blosc problem on import of ome.zarr into OMERO #76

pwalczysko · 2024-01-23T15:28:48Z

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

omero import --depth=10 18188.zarr
....
2024-01-23 13:50:08,928 5965       [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.UnsatisfiedLinkError: Unable to load library 'blosc': Native library (linux-aarch64/libblosc.so) not found in resource path 
...

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:

the error with the Unable to find library blosc was fixed, but, instead, we have an IndexOOBounds error which is described in Index Out Of Bounds when importing to OMERO docker #77

Full error in

omero import --depth=10 18188.zarr
...
2024-01-23 13:50:08,928 5965       [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.UnsatisfiedLinkError: Unable to load library 'blosc': Native library (linux-aarch64/libblosc.so) not found in resource path (lib/server/commons-collections4.jar:lib/server/objenesis.jar:lib/server/jgoodies-forms.jar:lib/server/omero-gateway.jar:lib/server/aircompressor.jar:lib/server/serializer.jar:lib/server/commons-lang.jar:lib/server/spring-context-support.jar:lib/server/omero-romio.jar:lib/server/spring-context.jar:lib/server/metrics-jvm.jar:lib/server/batik-gvt.jar:lib/server/lucene-core.jar:lib/server/sketches-core.jar:lib/server/turbojpeg.jar:lib/server/jackson-databind.jar:lib/server/omero-common.jar:lib/server/lucene-spellchecker.jar:lib/server/jblosc.jar:lib/server/metrics-graphite.jar:lib/server/calcite-linq4j.jar:lib/server/icegrid.jar:lib/server/jgoodies-common.jar:lib/server/hibernate-commons-annotations.jar:lib/server/xalan.jar:lib/server/rhino.jar:lib/server/metadata-extractor.jar:lib/server/udunits.jar:lib/server/jzarr.jar:lib/server/ehcache.jar:lib/server/commons-io.jar:lib/server/spring-messaging.jar:lib/server/batik-svg-dom.jar:lib/server/snakeyaml.jar:lib/server/spring-security-core.jar:lib/server/jackson-dataformat-yaml.jar:lib/server/metakit.jar:lib/server/fontbox.jar:lib/server/httpcore.jar:lib/server/batik-slideshow.jar:lib/server/xmpcore.jar:lib/server/lucene-highlighter.jar:lib/server/base.jar:lib/server/google-http-client-xml.jar:lib/server/minio.jar:lib/server/spring-expression.jar:lib/server/activation.jar:lib/server/lucene-memory.jar:lib/server/batik-anim.jar:lib/server/re2j.jar:lib/server/omero-server.jar:lib/server/jackson-annotations.jar:lib/server/spring-orm.jar:lib/server/commons-codec.jar:lib/server/json-path.jar:lib/server/quartz.jar:lib/server/lucene-spatial.jar:lib/server/batik-constants.jar:lib/server/metrics-logback.jar:lib/server/jhdf5.jar:lib/server/batik-codec.jar:lib/server/java-image-scaling.jar:lib/server/formats-bsd.jar:lib/server/specification.jar:lib/server/xmlgraphics-commons.jar:lib/server/btm.jar:lib/server/xml-apis.jar:lib/server/batik-css.jar:lib/server/javassist.jar:lib/server/xercesImpl.jar:lib/server/solr-core.jar:lib/server/httpmime.jar:lib/server/jul-to-slf4j.jar:lib/server/batik-script.jar:lib/server/jcip-annotations.jar:lib/server/metrics-core.jar:lib/server/batik-rasterizer-ext.jar:lib/server/perf4j.jar:lib/server/javax.mail.jar:lib/server/annotations.jar:lib/server/batik-rasterizer.jar:lib/server/java-getopt.jar:lib/server/memory.jar:lib/server/ome-codecs.jar:lib/server/xpp3.jar:lib/server/reflectasm.jar:lib/server/lucene-stempel.jar:lib/server/jython.jar:lib/server/hibernate-core.jar:lib/server/batik-ext.jar:lib/server/okio.jar:lib/server/batik-all.jar:lib/server/batik-gui-util.jar:lib/server/OMEZarrReader.jar:lib/server/kryo.jar:lib/server/solr-commons-csv.jar:lib/server/batik-swing.jar:lib/server/ome-jai.jar:lib/server/spring-beans.jar:lib/server/hibernate-search-analyzers.jar:lib/server/spring