[Bioperl-l] HTTP response size check in
Aaron J. Mackey
amackey at pcbi.upenn.edu
Thu Jul 21 12:09:37 EDT 2005
This is what I do to distinguish intermediate pages from , and it
seems to be stable (at least so far):
if ($html =~ m/Status=WAITING/iso)
On Jul 20, 2005, at 9:23 PM, Jason Stajich wrote:
> 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.
> 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 Markel, Ph.D.
>> Principal Bioinformatics Architect email: smarkel at 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 at portal.open-bio.org
> Jason Stajich
> Duke University
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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