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Task #2381 (closed)

Opened 14 years ago

Closed 14 years ago

BUG: importing li-flim

Reported by: jburel Owned by: cxallan
Priority: blocker Milestone: OMERO-Beta4.2
Component: Import Version: n.a.
Keywords: n.a. Cc: cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2010-05-13 (9)

Description 

2010-05-17 10:32:36,931 129957     [2-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - INTERNAL_EXCEPTION: /Users/jburel/Desktop/samples/li-flim/lifetime-extended.fli
java.lang.NullPointerException
	at ome.formats.OMEROMetadataStoreClient.getIObjectContainer(OMEROMetadataStoreClient.java:2308)
	at ome.formats.model.ShapeProcessor.process(ShapeProcessor.java:97)
	at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1738)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:251)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:436)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	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:417)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
	at java.util.concurrent.FutureTask.run(FutureTask.java:123)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:172)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676)

Change History (14)

comment:1 Changed 14 years ago by cxallan

  • Status changed from new to assigned

comment:2 Changed 14 years ago by cxallan

(In [7029]) Fixed shape processor's invalid usage of IMAGE_INDEX. (See #2381)

comment:3 Changed 14 years ago by cxallan

As of r7029 now fails with:

2010-05-18 11:47:47,021 14899      [2-thread-1] DEBUG      ome.formats.importer.gui.GuiImporter  - Error processing references.
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:150)
	at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1659)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:251)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:437)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149)
	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: java.lang.RuntimeException: Unable to synchronize reference Polyline:0:0 --> omero.model.Image:0:0
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:121)
	... 15 more

comment:4 Changed 14 years ago by cxallan

(In [7031]) Fixed missing TransmittanceRange? source object handler. (See #2381)

comment:5 Changed 14 years ago by cxallan

As of r7031 now fails with:

    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for FilterSet:0:0(ome.model.acquisition.FilterSet:Hash_408948456) --> Channel:0:0(ome.model.core.Channel:Hash_1765745570) reference.
                        	at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:464)
                        	at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:214)
                        	at sun.reflect.GeneratedMethodAccessor167.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:409)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:144)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175)
                        	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 $Proxy54.doWork(Unknown Source)
                        	at ome.services.util.Executor$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:146)
                        	at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:209)
                        	at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:99)
                        	at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:194)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:341)
                        	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)
                        "

comment:6 Changed 14 years ago by cxallan

(In [7032]) Fixed implementation of setChannelFilterSetRef(). (See #2381)

comment:7 Changed 14 years ago by cxallan

As of r7032 now fails with:

    serverStackTrace = "ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.acquisition.Filter.filterSet; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.acquisition.Filter.filterSet
                        	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:175)
                        	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 $Proxy54.doWork(Unknown Source)
                        	at ome.services.util.Executor$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:146)
                        	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)
                        "

comment:8 Changed 14 years ago by cxallan

Ignore the above, see the FV1000 ticket (#2388) for more information on its status. Current status for li-flim as of r7034:

2010-05-18 13:50:49,417 1038393    [2-thread-1] DEBUG      ome.formats.importer.gui.GuiImporter  - Error processing references.
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:150)
	at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1659)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:251)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:437)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149)
	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: java.lang.RuntimeException: Unable to synchronize reference Polyline:0:0 --> omero.model.Image:0:0
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:121)
	... 15 more

comment:9 Changed 14 years ago by cxallan

(In [7040]) Corrected ROI and Shape handling and removed all usage of *RefIndex?. (Fixes #2385; See #2381)

comment:10 Changed 14 years ago by cxallan

As of r7040 there is a missconfigured reference to a Shape rather than an Roi. The exception:

2010-05-18 17:44:24,143 158352     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: /Volumes/ome/data_repo/test_images_good/li-flim/lifetime-extended.fli
java.lang.RuntimeException: omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for Polyline:0:0(ome.model.roi.Polyline:Hash_1599453584) --> Image:0(ome.model.core.Image:Hash_1963576789) reference.
                                at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:489)
                                at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:214)
                                at sun.reflect.GeneratedMethodAccessor206.invoke(Unknown Source)
                                at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                                at java.lang.reflect.Method.invoke(Method.java:597)
                                at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                                at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:409)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at ome.security.basic.EventHandler.invoke(EventHandler.java:144)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175)
                                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 $Proxy54.doWork(Unknown Source)
                                at ome.services.util.Executor$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:146)
                                at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:209)
                                at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:99)
                                at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:194)
                                at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:341)
                                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)
                        "

The container and relevant reference:

2010-05-18 17:44:24,084 158293     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Polyline:0:0 == omero.model.PolylineI@ba97149,Polyline:0:0

2010-05-18 17:44:24,084 158293     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Image:0 == Polyline:0:0

This reference should be to Roi:0 not Polyline:0:0.

comment:11 Changed 14 years ago by cxallan

  • Owner changed from bwzloranger to mlinkert-x
  • Status changed from assigned to new

comment:12 Changed 14 years ago by mlinkert

Fixed in ​bio-formats:r6336.

comment:13 Changed 14 years ago by cxallan

  • Owner changed from mlinkert-x to cxallan
  • Status changed from new to assigned

comment:14 Changed 14 years ago by cxallan

  • Remaining Time set to 0
  • Resolution set to fixed
  • Status changed from assigned to closed

(In [7043]) Upgrading to ​bio-formats:r6340. (Fixes #2358, #2377, #2380, #2381, #2390)

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