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User Story #2941 (closed)

Opened 10 years ago

Closed 9 years ago

Import Errors with ome example files

Reported by: bwzloranger Owned by: mlinkert
Priority: major Milestone: Unscheduled
Component: Import Keywords: n.a.
Cc: cxallan, jburel, ajpatterson, jamoore Story Points: n.a.
Sprint: n.a. Importance: n.a.
Total Remaining Time: 0.0d Estimated Remaining Time: n.a.

Description (last modified by jburel)

Several of the current 'valid' OME example file located in the repo do not import (files located in specification/Documentation/Samples/). These file should import.

  • We should have a test to regularly test these files
  • Determine the cause of the failures (is this an importer bug or an issue with the stylesheets, for example).

Change History (9)

comment:1 Changed 10 years ago by bwzloranger

Should probably have a chain of tests here. Taking an importable older schema, doing a translation, and testing against both to make sure the translations are ok first, then seeing what imports.

comment:2 Changed 10 years ago by bwzloranger

  • Cc mlinkert-x jburel ajpatterson added

comment:3 Changed 10 years ago by bwzloranger

  • Type changed from Task to User Story

comment:4 Changed 10 years ago by bwzloranger

  • Cc jmoore added

comment:5 Changed 10 years ago by jburel

  • Description modified (diff)

comment:6 Changed 10 years ago by jburel

Brian: could you create tickets with the error that you have already noticed? thanks

comment:7 Changed 10 years ago by bwzloranger

Two errors here. I've listed the error along with some sample QA feedback numbers associated with them (should you require more details):

http://qa.openmicroscopy.org.uk/qa/feedback/2825/

java.lang.RuntimeException: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref
                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648)
                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
                        	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:222)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy56.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:339)
                        	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:147)
                        	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:167)
                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)
                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:211)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:333)
                        	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)

http://qa.openmicroscopy.org.uk/qa/feedback/2824/

java.lang.RuntimeException: omero.ApiUsageException
    serverStackTrace = ""
    serverExceptionClass = ""
    message = "omero.model.LightSource does not specify a valid class."
	at ome.formats.enums.IQueryEnumProvider.getEnumerations(IQueryEnumProvider.java:185)
	at ome.formats.enums.IQueryEnumProvider.getEnumeration(IQueryEnumProvider.java:132)
	at ome.formats.OMEROMetadataStoreClient.getEnumeration(OMEROMetadataStoreClient.java:957)
	at ome.formats.OMEROMetadataStoreClient.setLaserPump(OMEROMetadataStoreClient.java:4528)
	at loci.formats.meta.MetadataConverter.convertLightSources(MetadataConverter.java:2352)
	at loci.formats.meta.MetadataConverter.convertMetadata(MetadataConverter.java:1028)
	at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:404)
	at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:308)
	at loci.formats.FormatReader.setId(FormatReader.java:1074)
	at loci.formats.ImageReader.setId(ImageReader.java:650)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:244)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:255)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:447)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:384)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:216)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:637)

    

comment:8 Changed 9 years ago by mlinkert

  • Cc bwzloranger mlinkert-x removed
  • Owner set to mlinkert-x

comment:9 Changed 9 years ago by jburel

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