new_dvd11.pl

#!/usr/bin/perl

## Hussein Vastani

use CGI qw( :standard );
use Fcntl qw( :flock );

#get the clients ip address
$clientip = $ENV{'REMOTE_ADDR'};
$clientip =~ s/\./\-/g;
($sec,$min,$hr) = localtime();
$clientip = $clientip.'-'.$sec.'-'.$min.'-'.$hr;
$clientip = 'files'. $clientip;

print header, start_html( -title=>'Discrete Visualizer of Dynamics Web Interface', -script=>{-language=>'JavaScript',-src=>'fnct.js'});
print start_multipart_form(-name=>'form1', -method =>"POST", -onSubmit=>"return validate()");
print "<div style=\"font-family:Verdana,Arial\"><div id=\"tipDiv\" style=\"position:absolute\; visibility:hidden\; z-index:100\"></div>";
print "<table background=\"gradient.gif\" width=\"100%\"  border=\"0\" cellpadding=\"0\" cellspacing=\"10\">";
print "<tr><td align=\"center\" colspan=\"2\"><b><font size=\"5\">Discrete 
Visualizer of Dynamics (DVD) v1.0 </font></b><p>";
print "If this is your first time, please read the <a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html\" target=\"_blank\">tutorial</a>. It is important ";
print "that you follow the format specified in the tutorial.<br>Make your selections and provide inputs (if any) in the form below and click ";
print "Generate to run the software.<br> Note: The computation may take some time depending on your internet connection.</td></tr>";
print "<tr><td><table align=\"center\" border=\"0\" bgcolor=\"#ABABAB\"  cellpadding=\"1\" cellspacing=\"0\"><tr><td>";
print "<table border=\"0\" bgcolor=\"#FFFFCC\" width=\"100%\" cellspacing=\"0\" cellpadding=\"1\"><tr valign=\"top\"><td bgcolor=\"#FF8000\" nowrap>";
print "<strong><font color=\"#FFFFFF\">Network Description</font></strong></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr>";
print "<tr valign=\"top\"><td nowrap><font size=\"2\">Enter number of nodes: </font>",textfield(-name=>'n_nodes', -size=>2, -maxlength=>2, -default=>3);
print "&nbsp\;<a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html#N\" onmouseover=\"doTooltip(event,0)\" onmouseout=\"hideTip()\"><font size=\"1\">what is this?</font></a>";
print "</td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr><tr valign=\"top\"><td nowrap><font size=\"2\">Enter number of states per node: </font>";
print textfield(-name=>'p_value',-size=>2,-maxlength=>2, default=>3);
print "&nbsp\;<a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html#P\" onmouseover=\"doTooltip(event,1)\" onmouseout=\"hideTip()\"><font size=\"1\">what is this?</font></a>";
print "</td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr>";
print "<tr valign=\"top\"><td nowrap><font size=\"2\">Select format of input functions:";
print "&nbsp\;<a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html#F\" onmouseover=\"doTooltip(event,3)\" onmouseout=\"hideTip()\"><font size=\"1\">what is this?</font></a><br>";
print radio_group(-name=>'translate_box', -values=>['Polynomial','Boolean'], -default=>'Polynomial', -linebreak=>'true');
print "</font></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr><tr valign=\"top\"><td nowrap><font size=\"2\">Select the updating scheme for the functions:";
print "&nbsp\;<a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html#U\" onmouseover=\"doTooltip(event,4)\" onmouseout=\"hideTip()\"><font size=\"1\">what is this?</font></a><br>";
print radio_group(-name=>'update_box', -values=>['Synchronous', 'Sequential'], -default=>'Synchronous', -linebreak=>'true');
print "&nbsp\;&nbsp\;&nbsp\;&nbsp\;- Enter update schedule separated by spaces: ",textfield(-name=>'update_value', -size=>24);
print "</font></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr></table></td></tr></table></td>";
print "<td><table cellSpacing=\"0\" cellPadding=\"1\" align=\"center\" bgColor=\"#ababab\" border=\"0\"><tr><td><table cellSpacing=\"0\" cellPadding=\"1\" width=\"100%\" bgColor=\"#ffffcc\" border=\"0\">";
