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

Allen Day allenday at ucla.edu
Mon Oct 17 21:50:14 UTC 2005

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


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 id="feature/auto316726" type="type/SO:three_prime_UTR"
> name="auto316726">
> 	<LOC pos="region/chr21/26018728:26018820:-1"/>
> ...
> But I know that "auto316726" should be a child of "BC001178".
> Andrew, would your DAS/2 validator catch problems like this?
> 	Thanks,
> 	Gregg

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