[DAS2] biopackages.net out of synch with spec?

[Lincoln Stein]

I'll use your hand-edited examples for testing.

Lincoln

On Wednesday 15 March 2006 14:32, Andrew Dalke wrote:
> Lincoln:
> > I just ran through the source request on biopackages.net and it is
> > returning
> > something that is very different from the current spec (CVS updated as
> > of
> > this morning UK time).
>
> The server isn't synched with any specific version of the spec. For
> example, if I make a features request from
>
> http://das.biopackages.net/das/genome/yeast/S228C/feature?inside=chr1/
> 0:1000")
>
> I get
>
> <?xml version="1.0" standalone="no"?>
> <!DOCTYPE DAS2FEATURE SYSTEM
> "http://www.biodas.org/dtd/das2feature.dtd">
> <FEATURELIST
>    xmlns="http://www.biodas.org/ns/das/2.00"
>    xmlns:xlink="http://www.w3.org/1999/xlink"
>    xml:base="http://das.biopackages.net/das/genome/yeast/S228C/feature">
> </FEATURELIST>
>
> As from the discussion a few weeks ago we shouldn't be using the
>    standalone="no"
> since that says the document cannot be understood without consulting
> the DTD, which doesn't exist.  And I don't want a DTD.
>
> Also, the namespace needs to be
> "http://www.biodas.org/ns/das/genome/2.00"
> (It's missing the 'genome') and the 'FEATURELIST' was replaced with
> 'FEATURES' a year ago.
>
> In the types request
>
> <?xml version="1.0" standalone="no"?>
> <?xml-stylesheet type="text/xsl" href="/xsl/das-genome-type.xsl"?>
> <!DOCTYPE DAS2TYPES SYSTEM "http://www.biodas.org/dtd/das2types.dtd">
> <!--
>       xmlns="http://www.biodas.org/ns/das/genome/2.00"
> -->
> <TYPES
>       xmlns:xlink="http://www.w3.org/1999/xlink"
>       xml:base="http://das.biopackages.net/das/genome/yeast/S228C/type/">
>    <TYPE id="SO:ARS" ontology="/das/ontology/obo/1/ontology/SO/0000436"
> name="ARS" definition="A sequence that can autonomously replicate, as a
> plasmid, when transformed into a bacterial host.">
>
>
> the commented out namespace declaration needs to there, and the type
> id 'SO:ARS' needs to be escaped as it's treated as an identifier
> resolved
> with the "SO" protocol.  Plus, until yesterday I didn't know about the
> 'name' or 'definition' attributes.  These are now in the schema as
> 'title' and 'description'.
>
> There are a few other differences, like problems in the taxid and
> empty strings for timestamps.  I hand-updated examples from Allen's
> server yesterday, in cvs under das/das2/draft3/ucla .  I found some
> of these during the update, though others I pointed out about a
> year ago.
>
> Allen doesn't want to update the server until the spec is stable,
> for two reasons.  First, he doesn't like the churn of doing work only
> to have to make more changes.  Second, you're not the only one who says
>
> >  It is much more fun for me to code to a working
> > server because I have the opportunity to watch my code run.
>
> and Allen's setup doesn't have the ability to implement two versions
> at the same time.
>
> 					Andrew
> 					dalke at dalkescientific.com
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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