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

[Allen Day]

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

-Allen

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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