[BioSQL-l] _removeSequence

[Richard HOLLAND]

Well, technically that should work because BioJava simply issues a
delete against the seqfeature table, and therefore all features related
through foreign keys should automatically delete themselves as a result
without any further intervention by BioJava... beats me why it doesn't!
Unfortunately I don't currently use the MySQL implementation myself so I
can't help much. I hope someone on BioSQL-L knows a little more?

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: Martina [mailto:boehme at mpiib-berlin.mpg.de] 
> Sent: Monday, June 20, 2005 6:21 PM
> To: Richard HOLLAND
> Cc: biosql-l-bounces at portal.open-bio.org; BioJava; 
> biosql-l at open-bio.org
> Subject: Re: [BioSQL-l] _removeSequence
> 
> 
> My tables are all InnoDB tables and in the biosqldb-mysql.sql (v 1.40 
> 2004/11/04 01:49:41) which created them, it says ON DELETE CASCADE.
> Do I need to do anything else?
> 
> Thanks,
> Martina
> 
> Richard HOLLAND wrote:
> 
> > 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: biosql-l-bounces at portal.open-bio.org 
> >>[mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of 
> >>mark.schreiber at novartis.com
> >>Sent: Monday, June 20, 2005 5:57 PM
> >>To: Martina
> >>Cc: biosql-l-bounces at portal.open-bio.org; BioJava; 
> >>biosql-l at open-bio.org
> >>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 <boehme at mpiib-berlin.mpg.de>
> >>Sent by: biosql-l-bounces at portal.open-bio.org
> >>06/20/2005 05:43 PM
> >>
> >> 
> >>        To:     biosql-l at open-bio.org, BioJava 
> <biojava-l at 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
> >>
> >>_______________________________________________
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> >>BioSQL-l at open-bio.org
> >>http://open-bio.org/mailman/listinfo/biosql-l
> >>
> >>
> >>
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> > 
>