[BioSQL-l] SQLite support

[Peter]

On Sun, Jul 5, 2009 at 11:24 AM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Dec 15, 2008 at 11:43 AM, Peter<biopython at maubp.freeserve.co.uk> wrote:
>> On Mon, Dec 15, 2008, vanaquisl vanaquisl wrote:
>>>
>>> Hi folks,
>>>
>>> I am a brand new BioSQL user and I'd like to know if there will be a SQLite
>>> support in the near future?
>>
>> As far as I know, BioSQL does not currently include a schema for SQLite.
>
> This was one of the things Brad Chapman and I discussed with Hilmar Lapp
> last week at BOSC/ISMB 2009. I've just filed BioSQL enhancement Bug 2870
> on this: http://bugzilla.open-bio.org/show_bug.cgi?id=2870
>
>>> I am about to use SQLite for a standalone lightweight Biopython application
>>> and it would be very helpful if I could use BioSQL directly.
>>
>> Biopython can talk to a BioSQL database run on MySQL (using MySQLdb),
>> PostgreSQL (using either Psycopg or Psycopg2).  In theory it could be
>> extended to use any supported BioSQL database (provided there are
>> python bindings for the database software, in the case of SQLite using
>> pysqlite would probably fine).
>
> We have a proof of principle implementation of the Biopython BioSQL
> bindings working with BioSQL on SQLite, see enhancement Bug 2866:
> http://bugzilla.open-bio.org/show_bug.cgi?id=2866

Hi Hilmar,

I've filed a BioSQL enhancement bug 2870 for adding an SQLite
schema to BioSQL, and Brad has attached his proposed schema
(converted from that for MySQL) to the bug:

http://bugzilla.open-bio.org/show_bug.cgi?id=2870

Could you take a look at this please? If you are happy with it, we'd like
to have it included in BioSQL v1.0.2 (even if Biopython is initially the
only Bio* project to support it).

Thanks,

Peter