[Biopython-dev] zxJDBC support for BioSQL

[Peter]

On Thu, Dec 17, 2009 at 1:39 AM, Kyle Ellrott <kellrott at gmail.com> wrote:
>
> I've push pushed a patch to the BioSQL code that enables zxJDBC support.
> This means that Jython can now run BioSQL through mysql.  (SQLite hasn't
> been ported to Java yet)
> zxJDBC is a Jython module included in the standard distribution that
> provides a PythonDB interface through the java sql interfaces.  I've only
> ran the unit tests using the mysql-connector, but it should theoretically
> work with Oracle as well.

Sounds good, and ought to work on PostgreSQL too in theory.

I should be able to test it on MySQL.

> The biggest issues for changing code:
>  - Java expects ? instead of %s, so sql strings have to be altered (I
> override the execute method in the DBUtils to run a regular express
> before execution)
>  - A Sql string with a=? works, one with a='?' does not (Loader.py had some
> examples of this)
>  - Java returns unicode, not strings (recent patch to the mainline fixes
> this)

Some of those issues applied to SQLite (hence the changes on the
trunk from Brad).

> Code can be found at http://github.com/kellrott/biopython

Lovely. That's on your jython branch (along with lots of your other work)?

Peter