[DAS2] biopackages DAS/2 server passed validation

[Helt,Gregg]

I've fixed some bugs in IGB and now it is able to retrieve some genome
features from the biopackages server and visualize them.  For example
this feature query works:

http://das.biopackages.net/das/genome/human/17/feature?segment=http%3A%2
F%2Fdas.biopackages.net%2Fdas%2Fgenome%2Fhuman%2F17%2Fsegment%2Fchr21;ov
erlaps=26040000%3A26060000;type=SO%3AmRNA

with URL-decoded query params:
	
segment=http://das.biopackages.net/das/genome/human/17/segment/chr21
	overlaps=26040000:26060000
	type=SO:mRNA

However, not all feature queries work.  For example, another query,
exactly the same as the above except for a different type filter:

http://das.biopackages.net/das/genome/human/17/feature?segment=http%3A%2
F%2Fdas.biopackages.net%2Fdas%2Fgenome%2Fhuman%2F17%2Fsegment%2Fchr21;ov
erlaps=26040000%3A26060000;type=SO%3ACDS

with URL-decoded query params:
	
segment=http://das.biopackages.net/das/genome/human/17/segment/chr21
	overlaps=26040000:26060000
	type=SO:CDS

returns this error message:

<?xml version="1.0" encoding="UTF-8"?>
<FEATURES
    xmlns="http://biodas.org/documents/das2"
    xml:base="http://das.biopackages.net/das/genome/human/17/"
>

<error>
                         <code>500</code>
                         <description>Died at
/usr/lib/perl5/site_perl/5.8.3/Package/Base/Devel.pm line 425.
</description>
                       </error>

Should "SO:CDS" not be a searchable type?

Also, is the full URI for the type supposed to be 
	A) "SO:CDS" or 	
	B) "http://das.biopackages.net/das/genome/human/17/type/SO:CDS"
?
According to XML Base resolution rules, with "SO:CDS" as the value for
the TYPE uri attribute, then because there is a ":" before any "/", the
full URI is (A).  If the full URI is supposed to be (B), then the uri
attribute should be "./SO:CDS" (given that xml:base is
"http://das.biopackages.net/das/genome/human/17/type/").

	Thanks,
	Gregg

> -----Original Message-----
> From: das2-bounces at lists.open-bio.org [mailto:das2-bounces at lists.open-
> bio.org] On Behalf Of Helt,Gregg
> Sent: Tuesday, November 14, 2006 6:45 PM
> To: Brian O'Connor; das2 at lists.open-bio.org
> Subject: Re: [DAS2] biopackages DAS/2 server passed validation
> 
> Thanks!  Looks like most of the problem IGB was having with the
> biopackages server were due to the truncated 'type' attributes in
> CAPABILITY.
> 
> Using IGB I'm still not getting features back from the biopackages
> server from a features query with overlaps and type filters, but I
think
> that's a bug in IGB's request.  Hope to fix tonight.
> 
> 	Gregg
> 
> > -----Original Message-----
> > From: das2-bounces at lists.open-bio.org
[mailto:das2-bounces at lists.open-
> > bio.org] On Behalf Of Brian O'Connor
> > Sent: Tuesday, November 14, 2006 4:46 PM
> > To: das2 at lists.open-bio.org
> > Subject: [DAS2] biopackages DAS/2 server passed validation
> >
> > Hi,
> >
> > I finished validating the DAS/2 server at biopackages.net using
> Andrew's
> > validator.  After making a few small tweaks all document types pass.
> > Here are the URLs I validated with:
> >
> > * http://das.biopackages.net/das/genome
> > * http://das.biopackages.net/das/genome/human/17/segment
> > * http://das.biopackages.net/das/genome/human/17/type
> > *
> >
>
http://das.biopackages.net/das/genome/human/17/feature?segment=http%3A%2
> F%
> >
>
2Fwww.ncbi.nlm.nih.gov%2Fgenome%2FH_sapiens%2FB36.1%2Fdna%2Fchr1;overlap
> s=
> > 1:1000
> >
> > I also fixed the bug with the "type" attribute in the CAPABILITY
> > elements.  They now are "features", "types", or "segments" to be
> > compliant with the spec.
> >
> > --Brian
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das2
> 
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