[BioSQL-l] SQLite support

[Peter]

On Thu, Dec 10, 2009 at 3:03 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Brad and I are hoping to include BioSQL on SQLite support in the
> imminent release of Biopython 1.53, although we will stress in the
> release notes that this (and the schema) is still experimental.
>
> For this initial release, the user probably still have to manually
> create the SQLite database - this is something I hope we can make
> much more user friendly in the subsequent releases of Biopython
> (taking advantage of the fact the SQLite is included with Python 2.5
> onwards, so we can do this without any external dependencies).
>
> Peter
>
> See also:
> http://bugzilla.open-bio.org/show_bug.cgi?id=2870
> http://bugzilla.open-bio.org/show_bug.cgi?id=2866
>

To keep you guys informed, we released Biopython 1.53 at the
end of 2009, and this did include BioSQL on SQLite support
based on the draft schema:
http://news.open-bio.org/news/2009/12/biopython-release-153/

Even if a BioSQL v1.0.2 release isn't imminent, could the draft
SQLite schema be checked into BioSQL's SVN repository please?

Repository link to see the file (currently no revisions):
http://github.com/biopython/biopython/blob/master/Tests/BioSQL/biosqldb-sqlite.sql

Alternatively you can grab the file here:
http://biopython.open-bio.org/SRC/biopython/Tests/BioSQL/biosqldb-sqlite.sql
(updated hourly, not that we have any revisions planned)

As I said before, we'd like to make using BioSQL on SQLite
from within Biopython much easier (because unlike the other
database back ends, it is *very* simple to create or delete a
new SQLite database). This would require us to install a
copy of the schema as part of Biopython (currently we just
include a copy used for unit tests), so the sooner the schema
becomes "official", the better.

Regards,

Peter