[BioSQL-l] State of BioSql?

[Fields, Christopher J]

Peter, 

We should probably send issues to the  BioSQL bug tracker on redmine.open-bio.org.  It's possible the BioSQL-specific updates needed are mainly to allow other DBI that are now supported, but I suppose we need to have more specifics as to what exactly needs to be done.  Any BioPerl-specific stuff could be filed separately for BioPerl-DB.

(I'm all for a new BioSQL release, by the way…)

chris

On Sep 18, 2012, at 1:19 PM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Tue, Sep 18, 2012 at 6:58 PM, David Wilbur <wildboar at workwerks.com> wrote:
>> Hi,
>> 
>> i am working on a project that sees potential uses for BioSql. (which
>> we would be, if chosen, using with a current version of ruby, bioruby,
>> rails and postgres)
>> 
>> i am mostly interested in the state of the project, it appears to have
>> no changes since 2008.
> 
> No releases of BioSQL itself for a while I grant you, but the most recent
> change was last week https://github.com/biosql/biosql/commits/master
> (an update for the MySQL schema), and a year ago an SQLite schema
> was added.
> 
> I'd like to see another point release (to ship the SQLite schema) but
> it needs someone with Perl expertise to update the misc BioSQL
> Perl scripts. Adding support for BioSQL on SQLite to BioPerl etc
> would also be great (currently only available in Biopython I think).
> 
> When you say no changes since 2008 are you talking about a
> particular Bio* binding for BioSQL?
> 
>> ruby, bioruby, and postgres, have both changed a lot since that time.
>> eg: http://lists.open-bio.org/pipermail/biosql-l/2011-November/001795.html
>> has this better solution for transactions been worked on? and so on...
> 
> Good question - Biopython has some special case code to cope
> under PostrgreSQL with and without those special case rules
> needed under BioPerl.
> 
> Peter
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