Open Microscopy Environment

I'm getting an error [Unable to synchronize reference Annotation] on an in place import of an ome.tiff that seems valid based on tiffcomment and xmlvalid:

Code: Select all

thusharaw@denali bftools $ ./tiffcomment /allen/aics/microscopy/PRODUCTION/PIPELINE_4_OptimizationAutomation/3500000766/ZSD2/100X_FF/converted/3500000766_100X_20170328_FC.ome.tiff | ./xmlvalid
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
Validating <stdin>
No validation errors found.
thusharaw@denali bftools $


Here is the full stack trace of the import failure:

Code: Select all

INTERNAL_EXCEPTION: /allen/programs/allencell/data/proj0/b5/f150bcb96dc74136b629d18530d1c1b5
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=Error processing references.
at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:141)
at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1752)
at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(ManagedImportRequestI.java:623)
at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:501)
at omero.cmd.HandleI.steps(HandleI.java:438)
at omero.cmd.HandleI$1.doWork(HandleI.java:366)
at omero.cmd.HandleI$1.doWork(HandleI.java:362)
at sun.reflect.GeneratedMethodAccessor305.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy72.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:443)
at omero.cmd.HandleI.run(HandleI.java:360)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at ome.services.util.Executor$Impl$1.call(Executor.java:484)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Unable to synchronize reference Annotation:1337:135 --> omero.model.PlaneInfo:1:17
at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:118)
... 34 more
, message=Error processing references.}

at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:665)
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.lang.Thread.run(Thread.java:748)

java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=Error processing references.
at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:141)
at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1752)
at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(ManagedImportRequestI.java:623)
at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:501)
at omero.cmd.HandleI.steps(HandleI.java:438)
at omero.cmd.HandleI$1.doWork(HandleI.java:366)
at omero.cmd.HandleI$1.doWork(HandleI.java:362)
at sun.reflect.GeneratedMethodAccessor305.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy72.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:443)
at omero.cmd.HandleI.run(HandleI.java:360)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at ome.services.util.Executor$Impl$1.call(Executor.java:484)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Unable to synchronize reference Annotation:1337:135 --> omero.model.PlaneInfo:1:17
at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:118)
... 34 more
, message=Error processing references.}

at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:665) ~[blitz.jar:na]
at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) [blitz.jar:na]
at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) [blitz.jar:na]
at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) [blitz.jar:na]
at IceInternal.Incoming.invoke(Incoming.java:221) [ice.jar:na]
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) [ice.jar:na]
at Ice.ConnectionI.dispatch(ConnectionI.java:1145) [ice.jar:na]
at Ice.ConnectionI.message(ConnectionI.java:1056) [ice.jar:na]
at IceInternal.ThreadPool.run(ThreadPool.java:395) [ice.jar:na]
at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) [ice.jar:na]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_144]
2017-09-26 02:12:07,134 7891       [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import
java.lang.Exception: Import failure
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:560) ~[blitz.jar:na]
at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289) ~[blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289) [blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958) [blitz.jar:na]
2017-09-26 02:12:07,134 7891       [      main] INFO         ome.formats.importer.ImportLibrary - Exiting on error



I will upload the file to the q/a location.

Thank you for uploading the file. I've checked the OME-XML content, and I can't see any problems with the annotation IDs or the annotation references which would cause the problem. I've created this ticket to track the issue: https://trello.com/c/1sX3tep3/62-bug-cr ... s-on-plane

However, when checking the OME-XML metadata, I did notice that all but the first annotation have improperly escaped XML. That is, the annotations are not valid XML, they are XML with all the markup escaped as entities. This should be verbatim XML.

Kind regards,
Roger