- 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.
