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Task #6332 (closed)

Opened 8 years ago

Closed 6 years ago

BUG: HTD import - Feedback 3884

Reported by: omero-qa Owned by: mlinkert
Priority: major Milestone: 5.0.0-rc1
Component: Bio-Formats Version: 4.4.9
Keywords: n.a. Cc: jay_copeland@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by jmoore)

​http://qa.openmicroscopy.org.uk/qa/feedback/3884/

Comment: I attempted these imports using the 4.3.1 client against our new 4.3.0 server.

(stack below)

Change History (8)

comment:1 Changed 8 years ago by jmoore

  • Component changed from from QA to Import
  • Description modified (diff) 
java.lang.RuntimeException: omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for omero.model.OriginalFile:4(ome.model.core.OriginalFile:Hash_1320087030) --> Plate:0(ome.model.screen.Plate:Hash_1049156053) reference.
                        	at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:523)
                        	at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:237)
                        	at sun.reflect.GeneratedMethodAccessor234.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:440)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy64.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:371)
                        	at ome.services.throttling.Adapter.run(Adapter.java:51)
                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:150)
                        	at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:232)
                        	at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:106)
                        	at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:201)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:378)
                        	at IceInternal.Incoming.invoke(Incoming.java:159)
                        	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                        	at Ice.ConnectionI.message(ConnectionI.java:972)
                        	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                        	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                        	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                        "
    serverExceptionClass = "ome.conditions.ApiUsageException"
    message = "Missing reference handler for omero.model.OriginalFile:4(ome.model.core.OriginalFile:Hash_1320087030) --> Plate:0(ome.model.screen.Plate:Hash_1049156053) reference."
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2163)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:293)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:452)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6314)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1175)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for omero.model.OriginalFile:4(ome.model.core.OriginalFile:Hash_1320087030) --> Plate:0(ome.model.screen.Plate:Hash_1049156053) reference.
                        	at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:523)
                        	at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:237)
                        	at sun.reflect.GeneratedMethodAccessor234.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:440)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy64.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:371)
                        	at ome.services.throttling.Adapter.run(Adapter.java:51)
                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:150)
                        	at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:232)
                        	at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:106)
                        	at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:201)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:378)
                        	at IceInternal.Incoming.invoke(Incoming.java:159)
                        	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                        	at Ice.ConnectionI.message(ConnectionI.java:972)
                        	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                        	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                        	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                        "
    serverExceptionClass = "ome.conditions.ApiUsageException"
    message = "Missing reference handler for omero.model.OriginalFile:4(ome.model.core.OriginalFile:Hash_1320087030) --> Plate:0(ome.model.screen.Plate:Hash_1049156053) reference."
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._MetadataStoreDelM.updateReferences(_MetadataStoreDelM.java:315)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:460)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:432)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2147)
	... 14 more

comment:2 Changed 6 years ago by jamoore

  • Milestone changed from Unscheduled to 5.0.0-beta2
  • Resolution set to fixed
  • Status changed from new to closed
  • Version set to 4.4.9

Bug has subsequently been fixed in the 4.4 and 5.0 lines. Thanks for the feedback.

comment:3 Changed 6 years ago by pwalczysko

Huh, sorry, I was just trying to re-import the file from Apache 3884 using Insight and got a failed import.

java.lang.ArrayIndexOutOfBoundsException: -1
	at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:546)
	at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:386)
	at loci.formats.FormatReader.setId(FormatReader.java:1360)
	at loci.formats.ImageReader.setId(ImageReader.java:781)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.Memoizer.setId(Memoizer.java:471)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6469)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1194)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:662)
	at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:555)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:463)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6469)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1194)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
	at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:546)
	at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:386)
	at loci.formats.FormatReader.setId(FormatReader.java:1360)
	at loci.formats.ImageReader.setId(ImageReader.java:781)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.Memoizer.setId(Memoizer.java:471)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	... 16 more

comment:4 Changed 6 years ago by pwalczysko

And on Howe as well:

ava.lang.ArrayIndexOutOfBoundsException: -1
	at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:523)
	at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:372)
	at loci.formats.FormatReader.setId(FormatReader.java:1244)
	at loci.formats.ImageReader.setId(ImageReader.java:727)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:323)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6375)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1347)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6429)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1347)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
	at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:523)
	at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:372)
	at loci.formats.FormatReader.setId(FormatReader.java:1244)
	at loci.formats.ImageReader.setId(ImageReader.java:727)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:323)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6375)
	... 11 more

comment:5 Changed 6 years ago by pwalczysko

  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:6 Changed 6 years ago by pwalczysko

Sorry, although I was saying something else in Jabber, I got an e-mail from this ticket suggesting I should try and re-import the file. Which I did and it failed on bot branches => reopening the ticket.

comment:7 Changed 6 years ago by jamoore

  • Component changed from Import to Bio-Formats
  • Owner changed from cxallan to mlinkert
  • Priority changed from minor to major
  • Status changed from reopened to accepted

Melissa: could you take a quick look?

comment:8 Changed 6 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from accepted to closed

Should be fixed with: ​https://github.com/openmicroscopy/bioformats/pull/800

Note that QA 3884 is expected not to import (since all of the pixel data is missing), but that PR fixes the exception that is thrown.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

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