[DAS] LDAS/DasClient problems

[Lincoln Stein]

> > So I'm updating the LDAS server to do the following:
> >
> > 	1) <SEGMENTERROR> for reference servers
> > 	2) <SEGMENTUNKNOWN> for annotation servers
>
> What do you do for the above case (requested an out-of-bounds
> region of a known segment)?

Yes, that's a good point.  An annotation server should return a segment error 
in this case.  Is it worth it to distinguish between missing landmarks and 
out of bounds errors?  Something like:

	<SEGMENTERROR detail="unknown landmark" ....>
	<SEGMENTERROR detail="bounds error" ...>
	<SEGMENTERROR detail="version skew" ...>

> > 	3) pass the "id" attribute in the features request
> > 		to look up a feature by its ID
> > 		- can return several segments if the feature spans
> > 			them
> > 	4) the HTTP header to contain some capabilities information:
> > 		x-das-capabilities:  multiple-segments; segment-status; xff-format;
> > 				feature-by-id
> >

Are these additions OK with you as is?  If so, they'll go into LDAS & the 
spec now.

Lincoln


> > How do you feel about modifying XFF slightly in order to normalize
> > groups?  I would love to be able to give exons unique IDs and then to
> > explicitly assign them to different splice patterns, rather than
> > duplicating them within the document.
>
> It sounds a nice idea, at least in principle.  I'll dig out the
> example I came up with showing how this might be done.
>
> > With regards to Dmitry's original problem, I can either produce an
> > intermediate version of LDAS that will give empty segments when a
> > landmark is not recognized so that it will work with Dazzle right now, or
> > I can release a version with the above modifications.  This will require
> > coordinate changes in Dazzle, Bio::DAS, and any other client libs
> > floating around.  Or you can patch Dazzle to accept LDAS's silent
> > omission of missing landmarks.  Which do you prefer?
>
> It shouldn't be too hard to put a temporary patch into das-client,
> so I'll do that for now.
>
>     Thomas.

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================