[Bioperl-l] Bio::Tools::Run::RemoteBlast return codes

[Mark A. Jensen]

How about returning 1, 2, 4 for the non-zero cases, with some
error constants set for convenience? MAJ
----- Original Message ----- 
From: "Scott Markel" <SMarkel at accelrys.com>
To: <Bioperl-l at lists.open-bio.org>
Sent: Thursday, January 14, 2010 5:58 PM
Subject: [Bioperl-l] Bio::Tools::Run::RemoteBlast return codes


> We've been looking at Bio::Tools::Run::RemoteBlast after some feedback
> from our customers.  Due to network irregularities (not sure what else
> to call it) users see the getting of remote BLAST results as somewhat
> random.  When results come back the hits are fine, but sometimes no
> information comes back at all.  Retrying helps.
> 
> In looking at RemoteBlast.pm there are four "return -1" cases.
> 
> * $status eq 'ERROR'      (return on line 614)
> * $line =~ /ERROR/I       (return on line 628)
> * !$got_content           (return on line 648)
> * !$response->is_success  (return on line 655)
> 
> In the case of no content we'd like to retry remote BLAST.  We're happy
> to do that part in our Pipeline Pilot Perl code wrapper for the BioPerl
> module, but we only want to retry in that case, not the other three.
> 
> What would happen if that third "return -1" changed to a different
> return value?
> 
> Scott
> 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
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> 
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> Vice President, Board of Directors:
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> 
> 
> 
> 
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