[BioSQL-l] SQLite support

[Hilmar Lapp]

Hi Peter, yes, I know I'm remiss on doing that. Will do shortly.  
Please don't stop pestering if I seem to have forgotten :-)

	-hilmar

On Jan 13, 2010, at 6:37 AM, Peter wrote:

> 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
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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