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Subject:Re: [Biojava-l] Re: [BioSQL-l] _removeSequence
Hi Martina,
In fact you can, as rank is the field that allows this to happen. In
Biojava, currently it's just a linearily incremented number such that
you can have the same type and source IDs for a given bio
Hi Martina,
In fact you can, as rank is the field that allows this to happen. In
Biojava, currently it's just a linearily incremented number such that
you can have the same type and source IDs for a given bioentry.
For example, adding a Genbank entry with 10 CDS features for 1 bioentry
will
That means, that I can't have 2 features refering to the same bioentry
with the same type (= type_term_id)and source (=source_term_id) but
different parent features because of the composite key bioentry_id in
the seqfeature table? Or what does "rank" in that table mean (its part
of that key), h
Yes. When you insert a sequence you must be prepared that when inserting
its ontology term or tag/value annotation the term may already be
present because another bioentry uses it too.
Ok, the proper way is to catch the SQLException in BIOSQLFeature, test
if it is a Dublicate key entry, get
Hi Hilmar,
I wasn't aware of 2 different types of features.
I'm making features as described in
http://www.biojava.org/docs/bj_in_anger/feature.htm, and as far as I
can tell from the results, its the first type you describe.
The second type of feature is confusing me: as I understood the
featu
Hi,
so I have this new database (still biosqldb-mysql.sqlv 1.40 2004/11/04
01:49:41) and after removing all sequences, I do still have entries in
term, term_relationship,term_relationship_term and ontology. And of
course, in biodatabase. If I delete the entry in biodatabase too,
nothing chang
I droped the db and run the bioSql again - looks like its working now!
Must have stopped before the alter table statements - didn't had the
foreign keys - but I didn't know, that they had to be there.
Thanks!
Richard HOLLAND wrote:
Well, technically that should work because BioJava simply iss
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
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 In
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 da
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.
- M
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