[DAS] RELAX NG schema for "sequence" command

[Andy Jenkinson]

To put another way, the ERRORSEGMENT element is only valid if the server supports the error-segment capability. I guess the issue is that the only use of the RNG schemas upto now for validation has been by the registry.

Personally from a technical point of view, I think including the errorsegment element in the RNG schemas (this will apply to many commands not just sequence) is the "correct" interpretation. However that means the registry would need to apply it's errorsegment test separately rather than relying on the rng to flag it as invalid. It already does the reverse of this test separately so this makes sense to me (i.e. if I ask for a bad segment do you give me an errorsegment element?).

Cheers,
Andy

On 1 Mar 2011, at 15:54, Jonathan Warren wrote:

> Hi Andrew
> 
> I guess this depends on what you are using the RNG for. What are you using it for? The registry needs the result from a sequence request to conform to the sequence.rng as it is on the registry as if a sequence is requested the test region put into the registry should return a sequence, if it returns an ERRORSEGMENT the the registry wants that reported as invalid. If I add the errorsegment to that document as you suggest the registry won't pick it up as invalid.
> 
> On 1 Mar 2011, at 15:19, Andrew Roberts wrote:
> 
>> 	Alright, now I'm hitting the lack of support for ERRORSEGMENT within the sequence command response.  I think there needs to be a choice inside the oneOrMore, so that elements can be SEQUENCE or ERRORSEGMENT.  I attached what I'm using as a testing schema in the meantime, hopefully it's helpful.
>> 
>> Andrew
>> <sequence.rng>
>> 
>> 
>> On Mar 1, 2011, at 5:09 AM, Jonathan Warren wrote:
>> 
>>> This is fixed now.
>>> 
>>> On 28 Feb 2011, at 18:34, Andrew Roberts wrote:
>>> 
>>>> Hello,
>>>> 
>>>> 	I'm working on some validations, and I think I may have found an error in sequence.rng (www.dasregistry.org/validation1.6/sequence.rng).  It appears that this schema makes no provision for the actual text data that belongs to the sequence element (i.e. the bases themselves).  Is this a known issue?
>>>> 
>>>> 	If not, I think the solution is to add a <text/> element inside the sequence element.  Line 10 should read,
>>>> 
>>>>            <attribute name="start"><data type="integer"></data></attribute><attribute name="stop"><data type="integer"></data></attribute><optional><attribute name="version"><text></text></attribute></optional><optional><attribute name="label"><text></text></attribute></optional><text/></element>
>>>> 
>>>> Cheers,
>>>> 
>>>> Andrew
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>>> 
>>> Jonathan Warren
>>> Senior Developer and DAS coordinator
>>> blog: http://biodasman.wordpress.com/
>>> jw12 at sanger.ac.uk
>>> Ext: 2314
>>> Telephone: 01223 492314
>>> 
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>>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE.
>> 
> 
> Jonathan Warren
> Senior Developer and DAS coordinator
> blog: http://biodasman.wordpress.com/
> jw12 at sanger.ac.uk
> Ext: 2314
> Telephone: 01223 492314
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE._______________________________________________
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