Re: [Biojava-l] [BioSQL-l] Load/Update Genbank sequence issue

Thu, 22 May 2008 08:42:49 -0700 

Gang,
did you fix the problem?
If so could you kindly share the solution?
I tried your code last night and I couldn't clear those Term instances from the cache. Does RichObjectFactory.clearLRUCache() clear the first level or second level cache? 
Again, I am not an expert, so I apologize if my question is obvious.
Thanks.
Guido



On May 21, 2008, at 11:12 AM, gang wu wrote:
The scenario is quite simple: I'm using the database to store Genbank genome sequences. Later I've to update the sequences when Genbank has newer releases. The following two lines are loading the same sequence twice. The first time will insert a new BioEntry record. the second time will delete the existing record and insert a new record again. 

   sl.loadSeq("/genomeseq/bacteria/NC_005813.gbk", "genbank");
   sl.loadSeq("/genomeseq/bacteria/NC_005813.gbk", "genbank");
Following code is used to load multiple genome sequences by calling the loadSeq() method multiple times. All failed except the first time. 
   sl.loadSeq("/genomeseq/bacteria/NC_005813.gbk", "genbank");
   sl.loadSeq("/genomeseq/bacteria/NC_006723.gbk", "genbank");
   sl.loadSeq("/genomeseq/bacteria/NC_008945.gbk", "genbank");
The exception message has the details. Since all variables used in loadSeq() are local, and I did the session flush/clear/close, then it should be ok to call the method again. 

Thank you very much for your help.

Gang


Richard Holland wrote:

I'm not sure why you'd want to do that? Either way, as far as I know,
Hibernate sessions are not designed for that. If you want to delete
the sequence then replace it with a completely new sequence object,
you have to create a new sequence object - you can't reuse the one you just deleted. The session info is embedded into that object so even if 
you clear the session, the object still refers to it.
If you just want to load a sequence, modify it, then save it back, you 
should just load it then use saveOrUpdate to save it back again with
changes. If you want to replace objects in your database, don't load
them, just delete them, then use save to create new objects in their
place.

cheers,
Richard

2008/5/21 gang wu <[EMAIL PROTECTED]>:
I got another problem with almost the same code(see attached code and output). If I call the loadSeq() only once, everything works fine. The second call of the same method will fail. By the exception message, it looks like the session is not cleaned up yet though at the end of the method the 
session has been flush/clear/closed. Anything wrong?
Or does anyone have a sequence data loader would like to share? I'm quite frustrated after keeping trying to do this seems simple thing without success. If I can make it work, I'd like to post it on the mailing list. 
Thanks in advance.

Gang

====================================================
public class SequenceLoaderNew {
public void loadSeq(String fileName, String namespace) throws
FileNotFoundException, BioException, SQLException, InterruptedException { 
    SessionFactory sessionFactory = new
Configuration().configure().buildSessionFactory();
    Session session = sessionFactory.openSession();
    RichObjectFactory.connectToBioSQL(session);
    Namespace ns = (Namespace)
RichObjectFactory.getObject(SimpleNamespace.class, new Object[] {namespace}); 
    RichSequenceDB db = new BioSQLRichSequenceDB(session);
    System.out.println("Start loading file " + fileName + " at " +
System.currentTimeMillis());
BufferedReader br = new BufferedReader(new FileReader(fileName)); RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(br, 
ns);
    try {
        while (rsi.hasNext()) {
            RichSequence sequence = rsi.nextRichSequence();
System.out.println("Loaded sequence" + sequence.getAccession() 
+ ", identifier: " + sequence.getIdentifier());
            Transaction tx = session.beginTransaction();
            try {
                System.out.println("Delete sequence" +
sequence.getAccession() + " if exists.");
                db.removeSequence(sequence.getAccession());
                tx.commit();
                session.flush();
                session.clear();
            } catch (Exception ex) {
                if (tx != null) {
                    tx.rollback();
                }
            }
            try {
                tx = session.beginTransaction();
                System.out.println("Save sequence " +
sequence.getAccession());
                //session.save("BioEntry", sequence);
                //db.addSequence(sequence);
                db.addRichSequence(sequence);
                tx.commit();
                System.out.println("Finished savig sequence " +
sequence.getAccession() + "\n");
            } catch (HibernateException ex) {
                tx.rollback();
                ex.printStackTrace();
            }
        }
    } finally {
        session.flush();
        session.clear();
        session.close();
    }
}

