[Biojava-l] RE: [BioSQL-l] _removeSequence

[Richard HOLLAND]

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
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> -----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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> 
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