[Biojava-dev] XML Schema

[Ola Spjuth]

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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>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>