BUG: Importing Flex

[cxallan]

Exception during import:

2010-05-19 14:06:59,609 1098304    [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: /Users/callan/testimages/flex/Meas_01(2008-12-23_14-31-25).mea
java.lang.RuntimeException: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):
                        null
                                at ome.formats.OMEROMetadataStore.handle(OMEROMetadataStore.java:869)
                                at ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:253)
                                at ome.services.blitz.impl.MetadataStoreI$4.doWork(MetadataStoreI.java:198)
                                at sun.reflect.GeneratedMethodAccessor222.invoke(Unknown Source)
                                at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                                at java.lang.reflect.Method.invoke(Method.java:597)
                                at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                                at ome.services.util.Executor$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.updateObjects_async(MetadataStoreI.java:183)
                                at omero.api._MetadataStoreTie.updateObjects_async(_MetadataStoreTie.java:92)
                                at omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:173)
                                at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:337)
                                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)
                        "

Looks like Well and WellSamples? are not correctly linked up (the indexes are off):

2010-05-19 14:06:59,390 1098085    [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Well:0:0 == omero.model.WellI@3df6c65c,omero.model.Well:0:0

2010-05-19 14:06:59,392 1098087    [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.WellSample:0:50:0 == omero.model.WellSampleI@7264ef18,omero.model.WellSample:0:50:0

[mlinkert]

Should be fixed in ​bio-formats:r6352. There should be 384 Well objects; Well 50 (C3) should have a single WellSample? linked to it and every other Well should be empty.

[cxallan]

(In [7066]) Updating to ​bio-formats:r6355. (Fixes #2358, #2367, #2368, #2406)