[DAS2] Re: Apollo and DAS/2 priorities

[Andrew Dalke]

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