[From nobody Thu Jul 21 17:13:44 2005 Return-Path: <jason.stajich@duke.edu> Received: from gg.gbf.de (apl-gg.gbf-braunschweig.de [192.168.1.1]) by gbf.de (8.13.4/8.13.4/Debian-3) with ESMTP id j6L1OBwm007076 for <Guido.Dieterich@gbf.de>; Thu, 21 Jul 2005 03:24:12 +0200 Received: from rzgate.gbf.de (localhost [127.0.0.1]) by gg.gbf.de (8.11.6p2G/8.11.6) with ESMTP id j6L1OBX17782 for <Guido.Dieterich@gbf.de>; Thu, 21 Jul 2005 03:24:11 +0200 (CEST) Received: from mx01.gbf.de (193.175.244.4) by gg.gbf.de (smtprelay) with ESMTP Thu Jul 21 03:23:59 2005. Received: from dartagnan.duhs.duke.edu (dartagnan.duhs.duke.edu [152.16.195.68]) by mx01.gbf.de (8.13.4/8.13.4/Debian-3) with ESMTP id j6L1Nw51022819 for <Guido.Dieterich@gbf.de>; Thu, 21 Jul 2005 03:23:58 +0200 Received: from richalieu.duhs.duke.edu (richalieu.duhs.duke.edu [152.16.195.50]) by dartagnan.duhs.duke.edu (8.13.4/8.13.4) with ESMTP id j6L1Nh5q2646266 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=FAIL); Wed, 20 Jul 2005 21:23:43 -0400 Received: from [192.168.100.5] (cpe-024-211-136-187.nc.res.rr.com [24.211.136.187]) (authenticated bits=0) by richalieu.duhs.duke.edu (8.13.1/8.13.1) with ESMTP id j6L1NfiU014688 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NO); Wed, 20 Jul 2005 21:23:42 -0400 (EDT) In-Reply-To: <42DEBFE0.1080209@scitegic.com> References: <42DEBFE0.1080209@scitegic.com> Mime-version: 1.0 Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <013A3AB6-52F7-4813-A220-6F2A0F57B92F@duke.edu> Cc: Bioperl-l <bioperl-l@bioperl.org>, Guido Dieterich <Guido.Dieterich@gbf.de> From: Jason Stajich <jason.stajich@duke.edu> Subject: Re: [Bioperl-l] HTTP response size check in Bio::Tools::Run::RemoteBlast Date: Wed, 20 Jul 2005 21:23:35 -0400 To: Scott Markel <smarkel@scitegic.com> X-Mailer: Apple Mail (2.733) X-Scanned-By: MIMEDefang 2.51 on 152.16.195.68 X-AntiVirus: checked by AntiVir Milter (version: 1.1.0-6; AVE: 6.31.1.0; VDF: 6.31.1.0; host: rzlimes) X-AntiVirus: checked by AntiVir Milter (version: 1.1.0-6; AVE: 6.31.1.0; VDF: 6.31.1.0; host: mx01) X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on rzlimes.gbf-braunschweig.de X-Spam-Level: * X-Spam-Status: No, score=1.6 required=5.0 tests=BAYES_50 autolearn=no version=3.0.3 Status: Content-Transfer-Encoding: 7bit Content-Disposition: inline I got a email from Guido to the same effect. Guido - best to post to the mailing list in the future so I am not the bottleneck. I just haven't had time to actually make the changes. Really need someone else to maintain this module to be honest. Anyways, any ways to make the module more robust to NCBI changes would be appreciated - it really started as a simple hack - I don't know if it needs to mirror more closely the example code that NCBI provides for submitting remote blasts. -jason On Jul 20, 2005, at 5:19 PM, Scott Markel wrote: > Sometime last week NCBI made a change to the HTTP response > for remote BLAST requests. Based on when my regressions > started to fail, I think it was on the 14th. > > The if( $size > 1000 ) check in retrieve_blast() now passes > when it shouldn't, meaning that intermediate pages are assumed > to be final results. I'm now seeing response sizes of just > under 2000 for the intermediate pages. A customer of mine is > getting about the same. > > If this check is changed to 2000, then we're back in business. > We can't make the number too big or we'll start missing small > result sets. A request for a single BLASTp hit gives me a > result size of about 3400. > > Has anyone else seen this problem? Is this a reasonable fix > to propose? I'm a little concerned that whatever the number > is, it's very susceptible to changes at NCBI. > > Scott > > -- > Scott Markel, Ph.D. > Principal Bioinformatics Architect email: smarkel@scitegic.com > SciTegic Inc. mobile: +1 858 205 3653 > 9665 Chesapeake Drive, Suite 401 voice: +1 858 279 8800, ext. 253 > San Diego, CA 92123 fax: +1 858 279 8804 > USA web: http://www.scitegic.com > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12/ ]