-jdbc.jar:lib/server/okhttp.jar:lib/server/logback-core.jar:lib/server/batik-ttf2svg.jar:lib/server/lucene-misc.jar:lib/server/json.jar:lib/server/ome-mdbtools.jar:lib/server/ome-common.jar:lib/server/avatica-core.jar:lib/server/avatica-metrics.jar:lib/server/error_prone_annotations.jar:lib/server/junit.jar:lib/server/calcite-core.jar:lib/server/checker-qual.jar:lib/server/glacier2.jar:lib/server/spring-core.jar:lib/server/lucene-smartcn.jar:lib/server/minlog.jar:lib/server/slf4j-api.jar:lib/server/subethasmtp.jar:lib/server/formats-api.jar:lib/server/jxrlib-all.jar:lib/server/httpclient.jar:lib/server/c3p0.jar:lib/server/commons-lang3.jar:lib/server/lucene-analyzers.jar:lib/server/solr-analysis-extras.jar:lib/server/batik-svgrasterizer.jar:lib/server/hazelcast-all.jar:lib/server/listenablefuture.jar:lib/server/batik-dom.jar:lib/server/cdm-core.jar:lib/server/commons-logging.jar:lib/server/batik-awt-util.jar:lib/server/spring-tx.jar:lib/server/icestorm.jar:lib/server/commons-collections.jar:lib/server/bufr.jar:lib/server/antlr.jar:lib/server/spring-ldap-core.jar:lib/server/omero-renderer.jar:lib/server/sqlite-jdbc.jar:lib/server/failureaccess.jar:lib/server/native-lib-loader.jar:lib/server/hamcrest-core.jar:lib/server/hibernate-search.jar:lib/server/jta.jar:lib/server/dom4j.jar:lib/server/spring-aop.jar:lib/server/google-http-client.jar:lib/server/batik-util.jar:lib/server/batik-svgpp.jar:lib/server/formats-gpl.jar:lib/server/commons-compiler.jar:lib/server/janino.jar:lib/server/pdfbox.jar:lib/server/protobuf-java.jar:lib/server/commons-beanutils.jar:lib/server/batik-transcoder.jar:lib/server/jackson-core.jar:lib/server/batik-svgbrowser.jar:lib/server/hibernate-jpa-2.0-api.jar:lib/server/ini4j.jar:lib/server/omero-model.jar:lib/server/ome-poi.jar:lib/server/filters.jar:lib/server/batik-i18n.jar:lib/server/batik-squiggle.jar:lib/server/esri-geometry-api.jar:lib/server/javax.activation.jar:lib/server/batik-parser.jar:lib/server/spring-jms.jar:lib/server/aopalliance.jar:lib/server/xml-apis-ext.jar:lib/server/spring-security-ldap.jar:lib/server/batik-squiggle-ext.jar:lib/server/batik-svggen.jar:lib/server/jna.jar:lib/server/guava.jar:lib/server/httpservices.jar:lib/server/joda-time.jar:lib/server/postgresql.jar:lib/server/batik-xml.jar:lib/server/commons-dbcp2.jar:lib/server/commons-pool2.jar:lib/server/j2objc-annotations.jar:lib/server/batik-bridge.jar:lib/server/logback-classic.jar:lib/server/aggdesigner-algorithm.jar:lib/server/jamon.jar:lib/server/jcl-over-slf4j.jar:lib/server/JWlz.jar:lib/server/omero-blitz.jar:lib/server/ome-xml.jar:lib/server/batik-extension.jar:lib/server/ice.jar:lib/server/solr-solrj.jar:etc/::*:%OMERO_PROFILE%::%OMERO_PROFILE%*)
	at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:277)
	at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:403)
	at com.sun.jna.Native.register(Native.java:1529)
	at com.sun.jna.Native.register(Native.java:1252)
	at org.blosc.IBloscDll.<clinit>(IBloscDll.java:15)
	at com.bc.zarr.CompressorFactory$BloscCompressor.cbufferSizes(CompressorFactory.java:352)
	at com.bc.zarr.CompressorFactory$BloscCompressor.uncompress(CompressorFactory.java:338)
	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:465)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:167)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
	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$2.doWork(HandleI.java:380)
	at jdk.internal.reflect.GeneratedMethodAccessor299.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.Executor$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.$Proxy73.doWork(Unknown Source)
	at ome.services.util.Executor$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)

