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

[Brian Gilman]

<blushing> Eh hem, sorry...I was playing around....</blushing>

					-B
--
Brian Gilman
President Panther Informatics Inc.
E-Mail: gilmanb at pantherinformatics.com
         gilmanb at jforge.net
AIM: gilmanb1

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On Aug 10, 2006, at 4:14 PM, Steve Chervitz 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
>>>>
>>>>
>>>>
>>>>
>>
>
>