[Biojava-dev] maven progress

[mark.schreiber at novartis.com]

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
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