[DAS2] DAS/2 Code Sprint, August 14-18

[Steve Chervitz]

On Mon, 14 Aug 2006, Allen Day wrote:

> Ah, I may implement this.  Let's discuss tomorrow morning.  Is there an
> agenda set?  Is anyone teleconferencing in?

I haven't seen a specific agenda, but something like this seems 
reasonable:

* status reports, including what you want to focus on for the sprint
* establish a prioitized list of goals and deliverables for the
   current sprint

Teleconferencing will start at 9AM PST on the usual number:

TEL=800-531-3250 (US) or 303-928-2693 (Int'l)
ID=2879055
PIN=1365

Steve

>
> On 8/10/06, Chervitz, Steve <Steve_Chervitz at affymetrix.com> wrote:
>> 
>> The netaffxdas das/2 server is back up now. Turned out to be a memory
>> trouble. The server got some whomping queries thrown at it, such as these:
>> 
>> 
>> M_musculus_Aug_2005/features?overlaps=chr1/0:194923535;type=mrna;format=bps
>> 
>> H_sapiens_Mar_2006/features?overlaps=chr20/0:62435964;type=mrna;format=bps
>> 
>> Which it could not complete due to out of memory errors. But it could
>> handle
>> this sizeable query even after the above failed:
>> 
>> 
>> H_sapiens_May_2004/features?overlaps=chr20/0:62435964;type=refseq;format=brs
>> 
>> Eventually, Jetty just decided it had enough and shut down it's
>> connection,
>> shouting: WARN!! Stopping Acceptor ServerSocket
>> 
>> My fix was to restart the das/2 server giving the java process another
>> 200M
>> of maximal heap. However, both das/1 and das/2 servers can now potentially
>> claim 89% of physical ram on that box, which could become unhealthy.
>> 
>> Ed notes that we might want to prevent such big queries in the first
>> place.
>> There is an error code in the das spec for this (HTTP error 413 "Request
>> Entity Too Large"). But how do we determine the what's a reasonable
>> maximum
>> allowable query result? It will depend on the feature density on a
>> particular assembly. This could be a good action item for the code sprint.
>> 
>> Steve
>> 
>> 
>> 
>> > From: "Helt,Gregg" <Gregg_Helt at affymetrix.com>
>> > Date: Thu, 10 Aug 2006 09:39:12 -0700
>> > To: Brian Gilman <gilmanb at pantherinformatics.com>
>> > Cc: DAS/2 <das2 at lists.open-bio.org>, "Chervitz, Steve"
>> > <Steve_Chervitz at affymetrix.com>
>> > Conversation: [DAS2] DAS/2 Code Sprint, August 14-18
>> > Subject: RE: [DAS2] DAS/2 Code Sprint, August 14-18
>> >
>> > Apologies, it looks like we're currently having some problem with proxy
>> > redirection on the Affy DAS/2 server.  Steve, can you check on this?
>> > When I request anything but the top level ~/sequence, I'm getting back
>> > HTTP error 502 "Bad Gateway" with the message:
>> > "The proxy server received an invalid response from an upstream server."
>> >
>> > However, I just tried the biopackages server and it is working, though
>> > response times are slower than usual (unless the response has already
>> > been cached).  Here's a feature query I recently ran, so it will be
>> > returned quickly from the server cache:
>> >
>> > http://das.biopackages.net/das/genome/human/17/feature?overlaps=chr21/26
>> > 027736:26068042;type=SO:mRNA
>> >
>> > hope that helps,
>> > gregg
>> >
>> >> -----Original Message-----
>> >> From: Brian Gilman [mailto:gilmanb at pantherinformatics.com]
>> >> Sent: Thursday, August 10, 2006 8:10 AM
>> >> To: Helt,Gregg
>> >> Cc: DAS/2
>> >> Subject: Re: [DAS2] DAS/2 Code Sprint, August 14-18
>> >>
>> >> Trying to get a features document?
>> >>
>> >>     Hello Greg et al. I'm desperately trying to get a features
>> > document
>> >> out of one of the DAS 2 servers and have not been able to do it yet.
>> > Can
>> >> someone help me out!?
>> >>
>> >>                                            Thanks!
>> >>
>> >>                                               -B
>> >>
>> >> Helt,Gregg wrote:
>> >>
>> >>> Affymetrix is hosting a DAS/2 code sprint on August 14-18, to
>> > coincide
>> >>> with the CSB conference at Stanford.  The sprint will be held at
>> > Affy's
>> >>> Santa Clara location, which is about a 20 minute drive from the
>> > Stanford
>> >>> campus.  For those attending CSB, the proximity should make it easy
>> > to
>> >>> join in, even if it's just for a morning or afternoon.  We can
>> > provide
>> >>> transportation to and from CSB if needed.  If you are interested in
>> >>> attending please email me, and specify whether you'll need a
>> > workstation
>> >>> or will be bringing your own laptop.
>> >>>
>> >>> This is a code sprint, so the focus will be on DAS/2 client and
>> > server
>> >>> implementations.  As with previous sprints I'd like to start each day
>> >>> with a teleconference at 9 AM Pacific time.  If you can't be there
>> >>> physically but still want to participate, please join in!
>> >>>
>> >>>            Gregg
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> DAS2 mailing list
>> >>> DAS2 at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/das2
>> >>>
>> >>>
>> >>>
>> >>>
>> >
>> 
>> 
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>