Why do I get org.hibernate.HibernateException: IOException occurred reading a binary value

Question

I found this exception in my logs I have never seen it before, Im using Hibernate 4.1.7

Does this indicate that my database is corrupted , or this a bug in Hibernate. I found a reference to this error at http://lists.jboss.org/pipermail/hibernate-issues/2010-November/026487.html but this referred to a much earlier version of hibernate and was fixed for Hibernate 4.0

org.hiorg.hibernate.HibernateException: IOException occurred reading a binary value
    at org.hibernate.type.descriptor.java.DataHelper.extractBytes(DataHelper.java:187)
    at org.hibernate.type.descriptor.java.PrimitiveByteArrayTypeDescriptor.wrap(PrimitiveByteArrayTypeDescriptor.java:124)
    at org.hibernate.type.descriptor.java.PrimitiveByteArrayTypeDescriptor.wrap(PrimitiveByteArrayTypeDescriptor.java:41)
    at org.hibernate.type.descriptor.sql.BlobTypeDescriptor$5.doExtract(BlobTypeDescriptor.java:118)
    at org.hibernate.type.descriptor.sql.BasicExtractor.extract(BasicExtractor.java:65)
    at org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:269)
    at org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:265)
    at org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:238)
    at org.hibernate.type.AbstractStandardBasicType.hydrate(AbstractStandardBasicType.java:357)
    at org.hibernate.persister.entity.AbstractEntityPersister.hydrate(AbstractEntityPersister.java:2807)
    at org.hibernate.loader.Loader.loadFromResultSet(Loader.java:1545)
    at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1477)
    at org.hibernate.loader.Loader.getRow(Loader.java:1377)
    at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:644)
    at org.hibernate.loader.Loader.doQuery(Loader.java:854)
    at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:293)
    at org.hibernate.loader.Loader.doList(Loader.java:2382)
    at org.hibernate.loader.Loader.doList(Loader.java:2368)
    at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2198)
    at org.hibernate.loader.Loader.list(Loader.java:2193)
    at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:122)
    at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1618)
    at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:374)
    at com.jthink.songkong.db.SongCache.loadSongsFromDatabase(SongCache.java:57)
    at com.jthink.songkong.analyse.analyser.SongGroup.getSongs(SongGroup.java:48)
    at com.jthink.songkong.analyse.analyser.DiscogsSongGroupMatcher.call(DiscogsSongGroupMatcher.java:63)
    at com.jthink.songkong.analyse.analyser.DiscogsSongGroupMatcher.call(DiscogsSongGroupMatcher.java:28)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:722)
Caused by: java.io.IOException: org.h2.jdbc.JdbcSQLException: IO Exception: "Missing lob entry: 5587/4" [90028-172]
    at org.h2.message.DbException.convertToIOException(DbException.java:348)
    at org.h2.store.LobStorageBackend$LobInputStream.fillBuffer(LobStorageBackend.java:695)
    at org.h2.store.LobStorageBackend$LobInputStream.readFully(LobStorageBackend.java:668)
    at org.h2.store.LobStorageBackend$LobInputStream.read(LobStorageBackend.java:654)
    at org.hibernate.type.descriptor.java.DataHelper.extractBytes(DataHelper.java:179)
    ... 31 more
Caused by: org.h2.jdbc.JdbcSQLException: IO Exception: "Missing lob entry: 5587/4" [90028-172]
    at org.h2.message.DbException.getJdbcSQLException(DbException.java:329)
    at org.h2.message.DbException.get(DbException.java:169)
    at org.h2.message.DbException.get(DbException.java:146)
    at org.h2.store.LobStorageBackend.readBlock(LobStorageBackend.java:203)
    at org.h2.store.LobStorageBackend$LobInputStream.fillBuffer(LobStorageBackend.java:692)
    ... 34 more

Answer 1

Let's start from the Hibernate's doc:

@Lob indicates that the property should be persisted in a Blob or a Clob depending on the property type: java.sql.Clob, Character[], char[] and java.lang.String will be persisted in a Clob. java.sql.Blob, Byte[], byte[] and serializable type will be persisted in a Blob.

For example:

@Lob
public String getFullText() {
    return fullText;
}

@Lob 
public byte[] getFullCode() {
    return fullCode;
}

Knowing this, it could mean that the object is not in the database. Maybe it was deleted from the table but in a referenced table didn't. Let's say that from the table Blobs, the blob with id 5 were deleted, but in the table users_blobs it is stille referenced like:

| user_id | blob_id|
|    4    |    5   | //This entry blob were delete but is still referenced by that table
|    5    |    2   | 

If that's the case, you should redefine your users_blobs (for example) constraints so it will be deleted or put null if blob is deleted.

Also, this link could be useful too:

http://h2-database.66688.n3.nabble.com/IO-Exception-quot-Missing-lob-entry-1-0-quot-90028-171-when-trying-to-read-a-BLOB-longer-than-128-bye-td4026236.html

Answer 2

Seems to be you are trying to load a data register that has been already deleted, try synchronizing access to that hibernate DAO. Multi-thread apps should be using one connection per thread.

Answer 3

This is surely a problem with the database, not with hibernate. You have to look at the cause of the exception which is an exception thrown inside the h2 database code.

Caused by: org.h2.jdbc.JdbcSQLException: IO Exception: "Missing lob entry: 5587/4" [90028-172]
    at org.h2.message.DbException.getJdbcSQLException(DbException.java:329)
    at org.h2.message.DbException.get(DbException.java:169)
    at org.h2.message.DbException.get(DbException.java:146)
    at org.h2.store.LobStorageBackend.readBlock(LobStorageBackend.java:203)
    at org.h2.store.LobStorageBackend$LobInputStream.fillBuffer(LobStorageBackend.java:692)

Searching the internet for “h2 database Missing lob entry” shows that this is a h2 specific error message and answers like here: https://groups.google.com/forum/#!topic/h2-database/xey-czIhocM indicate that it’s very likely that the database is corrupt.

If this happens more often, more research about how this happened would be appropriate. But this is done best at that h2 group where the database developers are active.