[DAS2] Re: New DAS/2 server for codesprint

Andrew Dalke dalke at dalkescientific.com
Thu Feb 9 09:35:19 UTC 2006

In the das2/scratch directory is a program called "verify_examples.py"
I ran it against


as follows

[guest276:das/das2/scratch] dalke% python ./verify_examples.py
! expected root tag  
'{http://www.biodas.org/ns/das/genome/2.00}FEATURES' got  
[guest276:das/das2/scratch] dalke%

That is, it's a simple command language.  The command to
load a URL of the given type is

   load FEATURES "url"

In this case it warns that the top-level name is "FEATURELIST"
instead of "FEATURES", which is something that was changed
last summer, I think.

Saving locally and editing by hand I then get

! expected root tag  
'{http://www.biodas.org/ns/das/genome/2.00}FEATURES' got  

That's because


should be


according to the spec.  I don't like the namespace though.

*** Does anyone mind if we change the namespace URL?  ***

Next is
* fatal: file not found: http://www.biodas.org/dtd/das2feature.dtd

That occurs because the XML says that it requires the DTD
to be understood (with the 'standalone="no"' at the top)

Taking that out and the DTD link,

4: error: attribute "type" not allowed at this point; ignored

That should be "type_id" instead of "type".  I've used "id"
as a convention to indicate that something is a URL inside of
DAS.  Change it to "url" or "uri" instead?

The PARENT should be after the LOC.  However, I think that the
ordering requirement is too fragile so I'll change the schema
so the elements can go in more arbitrary order.

There was an issue with the <PROP> element.  I'll explain
in the next email.

57: error: element "LOC" from namespace  
"http://www.biodas.org/ns/das/genome/2.00" not allowed in this context

That came from


       <LOC id="segment/chrVII" range="319671:774428:-1"/>
       <LOC id="segment/chrVII" range="735985:736081:1"/>


The RNC had a bug - it only allowed a single LOC element.  Fixed.

I've updated the schema and committed a copy of a features
data set from Allen's server to CVS under

					dalke at dalkescientific.com

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