[Biojava-l] BioJAVA-X + BioSQL + no update

[Christian Köberle]

Hi  Mark,

it works but the code has to look like that:
...
        session.getTransaction().begin();
        session.saveOrUpdate("Sequence",seq);       
        session.getTransaction().commit();
it also works with:
       session.update("Sequence",seq); 

Thanks,
Christian

mark.schreiber at novartis.com wrote:
> With BioJavaX if you want any changes to a RichSequence object to persist 
> to the database you need to "save or add it" with Hibernate. 
>
>
> SessionFactory sessionFactory = new 
> Configuration().configure().buildSessionFactory(); 
> Session session = sessionFactory.openSession();  
> RichObjectFactory.connectToBioSQL(session);
>
> RichSequence rs = ...;                // some sequence you've made or 
> modified
> session.saveOrUpdate("Sequence",rs);  // persist the sequence
>
> ***
> Another way is to do everything inside a transaction (this example is from 
> the BioJavaX docbook in CVS)
>
> SessionFactory sessionFactory = new 
> Configuration().configure().buildSessionFactory(); 
> Session session = sessionFactory.openSession();  
> RichObjectFactory.connectToBioSQL(session);
>
> Transaction tx = session.beginTransaction();
> try {
>
>     // print out all the namespaces in the database
>
>     Query q = session.createQuery("from Namespace");
>     List namespaces = q.list();               // retrieve all the 
> namespaces from the db
>     for (Iterator i = namespaces.iterator(); i.hasNext(); ) {
>         Namespace ns = (Namespace)i.next();
>         System.out.println(ns.getName());     // print out the name of the 
> namespace
>
>         // print out all the sequences in the namespace
>         Query sq = session.createQuery("from BioEntry where namespace= 
> :nsp");
>         // set the named parameter "nsp" to ns
>         sq.setParameter("nsp",ns);
>         List sequences = sq.list();
>
>         for (Iterator j = sequences.iterator(); j.hasNext(); ) {
>             BioEntry be = (BioEntry)j.next();        // RichSequences are 
> BioEntrys too
>             System.out.println("   "+be.getName());  // print out the name 
> of the sequence
>
>             // if the sequence is called bloggs, change its description to 
> XYZ
>
>             if (be.getName().equals("bloggs")) {
>                 be.setDescription("XYZ");
>             }
>         }
>
>     }
>
>     // commit and tidy up
>     tx.commit(); 
>     System.out.println("Changes committed.");
>
>     // all sequences called bloggs now have a description of "XYZ" in the 
> database
>
> } catch (Exception e) {
>     tx.rollback(); 
>     System.out.println("Changes rolled back.");
>     e.printStackTrace(); 
> }
>
> session.close();
>
>
>
>
>
>
> Christian Köberle <koeberle at mpiib-berlin.mpg.de>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 03/14/2006 10:06 PM
>
>  
>         To:     bio java mailing list <biojava-l at biojava.org>
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] BioJAVA-X + BioSQL + no update
>
>
> Hi,
> I have following problem.
> I put a RichSequence-Object into a BioSQL-DB, using the new Classes from 
> BioJAVA-X.
> Later I get these Sequence-Object from the BioSQL-DB (also with 
> BioJAVA-X)  and create new Faeture-Objects and Note-Objects and add 
> these to the Sequence-Object.
> In the case of BioJAVA 1.4 all Features and Annotations are written into 
> the BioSQL-DB. In case of BioJAVA-X there are  no changes ind the DB.
> Includes BioJAVA-X a method to update the BioSQL-DB or how can I add the 
> changes into the DB.
>
> Thanks,
> Christian
>
>   


-- 
Christian Köberle

Max Planck Institute for Infection Biology
Department: Immunology
Schumannstr. 21/22
10117 Berlin

Tel: +49 30 28 460 562
e-mail: koeberle at mpiib-berlin.mpg.de