We tracked down the error to the fact that the Hilmar Oracle version (no
assertion is made about the complexity) uses CLOBs to store sequence while
the Len Oracle (no assertion about simplicity etc) version uses LONGs to
store sequence. The biojava support code seems to assume LONGs and
strangely until very recently the JDBC oracle dirver seems to let you
write LONGs to CLOBs although the data that comes out again is completely
munged.
It would be possible to modify the biojava adapters to check for LONG or
CLOB and behaive appropriately but this would cause lots of maintenance
problems later.
Given this situtation, unless some one complains very loudly, the biojava
oracle adapters will be changed to assume CLOBs. Note: This means if you
are using biojava and oracle and biosql now then it will break unless you
adopts Hilmar's version. It will not cause any changes to biojava users of
MySQL etc.
- Mark
Len Trigg <[EMAIL PROTECTED]>
04/18/2005 04:58 PM
To: Mark Schreiber/GP/[EMAIL PROTECTED]
cc: Hilmar Lapp <[EMAIL PROTECTED]>, Biosql <[EMAIL PROTECTED]>
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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