Skip to content

LockTimeout: Import in progress viewing FIBSEM_dino_masks.zarr #25

New issue
New issue
Open
Open
LockTimeout: Import in progress viewing FIBSEM_dino_masks.zarr#25
@will-moore

Description

@will-moore
will-moore
opened on Aug 18, 2025

This Microscopy Nodes sample image is available at a couple of locations, e.g. https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/microscopynodes/20250730/FIBSEM_dino_masks.zarr/

Tried to register it. Both times Images are created in OMERO, but fail to render on merge-ci server:

$ python register.py https://s3.embl.de/microscopynodes/FIBSEM_dino_masks.zarr --target 21519
...
lsid: s3://s3.embl.de/microscopynodes/FIBSEM_dino_masks.zarr/?anonymous=true
Created Image 34632
Linked to Dataset 21519

$ python register.py https://uk1s3.embassy.ebi.ac.uk/idr/share/microscopynodes/20250730/FIBSEM_dino_masks.zarr/ --target 21519
...
lsid: s3://uk1s3.embassy.ebi.ac.uk/idr/share/microscopynodes/20250730/FIBSEM_dino_masks.zarr/?anonymous=true
Created Image 34633
Linked to Dataset 21519

Blitzlog for 2nd image above (same as for 1st image):

2025-08-18 10:47:18,642 INFO  [                 org.perf4j.TimingLogger] (.Server-13) start[1755514038603] time[38] tag[createOmeNgffPixelBuffer()]
2025-08-18 10:47:18,642 INFO  [                 org.perf4j.TimingLogger] (.Server-13) start[1755514038602] time[40] tag[omero.call.exception]
2025-08-18 10:47:18,642 INFO  [        ome.services.util.ServiceHandler] (.Server-13)  Excp:	ome.conditions.LockTimeout: Import in progress.
2025-08-18 10:47:18,642 INFO  [                 org.perf4j.TimingLogger] (.Server-13) start[1755514038599] time[43] tag[omero.call.exception]
2025-08-18 10:47:18,642 INFO  [        ome.services.util.ServiceHandler] (.Server-13)  Excp:	ome.conditions.LockTimeout: Import in progress.
2025-08-18 10:47:18,642 DEBUG [                    omero.util.IceMapper] (.Server-13) Handling:
ome.conditions.LockTimeout: Import in progress.
	at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:656)
	at com.glencoesoftware.omero.zarr.ZarrPixelsService.getPixelBuffer(ZarrPixelsService.java:373)
	at ome.services.RenderingBean$12.doWork(RenderingBean.java:2205)
	at jdk.internal.reflect.GeneratedMethodAccessor300.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.Executor$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$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at ome.tools.hibernate.ProxyCleanupFilter$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.$Proxy74.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:447)
	at ome.services.util.Executor$Impl.execute(Executor.java:392)
	at ome.services.RenderingBean.getPixelBuffer(RenderingBean.java:2202)
	at ome.services.RenderingBean.load(RenderingBean.java:417)
	at jdk.internal.reflect.GeneratedMethodAccessor2338.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy123.load(Unknown Source)
	at jdk.internal.reflect.GeneratedMethodAccessor2338.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.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy123.load(Unknown Source)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
	at ome.services.throttling.Callback.run(Callback.java:56)
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
	at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at omero.cmd.CallContext.invoke(CallContext.java:85)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy125.load_async(Unknown Source)
	at omero.api._RenderingEngineTie.load_async(_RenderingEngineTie.java:248)
	at omero.api._RenderingEngineDisp.___load(_RenderingEngineDisp.java:1223)
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2405)
	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)
2025-08-18 10:47:18,643 DEBUG [                    omero.util.IceMapper] (.Server-13) Handling:
omero.LockTimeout: null
	at omero.util.IceMapper.handleException(IceMapper.java:1389)
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:174)
	at ome.services.throttling.Callback.run(Callback.java:56)
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
	at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	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 omero.cmd.CallContext.invoke(CallContext.java:85)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy125.load_async(Unknown Source)
	at omero.api._RenderingEngineTie.load_async(_RenderingEngineTie.java:248)
	at omero.api._RenderingEngineDisp.___load(_RenderingEngineDisp.java:1223)
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2405)
	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)
2025-08-18 10:47:18,644 INFO  [        ome.services.util.ServiceHandler] (.Server-17)  Meth:	interface ome.api.StatefulServiceInterface.close

cc @jburel

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions