[Biojava-dev] BioSQLRichSequenceDB and BioSQLBioEntryDB

[mark.schreiber at novartis.com]

'Tis a thing of great beauty!





"Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
Sent by: biojava-dev-bounces at portal.open-bio.org
01/24/2006 11:38 AM

 
        To:     Mark Schreiber/GP/Novartis at PH
        cc:     biojava-dev at biojava.org, biojava-dev-bounces at portal.open-bio.org
        Subject:        RE: [Biojava-dev] BioSQLRichSequenceDB and BioSQLBioEntryDB


Exactly.


Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: mark.schreiber at novartis.com 
> [mailto:mark.schreiber at novartis.com] 
> Sent: Tuesday, January 24, 2006 11:36 AM
> To: Richard HOLLAND
> Cc: biojava-dev at biojava.org; biojava-dev-bounces at portal.open-bio.org
> Subject: RE: [Biojava-dev] BioSQLRichSequenceDB and BioSQLBioEntryDB
> 
> 
> So I should be able to get atomic transactions by doing this...
> 
> Session sess = factory.openSession();
> Transaction tx;
> RichObjectFactory.connectToHibernate(session); // bind 
> BioJavaX to the 
> hibernate session
> RichSequenceDB db = new BioSQLRichSequenceDB(session);
> 
> RichSequence seq = ... //make a RichSequence
> 
> try {
>      tx = sess.beginTransaction();
>      //do something the the DB
>      db.addSequence(seq1);
>      tx.commit();
>  }
>  catch (Exception e) {
>      if (tx!=null) tx.rollback();
>      throw e;
>  }
>  finally {
>      sess.close();
>  }
> 
> 
> 
> 
> 
> "Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
> Sent by: biojava-dev-bounces at portal.open-bio.org
> 01/24/2006 11:22 AM
> 
> 
>         To:     Mark Schreiber/GP/Novartis at PH
>         cc:     biojava-dev at biojava.org
>         Subject:        RE: [Biojava-dev] 
> BioSQLRichSequenceDB and BioSQLBioEntryDB
> 
> 
> All BJX needs is a Hibernate session. By default, Hibernate
> auto-commits, but you can wrap any part of your application 
> in code like
> this to make it transactional (example from the Hibernate Session
> javadocs):
> 
>  Session sess = factory.openSession();
>  Transaction tx;
>  try {
>      tx = sess.beginTransaction();
>      //do some work
>      ...
>      tx.commit();
>  }
>  catch (Exception e) {
>      if (tx!=null) tx.rollback();
>      throw e;
>  }
>  finally {
>      sess.close();
>  }
> 
> 
> So BJX doesn't need to worry about transactions - its entirely the
> user's responsibility.
> 
> cheers,
> Richard
> 
> Richard Holland
> Bioinformatics Specialist
> GIS extension 8199
> ---------------------------------------------
> This email is confidential and may be privileged. If you are not the
> intended recipient, please delete it and notify us immediately. Please
> do not copy or use it for any purpose, or disclose its content to any
> other person. Thank you.
> ---------------------------------------------
> 
> 
> > -----Original Message-----
> > From: mark.schreiber at novartis.com 
> > [mailto:mark.schreiber at novartis.com] 
> > Sent: Tuesday, January 24, 2006 11:17 AM
> > To: Richard HOLLAND
> > Cc: biojava-dev at biojava.org
> > Subject: Re: [Biojava-dev] BioSQLRichSequenceDB and BioSQLBioEntryDB
> > 
> > 
> > Very cool use of reflection in there!
> > 
> > I don't see how commits and rollbacks are handled though??
> > 
> > - Mark
> > 
> > 
> > 
> > 
> > 
> > "Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
> > Sent by: biojava-dev-bounces at portal.open-bio.org
> > 01/24/2006 10:51 AM
> > 
> > 
> >         To:     <biojava-dev at biojava.org>
> >         cc:     Mark Schreiber/GP/Novartis at PH
> >         Subject:        [Biojava-dev] BioSQLRichSequenceDB 
> > and BioSQLBioEntryDB
> > 
> > 
> > We've added two new modules to BioJavaX that allow you to wrap a 
> > BioSQL/Hibernate database in a SequenceDB compatible wrapper. 
> > More for 
> > convenience sake than anything else (its not foolproof) but 
> > it might be 
> > useful. 
> > 
> > They are:
> > 
> >                  org.biojavax.bio.db.biosql.BioSQLBioEntryDB
> >                  org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
> > 
> > The code depends on you having unique values in the 'name' 
> > column of the 
> > BioEntry table in your BioSQL database. You'll get 
> > 'IllegalIDExceptions' 
> > thrown all over the place if this does not hold true. If this 
> > is the case, 
> > you should use Hibernate directly rather than this 
> > convenience wrapper 
> > code.
> > 
> > To use it, make sure Hibernate is on your classpath. Then 
> you can do 
> > things like this:
> > 
> >                  Session session = ...;  // get a Hibernate 
> > session from 
> > somewhere
> > 
> > 
> > RichObjectFactory.connectToHibernate(session); // bind 
> > BioJavaX to the hibernate session
> >                  RichSequenceDB db = new 
> > BioSQLRichSequenceDB(session); // 
> > connect the hibernate session to our SequenceDB
> > 
> >                  System.out.println(db.ids()); // prints out 
> > a list of all 
> > the values in the 'name' column of the BioEntry table in the 
> > database 
> > 
> >                  for (Iterator i = db.getRichSequences("bloggs"); 
> > i.hasNext(); ) {  // retrieve all sequences where the name 
> is 'bloggs'
> >                      RichSequence seq = 
> > (RichSequence)i.next(); // get the 
> > next one
> >                      ... // do something with it here
> >                  }
> > 
> > To add sequences to your database:
> > 
> >                  RichSequence seq = ...; // get a RichSequence from 
> > somewhere
> >                  db.addRichSequence(seq);
> > 
> > To remove them again:
> > 
> >                  db.removeRichSequence("bloggs"); // removes 
> > the sequence 
> > with the name 'bloggs'
> > 
> > The BioSQLBioEntryDB works in exactly the same way but returns only 
> > BioEntry objects - ie. sequences without the sequence data 
> > attached. This 
> > might help with performance in some cases.
> > 
> > Finally, we also added a GenbankRichSequenceDB object that 
> > behaves much 
> > like the old GenbankSequenceDB object but returns 
> > RichSequence objects 
> > instead.
> > 
> > cheers,
> > Richard
> > 
> > Richard Holland
> > Bioinformatics Specialist
> > Genome Institute of Singapore
> > 60 Biopolis Street, #02-01 Genome, Singapore 138672
> > Tel: (65) 6478 8000   DID: (65) 6478 8199
> > Email: hollandr at gis.a-star.edu.sg
> > ---------------------------------------------
> > This email is confidential and may be privileged. If you 
> are not the 
> > intended recipient, please delete it and notify us 
> > immediately. Please do 
> > not copy or use it for any purpose, or disclose its content 
> > to any other 
> > person. Thank you.
> > ---------------------------------------------
> > 
> > 
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> > 
> > 
> 
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