All a server does is send data to a user agent - and that data has the form of HTML with embedded javascript - it doesn' t have any kind of control over how the user agent interprets the data.

So all your script has to do is to send the same data as a web browser would do.

If you don't want a general solution, but only one that works for you, there might be shortcut. If you look at that function again:

function validate_form(form)
{
  if ( form.user_id.value == "" || form.password.value == "" )
  {
    alert( "Enter a username and password." );
    return false;
  }
  //short-cut if challenge/response is disabled.
  if ( !_useChallenge )
  {
    form.encoded_pw.value = base64encode( form.password.value );
    form.encoded_pw_unicode.value = b64_unicode( form.password.value )
+;
    form.password.value =  "";
    return true;
  }
  ...
}
[download]

There seems to be a chance that the system accepts login without challenge/response, so all you have to do is to login once manually, and record the the values that are stored in form.encoded_pw_unicode and in the username field, and then uses this data each time you want to log in.

Thank you very much to all the PerlMonks. I was finally able to figure out how to work around the Javascript problem. As moritz suggested, I recorded the values of encoded_pw and and encoded_pw_unicode (which were being set by Javascript) by logging in once using the browser. I used 'Tamper Data' add-on of Mozilla Firefox to get those values. It is a wonderful tool. Then, I used those values in my program. Here is my final working program:

#!/usr/bin/perl -w

use strict;
use LWP::UserAgent;
use WWW::Mechanize;
use HTTP::Cookies;
use HTTP::Request::Common qw(POST);
#use LWP::Debug qw(+);


my $user_name = '...';
my $encoded_pw = urldecode('...');
my $encoded_pw_unicode = urldecode('...');

my $base_url = 'https://courses.northwestern.edu/webapps/login/';
my $target_url = '...';

my $agent = WWW::Mechanize->new( autocheck => 1 );
$agent->cookie_jar(HTTP::Cookies->new);

#Get the page once to get the initial cookies and store them  
#in the cookie jar
$agent->get($base_url);
die $agent->response->status_line unless $agent->success;

my $req = POST $base_url,
        [ user_id => $user_name, 
        encoded_pw => $encoded_pw, 
        encoded_pw_unicode => $encoded_pw_unicode];

#This POSTs the form and also gets the new cookies and 
#stores them in the cookie jar        
$agent->request($req);
die $agent->response->status_line unless $agent->success;

#Get the desired page
my $res = $agent->get($target_url);
die $agent->response->status_line unless $agent->success;

print $agent->content();

...
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