On 21 May 2004, at 06:55, [EMAIL PROTECTED] wrote:
Hi -
I'm going to start using BioSQL fairly intensively soon and I was
wondering at what level the biojava bindings to biosql control
transactions. Specifically: if I get a reference to a Sequence object from
my SequenceDB does that reference lock the underlying entry (entries) in
the database or does it just give me a local copy to play with and then
release the lock on the DB?
Neither.
The code supports lazy loading, otherwise it would be easy to make it explode on anything remotely resembling a large sequence, so the Sequence objects you get back are dependent on the database. On the other hand, the schema is too complex to realistically consider "locking" a sequence. So you should only really have one BioSQLSequenceDB accessing a database at a given time.
If you need multiple applications accessing the database at once, can you put them all in a single appserver so that they can share a single BioSQLSequenceDB? Otherwise, reasonable options are:
- Having one server export an object-oriented view of the BioSQLSequenceDB to other application (Corba/SOAP/RMI/whatever). [Aside: it would be really nice to have some kind of client-server view on BioJava. If this was biojava-specific rather than trying to make it an interoperability point (like BioCorba/bsane/etc.) it might actually be usable]
- When you need a sequence, lock the database, get the sequence out of BioSQL, copy it into an in-memory object, then release the lock.
- Hack the BioSQL code to disable lazy loading.
Without knowing a lot more about your applications, I'm not really in a position to say which of these are more appropriate.
Thomas.
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