[DAS2] Re: Apollo and DAS/2 priorities

Ed Erwin ed_erwin at affymetrix.com
Mon Jan 30 22:41:23 UTC 2006

Thanks Andrew,

I've looked over the rnc and xml files and here are my few comments and 


In common.rnc in the definition of prop_list, I'd prefer to use
the string 'mimetype' rather than the ambiguous 'type'

prop_list = element PROP {

   attribute key { text },
   ( attribute value { text } |
     attribute href { text } |
    (attribute type { text },
     text )


I have some questions about the <FORMAT> elements in the sources.xml 

       <SET type="features" id="volvox/1/features">
           <FORMAT name="das2xml" mimetype="text/x-das-type+xml" />
       <SET type="residues" id="volvox/1/residues">
           <FORMAT name="fasta" mimetype="text/x-fasta" />
           <FORMAT name="raw" mimetype="text/x-raw-sequence" />

If multiple formats are listed, does that mean that
   1) every object of that type is available in each of those formats, or
   2) every object is available in at least one of those formats?

For the DAS-specific formats like "text/x-das-type+xml",
do we require that each server must support all of those?

If so, is that made explicit somewhere?


In this example in sources4.xml, would you be better-off using
URL-encoding ("/blah%3c2%3e.txt") rather than XML-encoding?
Or is there an assumption that the necessary URL-encoding will
be done at a later time?

   <SOURCE id="human/" title="Duke Human" doc_href="/blah&lt;2&gt;.txt">



Andrew Dalke wrote:
> I have just (within the last few minutes) completed the first draft
> of the update of the spec.
> It's not in HTML - that calls for too much work for this stage.
> It's text, in CVS under das/das2/new_spec.txt
> There are many parts which need clarification.  These are marked
> with a "XXX" along with my comments.
> The RNC files are in
>   das/das2/scratch/*.rnc
> along with some test XML files.  These XML files are not meant
> to be realistic.  They are meant more to check edge cases.

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