[DAS] LDAS/DasClient problems

[Thomas Down]

On Tue, Feb 05, 2002 at 12:39:35PM -0500, Lincoln Stein wrote:
> Hi Thomas,
> 
> Now it makes sense.  I thought you were asking for the annotation servers to 
> distinguish between SEGMENTERROR and LANDMARKNOTANNOTATED.

I think it's still legitimate for an annotation server to flag
an error under some conditions (the one which comes to mind
is a request for an out-of-bounds region of a landmark which
the server /does/ know about).  SEGMENTUNKNOWN (or whatever
you want to call it) is a distinct case from this, though.

> How do you feel about calling the latter tag <SEGMENTUNKNOWN> (to be issued 
> by annotation servers only), since it is completely noncommittal about 
> whether the segment is an error or just unannotated.

Fine by me.  Also looks rather less ugly than 

> 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)?

> 	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
> 
> 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.