[Biojava-l] RE: [BioSQL-l] release preparation

[Richard HOLLAND]

I looked into this in a bit more detail earlier today and found that,
since some version of Oracle around the 9i point in time, the official
Oracle JDBC driver API for accessing LOBs in changed. This means that
whereas before the same code could be used in BioJava to access both
Hilmar's and Len's versions of the database, since the 9i drivers this
has no longer been possible, and BioJava only works with Len's version.
The problem is due to the way in which Len's schema uses LONG values for
biosequence.seq, but Hilmar's uses CLOBs. 

(The nitty gritty - before 9i, Oracle JDBC allowed you to access both
LONG and CLOB columns using getString()/setString() methods to
manipulate them. Now, these methods only work with LONG columns, and you
have to do fancy tricks to get anything useful into/out of CLOBs).

After discussing this with Mark earlier this afternoon, I am planning on
changing BioJava to use the new Oracle CLOB API, at which point it will
no longer work with schemas set up using Len's version. No change to
BioSQL is required. This, from a BioJava point of view, would make the
simple schema redundant. I am not sure if there are people in the other
Bio* projects who use the simple schema though so we probably can't just
drop it.

Are there any objections? I have crossposted this to the BioJava list to
make sure everyone who might be affected gets a say.

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 Len Trigg
> Sent: Monday, April 18, 2005 4:58 PM
> To: mark.schreiber at novartis.com
> Cc: Hilmar Lapp; Biosql
> Subject: Re: [BioSQL-l] release preparation
> 
> 
> 
> Mark Schreiber wrote:
> > now, my bad! Agreed that from a SQL query perspective the 
> schemas are the 
> > same, one just has more complexity (if I can call it that) 
> under the hood.
> 
> Indeed, the complexity is more to do with the complexity of installing
> and understanding what's going on in all those files :-) (particularly
> if you are not an oracle expert and have only been looking at the
> BioSQL schemas for the other supported databases), and that's why I
> did the simple version.  That's partly confirmed by the fact that the
> bjia description of how to use the original schema is about 8KB, while
> the description for the simple schema is about 1KB.  I'm all for
> dumping the simple one if the barrier for entry for the original
> schema is lowered (maybe it already has been).
> 
> 
> > I would prefer to keep instructions for the less complex 
> version up for 
> > the time being as we are having difficulties getting 
> biojava to work 
> > seamlessly with the more complex version. This is almost 
> certainly a 
> > failing of biojava for which the oracle support seems to have been 
> > compiled against the 'simple' schema not the 'complex schema'.
> 
> It certainly was only tested against the simple version, because
> that's the only schema I had working when I wrote the Oracle support.
> I am a little surprised that you are having major difficulties though,
> since the original package has a compatibility layer that (supposedly)
> presents the same schema as the simple version.
> 
> 
> > I expect we will soon have biojava supporting your version 
> and we can drop 
> > the 'simple' schema. After all, there is not much point 
> using oracle if 
> > you don't make use of the features.
> 
> In my case, it was a matter of using Oracle because that was what was
> already installed :-)
> 
> 
> Cheers,
> Len.
> 
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