print "<tr vAlign=top><TD nowrap bgColor=\"#ff8000\"><strong><font color=\"#ffffff\">Input Functions</font></strong></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr>";
print "<tr valign=\"top\"><td nowrap><font size=\"2\">Select function file: </font>",filefield(-name=>'upload_file');
print "&nbsp\;<a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html#F\" onmouseover=\"doTooltip(event,2)\" onmouseout=\"hideTip()\"><font size=\"1\">what is this?</font></a>";
print "</td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr>";
print "<tr><td><div align=\"center\"><b>OR</b> <font size=\"2\" color=\"#006C00\">(Edit functions below)</font></div></td></tr>";
print "<tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr><tr valign=\"top\"><td nowrap><div align=\"center\">";
print textarea(-name=>'edit_functions',
               -default=>'f1 = x1+x2
f2 = x1*x2*x3
f3 = x1*x2+x3^2',
			   -rows=>8,
			   -columns=>50);
print "</div></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr></table></td></tr></table></td></tr>";
print"<tr><td><table align=\"center\" border=\"0\" bgcolor=\"#ABABAB\"  cellpadding=\"1\" cellspacing=\"0\"><tr><td>";
print"<table border=\"0\" bgcolor=\"#FFFFCC\" width=\"100%\" cellspacing=\"0\" cellpadding=\"1\"><tr valign=\"top\"><td bgcolor=\"#FF8000\" nowrap>";
print"<strong><font color=\"#FFFFFF\">State Space Specification</font></strong></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr>";
print"<tr valign=\"top\"><td nowrap><font size=\"2\">Generate state space of";
print"&nbsp\;<a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html#S\" onmouseover=\"doTooltip(event,5)\" onmouseout=\"hideTip()\"><font size=\"1\">what is this?</font></a><br>";
print radio_group(-name=>'option_box', -values=>['All trajectories from all possible initial states', 'One trajectory starting at an initial state'], -default=>'All trajectories from all possible initial states', -linebreak=>'true',); 
print "&nbsp\;&nbsp\;&nbsp\;&nbsp\;- Enter initialization separated by spaces: ",textfield(-name=>'trajectory_value', -size=>20);
print"</font></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr></table></td></tr></table></td><td>";
print"<table align=\"center\" border=\"0\" bgcolor=\"#ABABAB\" cellpadding=\"1\" cellspacing=\"0\"><tr><td>";
print"<table border=\"0\" bgcolor=\"#FFFFCC\" width=\"100%\" cellspacing=\"0\" cellpadding=\"1\"><tr valign=\"top\">";
print"<td bgcolor=\"#FF8000\" nowrap><b><font color=\"#FFFFFF\">Additional Output Specification &nbsp\;<span style=\"background-color:#808080\">(optional)</span></font></b>";
print"&nbsp\;&nbsp\;&nbsp\;</td>";
print"</tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr><tr valign=\"top\"><td nowrap><font size=\"2\">View";
print"&nbsp\;<a href=\"http://dvd.vbi.vt.edu/visualizer/tutorial.html#G\" onmouseover=\"doTooltip(event,6)\" onmouseout=\"hideTip()\"><font size=\"1\">what is this?</font></a><br>";
print"<font color=\"#006C00\"><i>Select graph(s) to view and image 
format.</i></font><br>";
print checkbox_group(-name=>'statespace', -value=>'State space graph', -label=>'State space graph'),"&nbsp\;&nbsp\;&nbsp\;", popup_menu(-name=>'SSformat',-values=>['*.gif','*.jpg','*.png','*.ps']),"<br>";
print checkbox_group(-name=>'regulatory', -value=>'Dependency graph', -label=>'Dependency graph'), "&nbsp\;&nbsp\;&nbsp\;", popup_menu(-name=>'DGformat',-values=>['*.gif','*.jpg','*.png','*.ps']);
print"</font></td></tr><tr><td BGCOLOR=\"#DCDCDC\" HEIGHT=\"1\"></td></tr></table></td></tr></table></td></tr><tr>";
print"<td align=\"center\" colspan=\"2\">",submit('button_name','Generate')," <br><font color=\"#006C00\"><br><i>Results will be displayed below.</i></font></td></tr></table></div>"; 
print end_form;
open(ACCESS, ">>access") or die("Failed to open file for writing");
flock(ACCESS, LOCK_EX) or die ("Could not get exclusive lock $!");
print ACCESS ($ENV{REMOTE_ADDR});
system("date >>access");
flock(ACCESS, LOCK_UN) or die ("Could not unlock file $!");
close(ACCESS);
#print ("Clientid is $clientip");

