[Biojava-dev] maven progress

[Andreas Prlic]

Hi Mark,

That's already done. ;-) Have a look at new biosql module and let us know if
it works for you.

Andreas





On Tue, Oct 6, 2009 at 8:30 PM, <mark.schreiber at novartis.com> wrote:

>
> Hi -
>
> Could I suggest that the biosql code be factored out into it's own module?
>
> The main argument for this is that it currently uses fairly old Hibernate
> specific ORM bindings.  The more modern way to do this would be to use JPA
> (either inside or outside a container) which could then use any ORM provider
> (Hibernate, EclipseLink, JDO etc etc) in a uniform way. This could be a new
> BioSQL module that could replace the old one allowing a simple migration
> from the current ORM code to a JPA compliant ORM code without having to rip
> apart the core module.
>
> Best regards,
>
> - Mark
>
> biojava-dev-bounces at lists.open-bio.org wrote on 08/31/2009 09:23:03 AM:
>
>
> > Hi,
> >
> > I started to split up biojava into submodules and am mavenizing the
> > build process. The new SVN location is emerging here:
> >
> >
> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava
> >
> > or in your browser:
> >
> >
> http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/biojava
> >
> > A few questions so far from my side.
> >
> > 1) bytecode.jar: at the present the core module depends on this.   So
> > far it is in the /jars subfolder of the module and needs to be
> > installed by hand. What is the best way to deal with this in SVN?
> >
> > 2) Sequence module (Richard's original biojava v.3 branch) Since this
> > consists of sub-modules I have set it up as a few hierarchically
> > organized submodules. There is some biosql code there as well.
> > Richard/Mark not sure now to arrange this. I think it would be good to
> > have a biosql module. Shall I refactor the current biosql code out of
> > core into a new biosql module or will the current code be obsoleted
> > and  replaced with the new code in the sequence module?
> >
> > Andreas
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
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