BUG:Feedback 2889 nd2 Error

[omero-qa]

​http://qa.openmicroscopy.org.uk/qa/feedback/2889/

Comment: Latest round of testing from 'test_images_good'.

[bwzloranger]

java.lang.RuntimeException: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: could not insert: [ome.model.core.PlaneInfo]; SQL [insert into planeinfo (deltaT, creation_id, external_id, group_id, owner_id, permissions, update_id, exposureTime, pixels, positionX, positionY, positionZ, theC, theT, theZ, version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; nested exception is org.hibernate.exception.DataException: could not insert: [ome.model.core.PlaneInfo]
                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:642)
                        	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:150)
                        	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)
                        "
    serverExceptionClass = "ome.conditions.ValidationException"
    message = "could not insert: [ome.model.core.PlaneInfo]; SQL [insert into planeinfo (deltaT, creation_id, external_id, group_id, owner_id, permissions, update_id, exposureTime, pixels, positionX, positionY, positionZ, theC, theT, theZ, version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; nested exception is org.hibernate.exception.DataException: could not insert: [ome.model.core.PlaneInfo]"
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2032)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:290)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:520)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:433)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:376)
	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)
Caused by: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: could not insert: [ome.model.core.PlaneInfo]; SQL [insert into planeinfo (deltaT, creation_id, external_id, group_id, owner_id, permissions, update_id, exposureTime, pixels, positionX, positionY, positionZ, theC, theT, theZ, version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; nested exception is org.hibernate.exception.DataException: could not insert: [ome.model.core.PlaneInfo]
                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:642)
                        	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:150)
                        	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)
                        "
    serverExceptionClass = "ome.conditions.ValidationException"
    message = "could not insert: [ome.model.core.PlaneInfo]; SQL [insert into planeinfo (deltaT, creation_id, external_id, group_id, owner_id, permissions, update_id, exposureTime, pixels, positionX, positionY, positionZ, theC, theT, theZ, version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; nested exception is org.hibernate.exception.DataException: could not insert: [ome.model.core.PlaneInfo]"
	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.saveToDB(_MetadataStoreDelM.java:162)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:254)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:226)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2017)
	... 15 more

[bwzloranger]

Value of deltaT being returned from bio-formats is outside the range of double precision (6.79929338E-316). Looks like a bio-formats bug.

[bwzloranger]

Value of deltaT being returned from bio-formats is outside the range of double precision (6.79929338E-316). Looks like a bio-formats bug. Did you want to have a look at this Melissa (I think the problem here is that Java can support 10x-1600 or something like that - way beyond standard double precision). Let me know if we should be filtering this to sane values or its something you want to do (or its just a quirky bug).

[mlinkert]

This particular bug should be fixed in ​bio-formats:r7137, but in general it would probably be a good idea for you to filter out float/double values that can't be handled. I know we've discussed this issue before (in the context of #803, if I recall), but if it's not feasible to filter the values within OMERO then the next best place to do it would probably be within the ome.xml.model.* classes. If possible, I really want to avoid checking every double value at the reader level.

[bwzloranger]

Fixed in r8409