[DAS2] Re: New problem with content-type header in DAS/2 server responses!

[Lincoln Stein]

On Monday 14 November 2005 06:47 am, Andrew Dalke wrote:
> Steve:
> > I raised some other issues regarding types and feature properties etc.
> > a
> > couple of weeks ago that I'd like you to chime in on:
> > http://portal.open-bio.org/pipermail/das2/2005-October/000271.html
> >
> > The latest message on this thread is:
> > http://portal.open-bio.org/pipermail/das2/2005-November/000278.html
>
> I'll take them part by part.
>
> That last message suggested
>
>    <FEATURES xmlns="http://www.biodas.org/ns/das/genome/2.00"
>              xmlns:das="http://www.biodas.org/ns/das/genome/2.00"
>              xml:base="http://www.wormbase.org/das/genome/volvox/1/"
>              xmlns:xlink="http://www.w3.org/1999/xlink"
>
> das:prop="http://www.biodas.org/ns/das/genome/2.00/properties">
>      <FEATURE das:id="feature/cTel54X.1.2"
>               das:type="type/curated_exon">
>        <PROP das:ptype="property/genefinder-score">29</PROP>
>        <PROP das:ptype="das:prop#phase">2</PROP>
>        <PROP das:ptype="das:prop#protein_translation"
>              xlink:type="simple"
>
> xlink:href="http://www.wormbase.org/das/protein/volvox/2/feature/
> CTEL54X.1
> />
>      </FEATURE>
>
>
> I couldn't figure out why the "das:" namespace was needed for the
> attributes.  Why can't they be in the default namespace?

The extras das: prefix is not needed since it is the same namespace as the 
default namespace.

My feeling is that we should NOT be using namespaces in attribute names but 
not in attribute values (e.g. das:ptype is ok, but "das:prop#phase" is not 
OK). For attribute values we should be using URIs consistently.

Lincoln

> The "das:" in the value of an attribute doesn't know anything about
> the currently defined namespaces.  So this "das:" must be something
> completely different from the xmlns:das=... definition.
>
> >  * the values of the 'das:id', 'das:type', and 'das:ptype' attributes
> >    are URLs relative to xml:base unless they begin with 'das:prop#', in
> >    which case they are relative to the das:prop namespace.
>
> And from what I can tell about XML, there's no standard way to implement
> this using one of the standard XML parsers.  How do you get the das:prop
> namespace for a given element?  The parser often does the expansion
> for you.  Eg, in one of the Python XML parsers it does the translations
> into Clark notation, like
>
>    {http://www.biodas.org/ns/das/genome/2.00}ptype
>
> For more info on XML namespaces, see http://www.jclark.com/xml/xmlns.htm
>
>
>
> 					Andrew
> 					dalke at dalkescientific.com
>
> _______________________________________________
> DAS2 mailing list
> DAS2 at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/das2

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING, 
PLEASE CONTACT MY ASSISTANT, 
SANDRA MICHELSEN, AT michelse at cshl.edu