[Biojava-dev] Biojava3 and BioSQL

[Thiago Satake]

Hi,

I was wandering if I should use hibernate or not in my BioSQL module. In my
point of the view we should avoid a lot of dependency to make things easy
to set up. But I am not sure it would be good for everyone...

In this module I am thinking to create a data access object strategy
typically exchange data with clients using Transfer Objects, and also, I
believe we need to create DAOFactory to encapsulate multiple types of data
source ( Oracle, Mysql and Postgres).

I will expose read() and write() functions using an session façade which
will encapsulate reused biojava3 component an data access object.

Is everything making sense ? ;-)



Thanks


Thiago Seito Satake





On 29 May 2012 12:00, Scooter Willis <HWillis at scripps.edu> wrote:

> Thiago
>
> If you get a chance can you look at the UniprotProxySequenceReader as a
> potential model for BioSQL integration. The underlying sequence objects in
> Biojava3-core don't care about the storage container for sequence data,
> annotations etc. You should be able to do a BioSQLProxySequenceReader
> which has knowledge of the BioSQL schema and connection parameters that
> you pass into the appropriate Sequence object.
>
> I think this makes the most sense to integrate BioSQL into Biojava3.
>
> Let me know what I can do to help.
>
> Scooter
>
> On 5/28/12 9:34 AM, "Thiago Satake" <maruco at gmail.com> wrote:
>
> >Thanks Andreas,
> >
> >
> >In my current project I will work with Java and BioSQL. I think that an
> >biojava3-biosql API would be very useful. Now I am getting a good
> >understanding of  biojava3 and deciding what is the best solution for
> >that.
> >Any suggestions would be good!!
> >
> >
> >For now, I have created a simple project in my local environment called
> >biojava3-biosql, after I've finished, I would like to share with all of
> >you. Is possible include in BioJava project ?
> >
> >
> >
> >Thanks,
> >
> >
> >Thiago Seito Satake
> >
> >
> >
> >
> >
> >
> >On 26 May 2012 20:34, Andreas Prlic <andreas at sdsc.edu> wrote:
> >
> >> No, biojava 3 does not have biosql bindings currently. Any patches are
> >> welcome...
> >>
> >> Andreas
> >>
> >> On Sat, May 26, 2012 at 12:13 PM, Thiago Satake <maruco at gmail.com>
> >>wrote:
> >> > Hi,
> >> >
> >> > I have noticed that there is a componet called biosql 1.8.1 which
> >>works
> >> > with biojava 1.8.
> >> >
> >> > Quick question, I would like to work with biojava3 and BioSQL. Is
> >>there a
> >> > componete for that ?
> >> >
> >> > Thanks
> >> >
> >> >
> >> > --
> >> > Thiago Seito Satake
> >> > _______________________________________________
> >> > biojava-dev mailing list
> >> > biojava-dev at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
> >
> >
> >--
> >Thiago Seito Satake
> >Tel: (041) 88428444
> >_______________________________________________
> >biojava-dev mailing list
> >biojava-dev at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


-- 
Thiago Seito Satake
Tel: (041) 88428444