Hello,
I have commited the hibernate mapping in the gmod cvs. You will find it in schema/JavaTools.

If you want some hints don't hesitate to ask.

Regards

Cyril

cpommier@versailles.inra.fr a écrit :
Selon John Osborne <ozborn@uab.edu>:

  
On Jul 27, 2007, at 1:18 AM, Cyril Pommier wrote:

    
Hello
I am about to commit an hibernate mapping into cvs. The only thing
I have to finish is to package correctly andromda (code generator)
to allow anybody to generate a valide mapping for its particular
flavor of chado.
If you are interressed, I'll let you know as soon as I have
commited this stuff.

      
This sounds great - could it handle updating existing ontologies in a
CHADO database with new releases from GO, SO, etc...?
    
The hibernate mapping is only a set of java persistent objects mapped to a
relational schemas. Those object can be used for easy navigation of data and
eases updating.
You still need another layer (DAO/Service) to do the buisness manipulation of
those objects. For instance changing the id of a particular cvterm or adding
more dbxref or chilterms before saving.

You still need to write the java code that parses a datasource (either obo or
chadoXML) and then injects the data into java objects.



  
Excuse my ignorance but when you say commit to CVS do you mean a
local CVS at your workplace or the gmod sourceforge site?
    

It will be the gmod one. it will be in schemas/chado/JavaTools


 If it is
  
the latter, what package would it be under?

  -John





    
Regards

Cyril


Chris Mungall a écrit :
      
Hi John

I believe Hibernate will fit in best with how the oboedit
architecture will evolve, so this would be my recommendation. We'd
also be interested in looking at your JDBC-level implementation.

Cheers
Chris

On Jul 26, 2007, at 8:30 AM, John Osborne wrote:


        
Along those lines is there someone on this list developing that is
developing an iBATIS or Hibernate based middleware for loading
ontologies?

I'm writing something right now to do basic loading of OBO files
into
the CV module using John Day Richter's OBOParser and a simple JDBC
driver, but I wanted to do something more flexible but I don't have
the time with the deadline I'm operating under.

I was thinking of using the Perl loader but our schema is slightly
different from CHADO and we're loading in SQL Server 2000 (not my
choice) so something like iBATIS is tempting since it is flexible
that way. If anyone else has something (or is writing something) I
wouldn't mind collaborating.

As it is I'm hoping to finish my simple loader today if I don't get
interrupted too much.

  -John




On Jul 24, 2007, at 7:05 PM, Brian Osborne wrote:


          
Chris,

Start here:

http://gmod.org/wiki/index.php/GMOD_Middleware

This links out to the individual presentations.


Brian O.


On 7/24/07 7:16 PM, "Chris Mungall" <cjm@fruitfly.org> wrote:


            
Are the results of the last GMOD middleware bake-off posted
anywhere?

What are the current recommendations for ensuring
interoperability of
new GMOD components?

After a long hiatus I may be writing a few infrastructural
components
for Chado - improving ontology loading and loaders for MAGE-TAB.
I am
most comfortable with language-independent XML based
approaches, ie
Chado-XML, but I would rather contribute towards a unified
approach
that will be used by the majority of GMOD folks.


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_____________________________
Cyril Pommier
Bioinformatic Engineer
INRA - URGI
523 place des terrasses
91034 Evry cedex
Tel.: 01-60-87-37-42
      06-64-30-81-85
Fax.: 01-60-87-37-00
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-- 
_____________________________
Cyril Pommier
Bioinformatic Engineer
INRA - URGI 
523 place des terrasses
91034 Evry cedex
Tel.: 01-60-87-37-42
      06-64-30-81-85
Fax.: 01-60-87-37-00
_____________________________