[Biojava-dev] XML Schema

[markjschreiber at gmail.com]

It would probably be less time consuming to write the bridge than wait for  
BJ3 which has no time frame as yet.

I also don't think there will be (or should be) a unified XML schema for  
BJ3 as it will be much more modular (by design). Possibly each module could  
have a schema if relevant. Generally it is hoped that each module will be  
compatible with bean like design (unless there is a good reason not to) so  
this would implicitly mean there will be simple XML schema generation.

- Mark

On Jan 13, 2009 9:47pm, Ola Spjuth <ola.spjuth at farmbio.uu.se> wrote:
> Hi,
>
>
>
> Seems a bit too time-consuming for me for the moment, I'll have to wait  
for BJ3. Is there a roadmap/timeframe for this?
>
>
>
> I just want to suggest (for BJ3 development) to have/generate an XML  
Schema. At least I would benefit from this since I generate service  
bindings on the fly and also want to validate data in remote services.
>
>
>
> Cheers,
>
>
>
> /Ola
>
>
>
> On 13 jan 2009, at 13.52, Mark Schreiber wrote:
>
>
>
>
> Hi -
>
>
>
> With JAXB you can annotate the POJOs with JAXB instructions although I
>
> believe if you have a beany object and no annotation you get default
>
> behavior if you don't annotate it. I think you can get a schema from
>
> an object or auto generate objects from a schema (unless it is a bit
>
> complex in which case you might need to put JAXB tags in the schema).
>
>
>
> There is no clearcut way to get from biojavax to XML. This is because
>
> of the heavy use of singletons and non-bean like objects in biojavax
>
> (something that BJ3 will hopefully get away from). If you want to make
>
> a custom XML serializer/ deserializer my recommendation would be to
>
> put in a middle (transport) layer of beans that operate like the DTO's
>
> of older EJB designs. They would basically be data holders that you
>
> can generate from biojavax objects and then send to XML. Going the
>
> other way you would generate these beans from XML and then use the
>
> beans to generate biojavax objects (with singletons etc).
>
>
>
> - Mark
>
>
>
> On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth ola.spjuth at farmbio.uu.se>  
wrote:
>
>
> Hi Mark,
>
>
>
> Thanks for the quick answer. Never used JAXB myself; does this procedure
>
> support generation of an XML schema from code? I assume you will annotate
>
> the POJO's with JAXB metadata? I usually work the other way around and
>
> generate my model code from a model (usually based on an XML Schema), I
>
> guess in the end it boils down to the same result?
>
>
>
> Anyway, what is the preferred way of serializing current Biojava(X)  
objects
>
> to XML? Via BioSQL in some way?
>
>
>
> Cheers,
>
>
>
> /Ola
>
>
>
> On 13 jan 2009, at 11.24, Mark Schreiber wrote:
>
>
>
>
> The plan for biojava3 is that most or all of it will be POJO enough to
>
> support JAXB binding. The JPA implementation of BioSQL objects in BJ3
>
> is already XML compatible as the objects are entity beans and can be
>
> transported via JAX-RPC.
>
>
>
> - Mark
>
>
>
> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth ola.spjuth at farmbio.uu.se>
>
> wrote:
>
>
>
>
> Hi,
>
>
>
> Does it exist an XML Schema (or compatible) for Biojava, or even better a
>
> common schema for the Bio* projects? If not, is this in the pipe for
>
> Biojava3?
>
>
>
> /Ola
>
>
>
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