[DAS] Adjacent feature extension

[Andy Jenkinson]

On 7 Mar 2011, at 14:11, Jonathan Warren wrote:

> 
> On 7 Mar 2011, at 12:43, Andy Jenkinson wrote:
> 
>> In particular, I can foresee servers not interpreting the "type" filter appropriately, being likely to process the adjacent query then apply the type filter, which would be wrong. I have a feeling most sources implement the type filter as a passive "post filter" rather than an active one. I can tell you right now that it is going to be really quite difficult for me to implement "adjacent" correctly for the ASTD gene/transcript/exon sources, and I suspect the same will be true for retrofitting lots of other sources.
> This is an optional capability though right?

Of course, I'm just saying it's difficult for servers to implement so we should expect to see bad implementations exactly as we do with feature-by-id.

>> 
>>>> 
>>>> As to feature-by-id, I know changing behaviour is potentially a very disruptive change, but I think we can potentially do this purely because servers don't tend to implement it correctly anyway. Clients can happily filter out any additional features returned by old servers, and if any clients are reliant on the server including all overlapping features then as far as I am concerned they are either a) targeting specific servers rather than DAS-wide and thus unaffected, or b) already broken :)
>>> So you agree feature-by_id should be changed if we have the stomach for it? - good and Gustavo too. Well done Andy - You have just agreed to write Spec 1.7 or 3??? ;) Your argument above can be used for leaving the spec as it is then as well - but ideally I agree and guess we can call it spec 1.61 assuming other people agree.
>> 
>> I already have a small list of changes for DAS 1.7 or whatever and think it's fine for that context. In any case, let's keep these two issues separate as Thomas says.
> 
> I was really hoping not to do another major spec revision for at least 3 years and to focus on extensions giving new capabilities- otherwise for the core capabilities everyone is always playing catch up! This maybe something to discuss at some point soon.
>> 
>>>> 
>>>> I have to admit that the feature-by-id capability is one of the (many) things I loathe having to explain and would love to change it. Doing so would be consistent with what we were trying to do with 1.6 (i.e. rationalise existing use of the spec) but I chickened out really.
>>>> 
>>>> Cheers,
>>>> Andy
>>> 
>>> 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.