[Biopython-dev] MySQL (BioSQL)

[Peter Cock]

On Fri, May 2, 2014 at 12:16 PM, Tiago Antao <tra at popgen.net> wrote:
> On Wed, 30 Apr 2014 11:38:29 +0100
> Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> Since mysqldb isn't being actively maintained, that seems like
>> a good plan - thanks :)
>
> I have a pull request on this (did not commit it directly because I do
> not trust myself on this).

https://github.com/biopython/biopython/pull/317

That turned out to be very little code to change in BioSQL,
I guess the standardised Python DB API worked nicely -
and we already handle the MySQL quirks.

> There are two main issues:
>
> 1. I have changed the test schema for mysql (removed the BINARY from
> VARCHAR BINARY). Does this make sense?

Why? If there is a good reason we should bring this up on the
BioSQL list http://lists.open-bio.org/mailman/listinfo/biosql-l or
on their GitHub https://github.com/biosql/biosql

My hunch would be this is a string unicode vs bytes issue?

> 2. Should we remove mysqldb completely (and use mysql.connector
> instead)?
>
> Comments appreciated as I am not a specialist on this...
>
> Tiago

If you want to drop the old C based Python library it would
mean a deprecation process.

Does the MySQL Connector/Python library work nicely on
Windows, Jython, PyPy? This is what you are using, right?:

http://dev.mysql.com/doc/connector-python/en/index.html
https://pypi.python.org/pypi/mysql-connector-python

Thanks,

Peter