public static void main(String[] args) throws BioException,
FileNotFoundException, InterruptedException, SQLException {
    SequenceLoaderNew sl = new SequenceLoaderNew();
    sl.loadSeq("/genomeseq/bacteria/NC_005813.gbk", "genbank");
    sl.loadSeq("/genomeseq/bacteria/NC_005813.gbk", "genbank");
}
}
====================================================
Start loading file /genomeseq/bacteria/NC_005813.gbk at 1211349859602 
Loaded sequenceNC_005813, identifier: 45478502
Delete sequenceNC_005813 if exists.
Save sequence NC_005813
Finished savig sequence NC_005813
Start loading file /genomeseq/bacteria/NC_005813.gbk at 1211349863761 
Loaded sequenceNC_005813, identifier: 45478502
Delete sequenceNC_005813 if exists.
Save sequence NC_005813
org.hibernate.NonUniqueObjectException: a different object with the same 
identifier value was already associated with the session: [Term#20]
    at
org .hibernate .engine .StatefulPersistenceContext .checkUniqueness(StatefulPersistenceContext.java:590) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .performUpdate(DefaultSaveOrUpdateEventListener.java:284) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .entityIsDetached(DefaultSaveOrUpdateEventListener.java:223) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:89) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) 
    at
org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java: 507) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) 
    at
org.hibernate.engine.CascadingAction $5.cascade(CascadingAction.java:218) 
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java: 169) 
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at
org .hibernate .event .def .AbstractSaveEventListener .cascadeBeforeSave(AbstractSaveEventListener.java:431) 
    at
org .hibernate .event .def .AbstractSaveEventListener .performSaveOrReplicate(AbstractSaveEventListener.java:265) 
    at
org .hibernate .event .def .AbstractSaveEventListener .performSave(AbstractSaveEventListener.java:181) 
    at
org .hibernate .event .def .AbstractSaveEventListener .saveWithGeneratedId(AbstractSaveEventListener.java:107) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .saveWithGeneratedOrRequestedId (DefaultSaveOrUpdateEventListener.java:187) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) 
    at
org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java: 507) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) 
    at
org.hibernate.engine.CascadingAction $5.cascade(CascadingAction.java:218) 
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java: 169) 
    at
org .hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java: 296) at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java: 242) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java: 169) 
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at
org .hibernate .event .def .AbstractSaveEventListener .cascadeAfterSave(AbstractSaveEventListener.java:456) 
    at
org .hibernate .event .def .AbstractSaveEventListener .performSaveOrReplicate(AbstractSaveEventListener.java:334) 
    at
org .hibernate .event .def .AbstractSaveEventListener .performSave(AbstractSaveEventListener.java:181) 
    at
org .hibernate .event .def .AbstractSaveEventListener .saveWithGeneratedId(AbstractSaveEventListener.java:107) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .saveWithGeneratedOrRequestedId (DefaultSaveOrUpdateEventListener.java:187) 
    at
org .hibernate .event .def .DefaultSaveEventListener .saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) 
    at
org .hibernate .event .def .DefaultSaveEventListener .performSaveOrUpdate(DefaultSaveEventListener.java:27) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) 
    at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)
    at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)
    at primerdb.SequenceLoaderNew.loadSeq(SequenceLoaderNew.java:51)
    at primerdb.SequenceLoaderNew.main(SequenceLoaderNew.java:69)
Exception in thread "main" org.hibernate.NonUniqueObjectException: a
different object with the same identifier value was already associated with 
the session: [Term#19]
    at
org .hibernate .engine .StatefulPersistenceContext .checkUniqueness(StatefulPersistenceContext.java:590) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .performUpdate(DefaultSaveOrUpdateEventListener.java:284) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .entityIsDetached(DefaultSaveOrUpdateEventListener.java:223) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:89) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) 
    at
org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java: 507) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) 
    at
org.hibernate.engine.CascadingAction $5.cascade(CascadingAction.java:218) 
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java: 169) 
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at
org .hibernate .event .def .AbstractSaveEventListener .cascadeBeforeSave(AbstractSaveEventListener.java:431) 
    at
org .hibernate .event .def .AbstractSaveEventListener .performSaveOrReplicate(AbstractSaveEventListener.java:265) 
    at
org .hibernate .event .def .AbstractSaveEventListener .performSave(AbstractSaveEventListener.java:181) 
    at
org .hibernate .event .def .AbstractSaveEventListener .saveWithGeneratedId(AbstractSaveEventListener.java:107) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .saveWithGeneratedOrRequestedId (DefaultSaveOrUpdateEventListener.java:187) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94) 
    at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) 
    at
org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java: 507) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) 
    at
org.hibernate.engine.CascadingAction $5.cascade(CascadingAction.java:218) 
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java: 169) 
    at
org .hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java: 296) at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java: 242) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java: 169) 
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at
org .hibernate .event .def .AbstractFlushingEventListener .cascadeOnFlush(AbstractFlushingEventListener.java:131) 
    at
org .hibernate .event .def .AbstractFlushingEventListener .prepareEntityFlushes(AbstractFlushingEventListener.java:122) 
    at
org .hibernate .event .def .AbstractFlushingEventListener .flushEverythingToExecutions(AbstractFlushingEventListener.java:65) 
    at
org .hibernate .event .def .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 26) 
    at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
    at primerdb.SequenceLoaderNew.loadSeq(SequenceLoaderNew.java:60)
    at primerdb.SequenceLoaderNew.main(SequenceLoaderNew.java:69)
====================================================

