 INFO [ ome.services.util.ServiceHandler] (.Server-10) Args: ()
2024-01-23 15:38:24,848 INFO [ ome.security.basic.BasicEventContext] (.Server-10) cctx: group=0
2024-01-23 15:38:24,850 INFO [ ome.security.basic.EventHandler] (.Server-10) Auth: user=0,group=0,event=null(User),sess=49050db0-d57a-43e3-b2e1-0f8439dc10ac
2024-01-23 15:38:24,850 INFO [ org.perf4j.TimingLogger] (.Server-10) start[1706024304848] time[2] tag[omero.call.success.ome.services.ThumbnailBean.close]
2024-01-23 15:38:24,850 INFO [ ome.services.util.ServiceHandler] (.Server-10) Rslt: null
2024-01-23 15:38:24,850 INFO [ ome.services.util.ServiceHandler] (.Server-10) Cleanup: ome.services.ThumbnailBean@7a12c407
2024-01-23 15:38:24,850 INFO [ omero.cmd.SessionI] (.Server-10) Unregistered servant:49050db0-d57a-43e3-b2e1-0f8439dc10ac/3a1d0c58-90b5-498f-a24f-4e53aa935497omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie@c7bd81ab)
2024-01-23 15:38:24,851 INFO [ omero.cmd.SessionI] (.Server-11) Unregistered servant:49050db0-d57a-43e3-b2e1-0f8439dc10ac/35813f3a-ff00-4626-baf5-2d5f96fa37adomero.api.MetadataStore(omero.api._MetadataStoreTie@d3b6fa14)
2024-01-23 15:38:24,851 INFO [ o.s.blitz.repo.ManagedImportRequestI] (2-thread-4) Cleaning up import.
2024-01-23 15:38:24,851 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Executor.doWork -- ome.services.blitz.impl.ServiceFactoryI.isGuest[]
2024-01-23 15:38:24,851 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Args: [null, InternalSF@1761040949]
...
I was able to fix the problem on a RHEL 9 server by
sudo dnf install blosc
Then the import started to work.
Nevertheless, if I install blosc into the docker image as delivered by https://github.com/ome/omero-server-docker/pull/87
(make a change in line https://github.com/ome/omero-server-docker/blob/45f9f7f1e9beb5949e6fcd970503e622c599c0a3/Dockerfile#L14 changing it to RUN dnf install -y ansible-core sudo ca-certificates blosc
then the error changes: Although the blosc is installed and used successfully, I have now
2024-01-23 16:18:15,889 6364 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /Users/pwalczysko/Work/18188.zarr/0/0/0
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=java.lang.IndexOutOfBoundsException
at java.base/java.io.DataInputStream.readFully(DataInputStream.java:197)
at com.bc.zarr.CompressorFactory$BloscCompressor.uncompress(CompressorFactory.java:342)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.read(ChunkReaderWriterImpl_Byte.java:50)
at com.bc.zarr.ZarrArray.read(ZarrArray.java:278)
at com.bc.zarr.ZarrArray.read(ZarrArray.java:255)
at loci.formats.services.JZarrServiceImpl.readBytes(JZarrServiceImpl.java:266)
at loci.formats.in.ZarrReader.openBytes(ZarrReader.java:362)
at loci.formats.ImageReader.openBytes(ImageReader.java:467)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:169)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:231)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:350)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:350)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:872)
at ome.services.blitz.repo.ManagedImportRequestI.parseData(ManagedImportRequestI.java:803)
at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:676)
at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:525)
at omero.cmd.HandleI.steps(HandleI.java:448)
at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)
at omero.cmd.HandleI$2.doWork(HandleI.java:383)
at omero.cmd.HandleI$2.doWork(HandleI.java:380)
at jdk.internal.reflect.GeneratedMethodAccessor281.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy82.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at omero.cmd.HandleI.run(HandleI.java:379)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at ome.services.util.Executor$Impl$1.call(Executor.java:488)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
, message=}
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)
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.base/java.lang.Thread.run(Thread.java:829)
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=java.lang.IndexOutOfBoundsException
at java.base/java.io.DataInputStream.readFully(DataInputStream.java:197)
at com.bc.zarr.CompressorFactory$BloscCompressor.uncompress(CompressorFactory.java:342)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.read(ChunkReaderWriterImpl_Byte.java:50)
at com.bc.zarr.ZarrArray.read(ZarrArray.java:278)
at com.bc.zarr.ZarrArray.read(ZarrArray.java:255)
at loci.formats.services.JZarrServiceImpl.readBytes(JZarrServiceImpl.java:266)
at loci.formats.in.ZarrReader.openBytes(ZarrReader.java:362)
at loci.formats.ImageReader.openBytes(ImageReader.java:467)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:169)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:231)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:350)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:350)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:872)
at ome.services.blitz.repo.ManagedImportRequestI.parseData(ManagedImportRequestI.java:803)
at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:676)
at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:525)
at omero.cmd.HandleI.steps(HandleI.java:448)
at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)
at omero.cmd.HandleI$2.doWork(HandleI.java:383)
at omero.cmd.HandleI$2.doWork(HandleI.java:380)
at jdk.internal.reflect.GeneratedMethodAccessor281.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy82.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at omero.cmd.HandleI.run(HandleI.java:379)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at ome.services.util.Executor$Impl$1.call(Executor.java:488)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
, message=}
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)
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.base/java.lang.Thread.run(Thread.java:829)
2024-01-23 16:18:15,893 6368 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import
java.lang.Exception: Import failure
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)
at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)
at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2024-01-23 16:18:15,893 6368 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error
cc @khaledk2 @jburel @sbesson
On 2 of our servers, we got an error on trying to import ome.zarr into OMERO.
server version 5.6.8 and 5.6.10 tested, same result M1 aarch64 docker image BioFormats 6.11.1 revision: 383bac974cd52e83908b54e4769ebb1e0d0673ee date: 1 December 2022
Edit: This problem got fixed by installing blosc into the docker. Tested two docker images, one built locally and one built by @khaledk2 and pushed to Dockerhub,
khaledk2/omero-server:arm
. Both of those tests had the same outcome:Unable to find library blosc
was fixed, but, instead, we have anIndexOOBounds
error which is described in https://github.com/ome/ZarrReader/issues/77Full error in
2. merge-ci server 5.6.10 CentOS 7 docker BioFormats 6.11.1 revision: 383bac974cd52e83908b54e4769ebb1e0d0673ee date: 1 December 2022
024-01-23 13:55:50,055 5609 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /Users/pwalczysko/Work/18188.zarr/0/0/0 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: import-request-failure Parameters: {stacktrace=java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll at com.bc.zarr.CompressorFactory$BloscCompressor.cbufferSizes(CompressorFactory.java:371)
Edit: This problem got fixed by installation of
blosc
inside the docker which runs the merge-ci server. After that, the import of ome.zarr is working on this server.full stacktrace in