[Biojava-dev] BioSQLRichSequenceDB and BioSQLBioEntryDB

[mark.schreiber at novartis.com]

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
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> -----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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