[Biojava-l] Biojava 1.21 & BioSQL
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
From: Thomas Down [mailto:email@example.com]
Sent: Monday, July 08, 2002 3:43 PM
To: Tim Burcham
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.