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

omero import --depth=10 18188.zarr

2024-01-23 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$BloscCompressor.cbufferSizes(CompressorFactory.java:371)
	at com.bc.zarr.CompressorFactory$BloscCompressor.uncompress(CompressorFactory.java:357)
	at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.read(ChunkReaderWriterImpl_Byte.java:50)
	at com.bc.zarr.ZarrArray.read(ZarrArray.java:282)
	at com.bc.zarr.ZarrArray.read(ZarrArray.java:259)
	at loci.formats.services.JZarrServiceImpl.readBytes(JZarrServiceImpl.java:266)
	at loci.formats.in.ZarrReader.openBytes(ZarrReader.java:491)
	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$2.doWork(HandleI.java:380)
	at jdk.internal.reflect.GeneratedMethodAccessor293.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.Executor$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.$Proxy81.doWork(Unknown Source)
	at ome.services.util.Executor$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=Could not initialize class org.blosc.IBloscDll}

	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.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
	at com.bc.zarr.CompressorFactory$BloscCompressor.cbufferSizes(CompressorFactory.java:371)
	at com.bc.zarr.CompressorFactory$BloscCompressor.uncompress(CompressorFactory.java:357)
	at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.read(ChunkReaderWriterImpl_Byte.java:50)
	at com.bc.zarr.ZarrArray.read(ZarrArray.java:282)
	at com.bc.zarr.ZarrArray.read(ZarrArray.java:259)
	at loci.formats.services.JZarrServiceImpl.readBytes(JZarrServiceImpl.java:266)
	at loci.formats.in.ZarrReader.openBytes(ZarrReader.java:491)
	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$2.doWork(HandleI.java:380)
	at jdk.internal.reflect.GeneratedMethodAccessor293.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.Executor$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.$Proxy81.doWork(Unknown Source)
	at ome.services.util.Executor$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=Could not initialize class org.blosc.IBloscDll}

	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 13:55:50,065 5619       [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 13:55:50,065 5619       [2-thread-1] INFO         ome.formats.importer.ImportLibrary - Exiting on error

The text was updated successfully, but these errors were encountered:

pwalczysko · 2024-01-23T15:29:02Z

cc @jburel @sbesson @will-moore

pwalczysko · 2024-01-23T15:52:13Z

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]
...

pwalczysko · 2024-01-23T16:29:29Z

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 ome/omero-server-docker#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

This was referenced Jan 23, 2024

WiP Blosc ome/omero-server-docker#88

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Index Out Of Bounds when importing to OMERO docker #77

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blosc problem on import of ome.zarr into OMERO #76

blosc problem on import of ome.zarr into OMERO #76

pwalczysko commented Jan 23, 2024 •

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pwalczysko commented Jan 23, 2024

pwalczysko commented Jan 23, 2024

pwalczysko commented Jan 23, 2024

blosc problem on import of ome.zarr into OMERO #76

blosc problem on import of ome.zarr into OMERO #76

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pwalczysko commented Jan 23, 2024

pwalczysko commented Jan 23, 2024

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