[Bioperl-l] DEBUGGED Remoteblast from Bio::Perl through proxy..cont

[Jason Stajich]

Sorry I meant just do this.
$remoteblast->ua->env_proxy;

The ua function is not currently written to accept storing a new ua  
object but of course you can just do:
  $remoteblast->{'_ua'} = LWP::UserAgent->new(env_proxy => 1).

-jason

On Jul 11, 2005, at 2:32 PM, Jason Stajich wrote:

> Thanks - I think you can just reset the LWP object directly if you  
> like in your script code w/o modifying the module:
>  $remoteblast->ua(LWP::UserAgent->new(env_proxy =>1));
>
> We can certainly update the module to add this default  
> initialization though.
>
> You should submit it as feature request at http://bugzilla.open- 
> bio.org/  so we can track whether or not someone has done it.
>
> On Jul 8, 2005, at 4:00 PM, CHANDAN SINGH wrote:
>
>
>> sorry for the reduplication of the mail but i had forgot to mention
>> the  more  bugging bug which is How come ,others dont get this  
>> problem or
>> have i misunderstood something .
>> do reply
>>
>> Hi eveybody
>> Those of u ,having problem in blasting sequences from Bio::Perl  
>> module through
>> proxy  and getting
>>                              "time  out "  or  " no route to host  
>> " errors
>> do  need to set the  environment proxy variable ( hello smarty we  
>> all know it )
>> and just give the following argument
>>                                                     ( env_proxy =>  
>> 1 )
>> to
>>                  $self->{'_ua'} = new LWP::UserAgent(  );
>> as
>>              $self->{'_ua'} = new LWP::UserAgent( env_proxy => 1 );
>>
>> in  the following sub in Bio::Tools::Run::RemoteBlast.pm
>> sub ua {
>>    my ($self, $value) = @_;
>>    if( ! defined $self->{'_ua'} ) {
>>        $self->{'_ua'} = new LWP::UserAgent(  );
>>        my $nm = ref($self);
>>        $nm =~ s/::/_/g;
>>        $self->{'_ua'}->agent("bioperl-$nm/$MODVERSION");
>>    }
>>    return $self->{'_ua'};
>> }
>> I saw this bug in the stable version and also in the one downloaded
>> from CVS yesterday .
>>
>> _______________________________________________
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>>
>>
>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
>
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>

--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/