[Bioperl-l] Problem with : EUtilities - Proxy

Anthony Ferrari ferraria at gmail.com
Wed Dec 20 10:40:34 EST 2006


Defining a "no_proxy" environment variable in my '.bashrc' file solved my
problem. I set it to "localhost".

It indeed corresponds to the line...       [    ...if (@{
$self->{'no_proxy'} }) ...    ]   (I guess!)


I really don't know why we are compelled to do this, but let's say that's
the way it is.

It works now !

Thanks a lot.

Tony




On 20/12/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Dec 20, 2006, at 5:04 AM, Anthony Ferrari wrote:
>
> > You might check out this bug report, which relates directly to your
> > issue:
> >
> > http://bugzilla.open-bio.org/show_bug.cgi?id=2109
> >
> > After I worked out the proxy issue Torsten got it working.  Let me
> > know if this doesn't help or fix the problem.
> >
> > chris
> >
> >
> > I carefully read this bug but that doesn't help because this has
> > already been modified in the now given GenericWebDBI.pm
> > So my problem does not come from a deep recursion loop.
> >
> > As Torsten did, I tried the command  " BIOPERLDEBUG=1 perl -I. -w t/
> > EUtilities.t " to see what's really happening.
> > And actually, all tests are skipped because of the same message error
> > -> "Can't use an undefined value as an ARRAY reference at /usr/lib/
> > perl5/site_perl/5.8.7/LWP/UserAgent.pm line 779."
> >
> > ***
> > I tried the same command with the modified LWP::UserAgent package
> > (which means I comment the line 779 and the corresponding '}') and
> > all 453 tests passed.
> > But not always. I made the tests several times and  it often
> > failed. And always on a test called "eXXX->cookie->cookie() query
> > key" (ending with query key). In those cases, I got back a html
> > message indicating that the error was thrown by the internal sever
> > of NCBI. So I guess that sometimes it is just NCBI server fault
> > (internal problem), and BioPerl is not implied..
> > But once more, I comment a line from a basic package so it is a bit
> > hazardous.
> > ***
> >
> > tony - a little bit lost.
>
> I'm cc'ing Torsten as he has a bit more experience with proxies.
>
> EUtilities is set up to check for an env. proxy and also take a set
> proxy with $agent->proxy() (see GenericWebDBI POD).  It would be easy
> to say this was a bug in LWP, but I think the problem is that
> something is undefined (i.e. an env. variable), or username/password.
>
> From the bug report, Torsten set his proxy variables using the
> following:
>
> --------------------------------------
> "Note: I am behind an _authenticating_ proxy.
> My $http_proxy and $HTTP_PROXY are both set to
> http://USER:PASS@proxy.monash.edu.au:80/"
> --------------------------------------
>
> Note the lowercase for $http_proxy, which can make a difference.
> After the recursion fix, I'm assuming he made no changes to the env.
> settings, and according to the bug everything was fine (is that
> correct Tortsen?).
>
> Also LWP::UserAgent has this:
>
> --------------------------------------
> "Load proxy settings from *_proxy environment variables. You might
> specify proxies like this (sh-syntax):
>
>        gopher_proxy=http://proxy.my.place/
>        wais_proxy=http://proxy.my.place/
>        no_proxy="localhost,my.domain"
>        export gopher_proxy wais_proxy no_proxy
>
>      csh or tcsh users should use the setenv command to define these
> environment variables.
>
> On systems with case insensitive environment variables there exists a
> name clash between the CGI environment variables and the HTTP_PROXY
> environment variable normally picked up by env_proxy(). Because of
> this HTTP_PROXY is not honored for CGI scripts. The CGI_HTTP_PROXY
> environment variable can be used instead."
> --------------------------------------
>
> chris
>


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