[Biojava-dev] XML Schema

[Richard Holland]

Sorry about that last one. I understand what you're getting at now.

There is no current roadmap/timeline for BJ3 as there is nobody
developing it except me and I've got lots of other things to do at the
moment, which involve getting paid and so sadly have to take priority.

Maybe there is someone out there who is willing to take responsibility
for it and project manage the BJ3 development?

cheers,
Richard

Ola Spjuth 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
>>>>>
>>>>> _______________________________________________
>>>>> biojava-dev mailing list
>>>>> biojava-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>>
> 
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-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/