[DAS2] Re: Problems with biopackages DAS2 server

Allen Day allenday at ucla.edu
Thu Oct 6 19:49:05 UTC 2005

On Thu, 6 Oct 2005, Helt,Gregg wrote:

> I'm having some problems with feature responses from the DAS/2 server at
> das.biopackages.net.  It looks like in the das2feature XML at least some
> features are now pointing to themselves as parents.  For example, as

Yes, I know about this one.  It's an artifact of the performance
improvements I pushed to the production server (the one you use).  It can
be fixed quickly -- like by Friday.

> part of response to
> http://das.biopackages.net/das/genome/human/17/feature?overlaps=chr21/19
> 301959:21567303;type=SO:mRNA
> ...
> <FEATURE id="feature/U75330" type="type/SO:mRNA" name="U75330">
>     <PARENT id="feature/U75330"/>
>     <LOC pos="region/chr21/21292691:21834284:1"/>
>     ...
> ...
> Another problem I'm seeing is server internal errors in response to
> combination of an overlaps and inside feature filter, for example:

Now that you've mentioned it, I could have predicted this error.  I'll add
a unit test for overlaps+inside combined queries.  So the good news is
that once I fix it and add a test for this type of error, it won't happen

The bad news is that this fix may take several days as I have several
other urgent things in my queue.

> http://das.biopackages.net/das/genome/human/17/feature?overlaps=chr21/25
> 108802:26550995;inside=chr21/21567303:46976097;type=SO:mRNA
> returns an HTTP status code of 500, "Internal Server Error".
> Has the combination of overlaps/inside filter not been implemented yet?
> Or is this possibly because of the size of the inside filter's region?
> I haven't noticed either of these problems before, but for the last
> several weeks I've only been testing the higher-level responses
> (sources, regions, types) while redoing the client GUI, so I'm not sure
> when this started happening.

These are new errors as of last week, when I pushed out the new range 
query optimizations.


>             gregg

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