To do cascading deletes in MySQL requires the tables to have been set up using the InnoDB table style (as opposed to the default MyISAM tables). In InnoDB, foreign keys are actually enforced and deletes will cascade, whereas in MyISAM it has no concept of foreign keys and so is unable to enforce data integrity. The people on the BioSQL-L mailing list will be able to help you there.
The next version of BioJava's database interfaces after the 1.4 release will assume that the underlying database does have cascading deletes turned on. The existing version half-attempts to make up for the lack of cascading deletes in databases that don't support it, but it doesn't do it well at all, hence the problems you are seeing. After consulting with Hilmar last week we decided it was a fair assumption to make that all BioSQL instances are installed with cascading deletes enabled. BioPerl-db already makes this assumption. 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: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > [EMAIL PROTECTED] > Sent: Monday, June 20, 2005 5:57 PM > To: Martina > Cc: [EMAIL PROTECTED]; BioJava; > [EMAIL PROTECTED] > Subject: Re: [BioSQL-l] _removeSequence > > > Biojava doesn't attempt to recusivley remove features by > itself. It relies > on cascading deletes in the database. I know Oracle can be > set to do this > (and it works very well). If MySQL has equivalent > functionality you may > need to turn it on. I'm pretty sure it does but you need to set it up. > > - Mark > > > > > > Martina <[EMAIL PROTECTED]> > Sent by: [EMAIL PROTECTED] > 06/20/2005 05:43 PM > > > To: [EMAIL PROTECTED], BioJava <biojava-l@biojava.org> > cc: (bcc: Mark Schreiber/GP/Novartis) > Subject: [BioSQL-l] _removeSequence > > > Hi, > > Im trying to delete a sequence and recursivly all its features. > > So: > > for (SequenceIterator si = db.sequenceIterator(); si.hasNext();) { > Sequence s = si.nextSequence(); > String name = s.getName(); > s = null; > db.removeSequence(name); > } > > But if I look in the database (MySQL 4.1.12) I can still see plenty > of entries and I have problems entering the same features again, > because of dublicate key error. I would like to know if > _removeSequence(String) in BioSQLSequenceDB is supposed to remove > features recursivly or just the features of the removed sequence? > If so - what is the best way do delete the features of the features > (and so on)? And how to empty the db completly? > > Martina > > _______________________________________________ > BioSQL-l mailing list > [EMAIL PROTECTED] > http://open-bio.org/mailman/listinfo/biosql-l > > > > _______________________________________________ > BioSQL-l mailing list > [EMAIL PROTECTED] > http://open-bio.org/mailman/listinfo/biosql-l > _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
