[Bioperl-l] Bio::DB::RefSeq and iPrism Web Filter

Chris Fields cjfields at illinois.edu
Thu Mar 18 13:21:22 EDT 2010


No caching occurs that I know of.  If you have a environment proxy set somehow it will use that, using LWP::UserAgent and env_proxy() (your logging in via iPrism makes me think it is something along those lines). Otherwise the proxy has to be explicitly set for each object, so no caching is apparent.  Could you have a local environment proxy set that you're unaware of?  See here for examples:


You could try something like this after you create the instances, which accesses the LWP::UserAgent instance cached in the relevant class and shuts off proxies:


Otherwise, you can try coming up with a minimal test case indicating what happens (including any output) and file a bug report, just in case.


On Mar 18, 2010, at 11:27 AM, <armendarez77 at hotmail.com> wrote:

> Hello,
> I'm having a problem involving my company's StBernard iPrism Web Filter.  I would like to be able to run my scripts (include Bio::DB::RefSeq, Bio::DB::GenBank) via crontab, however the web filter requires me to log in every 8 hours.  The administrator removed the filter however, my scripts still failed.  I then logged into iPrism and the scripts worked.  
> The system administrators say its the script; that it is somehow caching information and preventing itself from accessing the internet.  I'm using the following modules: strict, DBI, Bio::Perl, Bio::SeqIO, Getopt::Long and Bio::Tools::Run::StandAloneBlast.  
> I would include the script, but it's a bit involved and passes arguments to other scripts.  
> Thank you,
> Veronica
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