[DAS] RELAX NG schema for "sequence" command

[Jonathan Warren]

If your data source is publicaly available you can test it by making a  
request like this:
http://www.dasregistry.org/validate?url=http://das.sanger.ac.uk/das/otter_das/&testcode=22:19173435,19372173

which returns properties for the status of each command. Or you can  
use the validation page on the registry interface to do the same thing.

Some people here are working on some XSD documents in order to use  
JAXB which will probably be of use to you as they should be structured  
more as you suggest.

We maybe need to make it more clear how we use these RNG documents in  
the documentation.

Thanks for the feedback!

On 1 Mar 2011, at 16:20, Andrew Roberts wrote:

> Ah, interesting. I'm exercising my implementations of the das  
> commands, and then validating the XML against the rng as a  
> correctness test. I had been assuming that the rng was a description  
> of all possible server responses, including error cases, but I now  
> see what you guys are using them for.
>
> Thanks!
>
>
>
> On Mar 1, 2011, at 10:54 AM, Jonathan Warren <jw12 at sanger.ac.uk>  
> 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
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>> 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.
>>>
>>
>> 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.

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.