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

[Andrew Dalke]

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

http://das.biopackages.net/das/genome/yeast/S228C/feature?overlaps=chrVI
I/364251:366080;type=SO:gene

as follows

[guest276:das/das2/scratch] dalke% python ./verify_examples.py
load FEATURES  
"http://das.biopackages.net/das/genome/yeast/S228C/feature? 
overlaps=chrVII/364251:366080;type=SO:gene"
! expected root tag  
'{http://www.biodas.org/ns/das/genome/2.00}FEATURES' got  
'{http://www.biodas.org/ns/das/2.00}FEATURELIST'
^D
[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  
'{http://www.biodas.org/ns/das/2.00}FEATURES'

That's because

<FEATURES
   xmlns="http://www.biodas.org/ns/das/2.00"

should be

<FEATURES
   xmlns="http://www.biodas.org/ns/das/genome/2.00"

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,

*  
file:///Users/dalke/cvses/das/das2/scratch/biopackages_features.xml:10: 
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.

*  
file:///Users/dalke/cvses/das/das2/scratch/biopackages_features.xml:95: 
57: error: element "LOC" from namespace  
"http://www.biodas.org/ns/das/genome/2.00" not allowed in this context

That came from

   <FEATURE
     id="feature/Affymetrix_YG-S98:3128_at"
     type_id="type/SO:PCR_product"
     name="Affymetrix_YG-S98:3128_at"
   >

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

   </FEATURE>


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
    das/das2/scratch/biopackages_features.xml


					Andrew
					dalke at dalkescientific.com