[DAS2] hrefs and xml:base

Lincoln Stein lstein at cshl.edu
Wed May 4 23:59:04 UTC 2005


I think that the current spec uses xml:base in the way that the standard 
intends, but please feel free to insert clarifications & corrections.  As far 
as putting the bg: prefix into the key name, it was intended to indicate that 
the key "glyph" belongs to the list of properties located at 
http://www.bioperl.org/biographics/properties.  Now, I didn't find any 
references to tell me how to namespace an attribute value, so I just fudged 
things. Are there better ways to do this?


On Wednesday 04 May 2005 17:46, Andrew Dalke wrote:
> Gregg:
> > If we want to fully adopt the xml:base standard (which I think we do),
> > then my interpretation is that xml:base is lexically scoped and within
> > its scope allows any attribute that requires a URI to be potentially
> > specified as a relative URI (relative to the xml:base) instead of an
> > absolute URI.
> That's what I figured, and what I did in my code.
> I'll edit the docs to flag which fields are expanded by xml:base.
> Now for part 2 of the question, in the <PROP> tag will
> the values ever take relative URLs?  Eg, suppose some
> server has an SVG description of how to draw the type
>      <PROP key="depict"  value="/svg/tRNAscan.svg" />
> In a related topic, the TYPES example we have says
>       xmlns="http://www.biodas.org/ns/das/genome/2.00"
>       xmlns:xlink="http://www.w3.org/1999/xlink"
>       xmlns:bg="http://www.bioperl.org/biographics/properties"
>       xmlns:das="http://www.biodas.org/ns/das/genome/2.00"
>       xml:base="http://www.wormbase.org/das/genome/volvox/1/type/">
> ..
>      <PROP key="bg:glyph"     value="box" />
>      <PROP key="bg:bgcolor"   value="white" />
>      <PROP key="bg:fgcolor"   value="black" />
>      <PROP key="bg:key"       value="tRNAs" />
>      <PROP key="bg:citation"  value="tRNA predictions made using Sean
> Eddy's tRNAscan program." />
>      <PROP key="bg:fontcolor" value="slateblue" />
>      <PROP key="bg:height"    value="3" />
> Is the "bg" in the XML namespace "bg" supposed to be inserted
> into the key name as a string?  If so, how?  Using universal
> names ( http://www.jclark.com/xml/xmlns.htm ) like
>   "{http://www.bioperl.org/biographics/properties}height"
> Or is the xmlns:bg definition there in error?
> This is a problem for me because the parsers I use treat
> XML namespaces as things that only apply to tags and attributes
> and throw away the namespace scope.
> There aren't that many people using DAS nor will there
> be.  We could just say that certain prefixes are reserved
> and that people may pick a unused namespace prefix as desired.
> 					Andrew
> 					dalke at dalkescientific.com
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