Richard Holland wrote:


Forgot to copy my reply back to the lists!


---------- Forwarded message ----------
From: Richard Holland <[EMAIL PROTECTED]>
Date: 2008/5/20
Subject: Re: [BioSQL-l] Load/Update Genbank sequence issue
To: gang wu <[EMAIL PROTECTED]>


You need to substitute this line:
RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(br, new 
SimpleNamespace(namespace));

with this line:

Namespace ns =
(Namespace)RichObjectFactory.getObject(SimpleNamespace.class,new
Object[]{namespace});
RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(br, ns); 

cheers,
Richard

PS. You're the second person who has quoted this section of code on
this list recently, and had the same problem with it. If you got it
from a website somewhere, could you send me the URL so I can get in
touch with the authors and get them to correct it? Thanks!

2008/5/20 gang wu <[EMAIL PROTECTED]>:



Hi all,

I'm trying to load Genbank sequence into BioSQL database with
BioJavax/Hibernate. It's Ok to load the first sequence. Then I got the exception when loading new sequences or reloading the same sequence. 
Seems
the Hibernate is trying to insert "genbank" namespace again. Can anybody 
tell me what I did wrong? Thanks in advance.

Gang

================================================================
public class SequenceLoaderNew {
public void loadSeq(String fileName, String namespace) throws
FileNotFoundException, BioException {
   System.out.println("Start loading file " + fileName + " at " +
System.currentTimeMillis());
BufferedReader br = new BufferedReader(new FileReader(fileName)); 
   Session session = new
Configuration().configure().buildSessionFactory().openSession();
   RichObjectFactory.connectToBioSQL(session);
   RichSequenceDB db = new BioSQLRichSequenceDB(session);
RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(br, 
new
SimpleNamespace(namespace));
   while (rsi.hasNext()) {
       Transaction tx = session.beginTransaction();
       RichSequence sequence = rsi.nextRichSequence();
System.out.println("Loaded sequence" + sequence.getAccession() + 
", identifier: " + sequence.getIdentifier());
       try {
           System.out.println("Delete sequence" +
sequence.getAccession()
+ " if exists.");
           db.removeSequence(sequence.getAccession());
       } catch (Exception ex) {
       }
       try {
           System.out.println("Save sequence " +
sequence.getAccession());
           session.save("BioEntry", sequence);
           tx.commit();
           session.flush();
           session.clear();
       } catch (HibernateException ex) {
           tx.rollback();
           ex.printStackTrace();
       }
   }
}

