#!/usr/bin/perl
#use strict; 
 
use WWW::Mechanize;	# this package is based on LWP, but behaves more like a browser
					# we need it here for easy managment of cookies, needed for logon
use Switch; 		# may not be used here, implements case:switch 

my $numArgs = $#ARGV+1;

if ($numArgs != 2) {
	print "\n";
	print "usage: gseaRobot <inputDir> <outputDir>\n";
	exit();
}

my $inputDir = $ARGV[0];
my $outputDir = $ARGV[1];

my $username = 'kburns@jhmi.edu';
my $loginUrl = 'http://www.broadinstitute.org/gsea/login.jsp';
my $queryUrl = 'http://www.broadinstitute.org/gsea/msigdb/annotate.jsp';
my $geneList = "$geneList";
#print $geneList,"\n";
my $geneSetName = "";
my $platform = "GENE_SYMBOL";
my $m = WWW::Mechanize->new();
## LOGIN
$m->get($loginUrl);
$m->form_name('loginForm');
$m->field('j_username',$username);
$m->field('j_password','password');
$response = $m->submit();

opendir (DIR, $inputDir) or die $!;            

while ($filename = readdir(DIR) ) {               
      if($filename=~/.*\.txt/){
      	open IN, "</$inputDir/$filename";
      	#@genes=<IN>;
      	while ($line=<IN>){
            	$geneList=$line;
            	print "$geneList\n";
            	
            	$m->get($queryUrl);
       			$m->form_name('computeOverlapsForm');
       			$m->field('platform',$platform);
       			$m->field('geneList',$geneList);
       			$m->field('geneSetName','');
       			$m->field('collection','C2');
       			##'CP:KEGG',
       			##'CP:REACTOME',
       			##'CP',
       			##'CGP',
      			##'CP:BIOCARTA';

       			$response = $m->submit();

       			## PERFORM DOWNLOAD
       			$m->form_name('downloadForm');
       			$m->field('platform',$platform);
       			$m->field('maxShown','10');
       			$m->field('geneList',$geneList);
       			$m->field('geneSetName','');
       			$m->field('collection','C2');
       			

       			$response = $m->submit();
       			###Write to outfile in output directory stated on command line
       			$outfile=$outputDir."/".$filename;
       			$m->save_content($outfile);
       			print $response->content();
       			close IN;
       			}
       			}
       			}