Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Index Out Of Bounds when importing to OMERO docker #77

Open
pwalczysko opened this issue Jan 25, 2024 · 0 comments
Open

Index Out Of Bounds when importing to OMERO docker #77

pwalczysko opened this issue Jan 25, 2024 · 0 comments

Comments

@pwalczysko
Copy link
Member

pwalczysko commented Jan 25, 2024 •
edited
Loading

Workflow:

On Mac M1,

  1. pull the image khaledk2/omero-server:arm where there is blosc installed.
  2. Run the image via docker-compose up inside the docker-example-omero repo - see my docker-compose.yml file on a branch https://github.com/pwalczysko/docker-example-omero/blob/server-good/docker-compose.yml
  3. Try to import an ...ome.zarr file compressed with blosc, observe error IndexOutOfBounds...

cc @khaledk2 @dgault @sbesson @will-moore

See also #76.

Note: three setups with the same docker-compose.yml file tried

  • on merge-ci
  • on Mac with amd architecture
  • on Mac with arm architecture (M1)

this problem only occurs in the M1 case.

2024-01-25 13:15:45,470 10394      [l.Client-1] 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$2.doWork(HandleI.java:380)
	at jdk.internal.reflect.GeneratedMethodAccessor270.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.Executor$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$2.doWork(HandleI.java:380)
	at jdk.internal.reflect.GeneratedMethodAccessor270.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.Executor$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)
2024-01-25 13:15:45,484 10408      [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)
2024-01-25 13:15:45,484 10408      [2-thread-1] INFO         ome.formats.importer.ImportLibrary - Exiting on error
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@pwalczysko