How to properly handle the interrupt waiting for logs?

I have started an import task that works very well, until a couple of days ago, when the number of objects increased sharply.

What will happen is that I got an excess of waiting for a lock wait. Then the application retries and an exception is thrown, as I call em.getTransaction (). Begin (); again.

To get rid of this problem, I changed innodb_lock_wait_timeout to 120 and reduced the party side to 50 objects.

I cannot figure out how to properly handle all this in code. I do not want all imports to fail due to blocking. How would you handle this? Do you have an example code? Maybe some other thoughts? Please go nuts!

My BatchPersister:

public class BatchPersister implements Persister {

    private final static Log log = getLog(BatchPersister.class);
    private WorkLogger workLog = WorkLogger.instance();

    private static final int BATCH_SIZE = 500;

    private int persistedObjects;
    private long startTime;
    private UpdateBatch batch;
    private String dataSource;


    public BatchPersister(String dataSource) {
        this.dataSource = dataSource;        
    }

    public void persist(Persistable obj) {

        persistedObjects++;
        logProgress(100);

        if (batch == null)
            batch = new UpdateBatch(BATCH_SIZE, dataSource);

        batch.add(obj);

        if (batch.isFull()) {
            batch.persist();
            batch = null;
        }
    }
}

Updatebatch

public class UpdateBatch {

    private final static Log log = LogFactory.getLog(UpdateBatch.class);
    private WorkLogger workLogger = WorkLogger.instance();

    private final Map<Object, Persistable> batch;
    private final EntityManager em;
    private int size;

    /**
     * Initializes the batch and specifies its size.
     */
    public UpdateBatch(int size, String dataSource) {
        this.size = size;
        batch = new LinkedHashMap<Object, Persistable>();
        em = EmFactory.getEm(dataSource);
    }    

    public void persist() {
        log.info("Persisting " + this);
        em.getTransaction().begin();    
        persistAllToDB();
        em.getTransaction().commit();

        WorkLog batchLog = new WorkLog(IMPORT_PERSIST, IN_PROGRESS);
        batchLog.setAffectedItems(batch.size());
        workLogger.log(batchLog);
        em.close();
   }

/**
  * Persists all data in this update batch
  */
    private void persistAllToDB() {
        for (Persistable persistable : batch.values())
            em.persist(persistable);
        }

        @Override
        public String toString() {
            final ArrayList<Persistable> values = new ArrayList<Persistable>(batch.values());
            Persistable first = values.get(0);
            Persistable last = values.get(values.size() - 1);
            return "UpdateBatch[" +
                first.getClass().getSimpleName() + "(" + first.getId() + ")" +
                " - " +
                last.getClass().getSimpleName() + "(" + last.getId() + ")" +
                "]";
         }
    }
}