[DAS2] Re: Apollo and DAS/2 priorities

[Allen Day]

The XML is now as you requested, please confirm.

After some thought today I realized the new SOURCES response is fully
compatible with the existing server.  The doc at:

http://das.biopackages.net/codesprint/sequence

is now simply a static XML doc that points into the stable server (plus
the new "segments" response) implementation at:

http://das.biopackages.net/das/genome

The headers for the static document don't include the correct Content-Type
"application/x-das-blah ; version = XxX", it's simply "text/xml".  I'll
add the headers in the morning GMT+8.

There are probably also some other Content-Type headers that need to be
changed for the other responses -- let me know if you spot them.

-Allen



On Mon, 6 Feb 2006, Andrew Dalke wrote:

> Allen:
> > After looking closely over this first draft of new_spec.txt, it's 
> > apparent
> > that there are still some holes, e.g. what should the response to the
> > following requests look like?
> >
> > http://das.biopackages.net/codesprint/sequence/yeast
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <SOURCES
>        xmlns:xlink="http://www.w3.org/1999/xlink"
>        xml:base="http://radius.genomics.ctrl.ucla.edu/das/sequence/">
> taxon="Yeast">
>        <VERSION id="yeast/S228C" title="Sce" created="" modified="">
> 
>        <COORDINATES taxid="" source="" authority="">
>          <VERSION name=""/>
>        </COORDINATES>
> 
>        <ASSEMBLY>
>          <LINK href="" priority=""/>
>        </ASSEMBLY>
> 
>        <PROP key="" value=""/>
> 
>        <CATEGORY type="features" query_id="yeast/S228C/feature">
>          <!-- list non-das2xml templates here -->
>        </CATEGORY>
>        <CATEGORY type="segments" query_id="yeast/S228C/segment"/>
>        <CATEGORY type="types"    query_id="yeast/S228C/type"/>
>        <CATEGORY type="locks"    query_id="yeast/S228C/lock"/>
> 
>      </VERSION>
> 
>    </SOURCE>
> </SOURCES>
> 
> 
> > http://das.biopackages.net/codesprint/sequence/yeast/S228C
> 
> The same for this case.  There is only on VERSION for "yeast".
> 
> 
> Your XML, btw, starts
> 
> <?xml version="1.0" standalone="no"?>
> <?xml-stylesheet type="text/xsl" href="/xsl/das.xsl"?>
> <!DOCTYPE DAS2DSN SYSTEM "http://www.biodas.org/dtd/das2dsn.dtd">
> <!-- this doesn't work and screws up the xsl     
> xmlns="http://www.biodas.org/ns/das/genome/2.00" -->
> <SOURCES
>        xmlns:xlink="http://www.w3.org/1999/xlink"
>        xml:base="http://radius.genomics.ctrl.ucla.edu/das/sequence/">
> 
> The "standalone" means that the DTD may affect the content of the
> documentation.
>    http://www.stylusstudio.com/w3c/xml11/sec-rmd.htm
> 
> > Markup declarations can affect the content of the document, as passed 
> > from an XML Processor to an application; examples are attribute 
> > defaults and entity declarations. The standalone document declaration, 
> > which MAY appear as a component of the XML declaration, signals 
> > whether or not there are such declarations which appear external to 
> > the Document Entity or in parameter entities. An external markup 
> > declaration is defined as a markup declaration occurring in the 
> > external subset or in a parameter entity (external or internal, the 
> > latter being included because non-validating processors are not 
> > required to read them).
> 
> For what we're doing, we don't need nor (I think) want that.  There's
> no reason for a client to consult the DTD to figure out the XML.
> 
> Instead, use
> 
> <?xml version="1.0"?>
> 
> and probably have the encoding
> 
> <?xml version="1.0" encoding="UTF-8"?>
> 
> That also means you can get rid of the
> 
> <!DOCTYPE DAS2DSN SYSTEM "http://www.biodas.org/dtd/das2dsn.dtd">
> 
> statements.
> 
> 					Andrew
> 					dalke at dalkescientific.com
> 
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