Issue #799: javax.jdo.JDONullIdentityException: The identity must not be null.

When stopping my JEE 6 Web Profile application in Glassfish 3.1.1, I sometimes get this exception, yielding in not merging athene.odb and athene.odb$. A bug in objectdb? 

bjjl@ps2:~$ ls -l /var/db/athene/
total 122080
-rw-r--r-- 1 bjjl webservd   2621440 2012-05-24 16:40 athene.odb
-rw-r--r-- 1 bjjl webservd 122265952 2012-05-24 16:40 athene.odb$
bjjl@ps2:~$

[#|2012-05-24T14:40:38.313+0200|SEVERE|glassfish3.1.1|javax.enterprise.system.tools.admin.org.glassfish.deployment.admin|_ThreadID=24;_ThreadName=Thread-2;|Cannot stop module
web
[ObjectDB 2.3.7_25] javax.persistence.PersistenceException
Exceptions during EntityManagerFactory close (error 512)
        at net.pocketservices.athene.lib.EntityManagerFilter.destroy(EntityManagerFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterConfig.release(ApplicationFilterConfig.java:319)
        at org.apache.catalina.core.StandardContext.filterStop(StandardContext.java:4717)
        at org.apache.catalina.core.StandardContext.stop(StandardContext.java:5564)
        at com.sun.enterprise.web.WebModule.stop(WebModule.java:527)
        at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:1049)

[...]

Caused by: javax.jdo.JDONullIdentityException: The identity must not be null.
        at javax.jdo.identity.SingleFieldIdentity.assertKeyNotNull(SingleFieldIdentity.java:92)
        at javax.jdo.identity.ObjectIdentity.<init>(ObjectIdentity.java:60)
        at com.objectdb.o.UTY.aK(UTY.java:1410)
        at com.objectdb.spi.DetachedTracker.<init>(DetachedTracker.java:82)
        at com.objectdb.o.ENT.getDetachTracker(ENT.java:939)
        at com.objectdb.o.ENT.w(ENT.java:329)
        at com.objectdb.o.STA.ae(STA.java:819)
        at com.objectdb.o.STM.D(STM.java:371)
        at com.objectdb.o.OBC.ae(OBC.java:222)
        at com.objectdb.o.OBM.close(OBM.java:184)
        at com.objectdb.o.OMF.close(OMF.java:867)
        ... 67 more

After this crash, the database seems to be corrupted, I cannot execute my pages anymore after restart of the web application: com.objectdb.o._PersistenceException: Failed to open file '/var/db/athene/athene.odb'

So this is a critical issue for me.

Caused by: com.objectdb.o.UserException: Failed to open file '/var/db/athene/athene.odb'
        at com.objectdb.o.MSG.d(MSG.java:74)
        at com.objectdb.o.LFL.Y(LFL.java:1174)
        at com.objectdb.o.LFL.I(LFL.java:873)
        at com.objectdb.o.LFL.I(LFL.java:769)
        at com.objectdb.o.SFL.<init>(SFL.java:225)
        at com.objectdb.o.MST.<init>(MST.java:109)
        at com.objectdb.o.MST.aJ(MST.java:94)
        at com.objectdb.o.MSF.UJ(MSF.java:178)
        at com.objectdb.o.OMF.am(OMF.java:746)
        at com.objectdb.jpa.EMF.am(EMF.java:156)
        at com.objectdb.o.OMF.al(OMF.java:692)
        at com.objectdb.jpa.EMF.createEntityManager(EMF.java:173)
        ... 27 more
Caused by: java.nio.channels.OverlappingFileLockException
        at sun.nio.ch.FileChannelImpl$SharedFileLockTable.checkList(FileChannelImpl.java:1166)
        at sun.nio.ch.FileChannelImpl$SharedFileLockTable.add(FileChannelImpl.java:1068)
        at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:868)
        at java.nio.channels.FileChannel.tryLock(FileChannel.java:962)
        at com.objectdb.o.LFL.O(LFL.java:908)
        at com.objectdb.o.LFL.I(LFL.java:859)
        ... 36 more

The exception in #2 reflects a locked database file (due to a failure during close) and not a corrupted database. Anyway, please try build 2.4.0_03 that should fix this issue.

Thank you for the quick fix. Replaced the library already, and will report if anything goes wrong again (hopefully not).

How is the main db file and the one with $ appended actually playing together? Is it some kind of cache?

The $ file is the recovery file.