public static void main(String[] args) throws BioException,
FileNotFoundException {
   SequenceLoaderNew sl = new SequenceLoaderNew();
   //sl.loadSeq("/genomeseq/bacteria/NC_005813.gbk", "genbank");
   sl.loadSeq("/genomeseq/bacteria/NC_004349.gbk", "genbank");
}
}
================================================================
org.hibernate.exception.ConstraintViolationException: could not insert: 
[Namespace]
   at
org .hibernate .exception.SQLStateConverter.convert(SQLStateConverter.java:71) 
   at
org .hibernate .exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java: 43) 
   at
org .hibernate .id .insert .AbstractReturningDelegate .performInsert(AbstractReturningDelegate.java:40) 
   at
org .hibernate .persister .entity .AbstractEntityPersister.insert(AbstractEntityPersister.java:2163) 
   at
org .hibernate .persister .entity .AbstractEntityPersister.insert(AbstractEntityPersister.java:2643) 
   at
org .hibernate .action .EntityIdentityInsertAction .execute(EntityIdentityInsertAction.java:51) at org.hibernate.engine.ActionQueue.execute(ActionQueue.java: 279) 
   at
org .hibernate .event .def .AbstractSaveEventListener .performSaveOrReplicate(AbstractSaveEventListener.java:298) 
   at
org .hibernate .event .def .AbstractSaveEventListener .performSave(AbstractSaveEventListener.java:181) 
   at
org .hibernate .event .def .AbstractSaveEventListener .saveWithGeneratedId(AbstractSaveEventListener.java:107) 
   at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .saveWithGeneratedOrRequestedId (DefaultSaveOrUpdateEventListener.java:187) 
   at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) 
   at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94) 
   at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) 
   at
org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java: 507) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) 
   at
org.hibernate.engine.CascadingAction $5.cascade(CascadingAction.java:218) 
   at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java: 169) 
   at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
   at
org .hibernate .event .def .AbstractSaveEventListener .cascadeBeforeSave(AbstractSaveEventListener.java:431) 
   at
org .hibernate .event .def .AbstractSaveEventListener .performSaveOrReplicate(AbstractSaveEventListener.java:265) 
   at
org .hibernate .event .def .AbstractSaveEventListener .performSave(AbstractSaveEventListener.java:181) 
   at
org .hibernate .event .def .AbstractSaveEventListener .saveWithGeneratedId(AbstractSaveEventListener.java:107) 
   at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .saveWithGeneratedOrRequestedId (DefaultSaveOrUpdateEventListener.java:187) 
   at
org .hibernate .event .def .DefaultSaveEventListener .saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33) 
   at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) 
   at
org .hibernate .event .def .DefaultSaveEventListener .performSaveOrUpdate(DefaultSaveEventListener.java:27) 
   at
org .hibernate .event .def .DefaultSaveOrUpdateEventListener .onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java: 535) 
   at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)
at primerdb.SequenceLoaderNew.loadSeq(SequenceLoaderNew.java: 38) 
   at primerdb.SequenceLoaderNew.main(SequenceLoaderNew.java:52)
Caused by:
com .mysql.jdbc.exceptions.MySQLIntegrityConstraintViolationException: 
Duplicate entry 'genbank' for key 'name'
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java: 1011) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java: 956) 
   at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3491)
   at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3423)
   at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1936)
   at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2060)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java: 2542) 
   at
com .mysql .jdbc.PreparedStatement.executeInternal(PreparedStatement.java: 1734) 
   at
com .mysql .jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2019) 
   at
com .mysql .jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1937) 
   at
com .mysql .jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1922) 
   at
org.hibernate.id.IdentityGenerator $ GetGeneratedKeysDelegate .executeAndExtract(IdentityGenerator.java:73) 
   at
org .hibernate .id .insert .AbstractReturningDelegate .performInsert(AbstractReturningDelegate.java:33) 
   ... 31 more
================================================================

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