[Biojava-l] Biojava 1.21 & BioSQL

Tim Burcham TBurcham@diadexus.com
Mon, 8 Jul 2002 15:47:59 -0700

I think moving to mysql 4 is the way to go. The SQL syntax is completely
standard. I just wanted to be sure we weren't missing something. Btw, I
added just a bit of code to the _removeSequence method that makes this work
in mysql 3, so a work-around is not impossible.

Could you/we just add a note to the source or docs that says which versions
of which DBMS this code works with?

Thanks - Tim

-----Original Message-----
From: Thomas Down [mailto:td2@sanger.ac.uk] 
Sent: Monday, July 08, 2002 3:43 PM
To: Tim Burcham
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] Biojava 1.21 & BioSQL

On Mon, Jul 08, 2002 at 10:05:05AM -0700, Tim Burcham wrote:
> I realize that this has probably been discussed before, but I have 
> looked at the docs & the list archives...
> BioJava 1.21 expects BioSQL running on MySQL version 4.0 or higher 
> correct? MySQL version 3 does not support the DELETE syntax as 
> expressed in BioSQLSequenceDB._removeSequence. Or is something else 
> wrong with our installation?

No, you're right -- DELETE queries with joins in them don't seem to be
supported in older versions of MySQL.  This leaves a bit of a problem since,
unless there's a MySQL feature which I'm missing, it looks like the
offending DELETEs are going to have to be replaced by a SELECT and a
large) number of DELETEs.

Unless there are any MySQL gurus out there who know of a
better solution, I guess this is the way to go.  I'll try
to implement it as a fall-back, so MySQL 4 and PostgreSQL
can still use the efficient, multi-table DELETE.

Any suggestions?