[DAS2] DAS/2 Server on Biopackages.net

[Brian O'Connor]

Hi,

I brought the DAS/2 server back online and the bug with empty 
domain/source/versioned source documents should now be fixed.  See: 
http://das.biopackages.net/das/genome.  Also, I temporarily turned 
server caching off so I can make sure the server is responding 
correctly.  I'll turn caching back on tomorrow after I've finished 
debugging/checking the responses.  The server is now using CVS HEAD.

Anyway, I've been looking over the output from our server and comparing 
it to the HTML spec and the RNC schema doc from cvs.  I have a few 
comments/questions/bugs:

Potential bugs on das.biopackages.net:

* FIXED: segments response was missing xmlns
* FIXED: domain/source/versioned source docs are not populated correctly
* Coordinates is missing the source attribute (it's empty) which is 
required in the RNC
* The capability responses look like:
 >>>>
<CAPABILITY type="type" query_uri="human/17/type">
<CAPABILITY type="feature" query_uri="human/17/feature">
<CAPABILITY type="segment" query_uri="human/17/segment">
<<<<
Whereas the HTML spec and RNC doc use "features", "types", and 
"segments".  Should this be changed on the biopackages.net server?

Questions about HTML spec/RNC doc:

* The segments element has a required attribute of "uri" in the RNC doc, 
is this correct?  The biopackages.net server only has a uri for a given 
segment and the examples from the HTML are the same.
* It's a little confusing to have the "overview" and "detailed" sections 
separate in the HTML spec.  I think it would make more sense to put the 
detailed section right after each overview or at least provide an anchor 
link at the end of each overview.
* Anchor links are broken throughout the html doc.
* the RNC mentions the type attribute under capability with:
 >>>>
  # A term describing the capability.  The following are reserved
  # terms: segments, features, locks, writeback, das1:segments,
  #  das1:types, das1:features
  attribute type { text },
<<<<
Types should be listed here too.  Also, could this be defined with:

attribute type { "segments" | "features" | "types" | "locks" | "..." }

to make it more clear?


Please let Allen or I know if you have any problems using the biopackages.net server.

--Brian