[DAS2] RE: Problem with parent/child features in biopackages server feature response

[Helt,Gregg]

Thanks for the quick fix!

Now I'm seeing another problem though.  Some feature queries with a
combination of one "overlaps" and one "inside" filter are giving weird
errors.  But some return correctly.

For example, 
http://das.biopackages.net/das/genome/human/17/feature?overlaps=chr21/26
104961:26271647;inside=chr21/26104961:46976097;type=SO:mRNA
returns correctly.

But
http://das.biopackages.net/das/genome/human/17/feature?overlaps=chr21/25
854314:26027736;inside=chr21/0:26027736;type=SO:mRNA
does not, instead returning these headers:
	HTTP/1.1 200 OK
	Date: Mon, 17 Oct 2005 22:40:54 GMT
	Server: Apache/2.0.51 (Fedora)
	X-DAS-Version: DAS/2.0
	X-DAS-Server: GMOD/0.0
	X-DAS-Content-Type: text/x-das-feature+xml
	X-DAS-Status-Details: Died at
/usr/lib/perl5/site_perl/5.8.3/Package/Base/Devel.pm line 425.

and then what appears to be more headers but is designated as content
(so I'm guessing a header-terminating blank line got inserted before
these):
	X-DAS-Status: 500
	X-DAS-Status: 200
	Content-Length: 0
	Keep-Alive: timeout=15, max=100
	Connection: Keep-Alive
	Content-Type: text/xml

The combination of an "overlaps" and "inside" filter is an important
part of IGB's client-side query optimizations.  I can turn this
optimization off for now, but I'm hoping you can diagnose and fix the
problem.

	Thanks again,
	Gregg

> -----Original Message-----
> From: Allen Day [mailto:allenday at ucla.edu]
> Sent: Monday, October 17, 2005 2:50 PM
> To: Helt,Gregg
> Cc: das2 at portal.open-bio.org
> Subject: Re: Problem with parent/child features in biopackages server
> feature response
> 
> Hi Gregg,
> 
> There was a logic inversion in my code.  PARENT/PART relationships
should
> now be restored.
> 
> Andrew, I'd also like to know if there is some code already written
that
> can be written into my regression tests.
> 
> I understand that it's really irritating to have non-fatal errors of
> different types continuously appearing.  Maybe I should spend some
time
> beefing up the regression test suite to do things like diff feature
graphs
> and make sure they are identical?  Something to discuss on the
conference
> call...
> 
> -Allen
> 
> On Mon, 17 Oct 2005, Helt,Gregg wrote:
> 
> > I finally got back to testing DAS/2 feature requests/responses in my
IGB
> > client.  I'm seeing a new problem in responses from the biopackages
> > server, there are no <CHILD> or <PARENT> elements for features at
all.
> >
> > See for example the returned XML from my standard test query:
> >
http://das.biopackages.net/das/genome/human/17/feature?overlaps=chr21/26
> > 027736:26068042;type=SO:mRNA
> >
> > ...
> > <FEATURE id="feature/BC001178" type="type/SO:mRNA" name="BC001178">
> > 	<LOC pos="region/chr21/26018728:26029854:-1"/>
> > 	...
> > </FEATURE>
> > <FEATURE id="feature/auto316726" type="type/SO:three_prime_UTR"
> > name="auto316726">
> > 	<LOC pos="region/chr21/26018728:26018820:-1"/>
> > </FEATURE>
> > ...
> >
> > But I know that "auto316726" should be a child of "BC001178".
> >
> > Andrew, would your DAS/2 validator catch problems like this?
> >
> >
> > 	Thanks,
> > 	Gregg
> >
> >