$p_value = param('p_value');
$n_nodes = param('n_nodes');
$upload_file = upload('upload_file');
$option_box = param('option_box');
$translate_box = param('translate_box');
$update_box = param('update_box');
$update_value = param('update_value');
$trajectory_box = param('trajectory_box');
$trajectory_value = param('trajectory_value');
$statespace = param('statespace');
$regulatory = param('regulatory');
$edit_functions = param('edit_functions');
$SSformat = param('SSformat');
$DGformat = param('DGformat');

my $bytesread = "";
my $buffer = "";

$fileuploaded = 0;
$SSformat =~ s/\*\.//;
$DGformat =~ s/\*\.//;

if($p_value && $n_nodes)
{
    open (OUTFILE, ">$clientip.functionfile.txt");
	if($upload_file)
	{
	  $fileuploaded = 1;
      flock(OUTFILE, LOCK_EX) or die ("Could not get exclusive lock $!");
      while($bytesread=read($upload_file, $buffer, 1024))
      {
            print OUTFILE $buffer;
      }
      flock(OUTFILE, LOCK_UN) or die ("Could not unlock file $!");
	  close $upload_file;
	}
	else  # user has not uploaded any file. so use the textarea value
	{
	  if($edit_functions)
	  {
		#read value from editfunctions and print it to outfile
		flock(OUTFILE, LOCK_EX) or die ("Could not get exclusive lock $!");
		print OUTFILE $edit_functions;
		flock(OUTFILE, LOCK_UN) or die ("Could not unlock file $!");
	  }
	  else # no functions provided
	   {
		print "<font color=\"red\">Error: No functions provided. Please upload a function file or type in your functions in the edit box</font><br>";
		close(OUTFILE);
		die("No function file provided by user");
	   }
	}	
    close(OUTFILE);
	#remove any ^M characters
    `perl -pi -e 's/\r//g' "$clientip.functionfile.txt"`;
    $bytesread = "";
    $buffer = "";  
	$filename = "";
	if($translate_box eq "Boolean")
    {
		if($n_nodes > 21  || ($p_value**$n_nodes >= 2**22)) {
            print "<font color=red><i>Sorry. Unable to compute statistics for very large networks. It is suggested you download the standalone version which has no limitations</i></font><br>";
                `rm -f $clientip.functionfile.txt`;
                die("Translation unsuccessful");
        }
        else {
            system("perl translator.pl $clientip.functionfile.txt $clientip.trfunctionfile.txt $n_nodes");
            $filename = "$clientip.trfunctionfile.txt";
            if(-e "$clientip.trfunctionfile.txt") {
                print  "<A href=\"$clientip.trfunctionfile.txt\" target=\"_blank\"><font color=green><i>Translation from Boolean functions to Polynomail was successful.</i></font></A><br><br>";
            }
            else {
                print "<font color=red>Translation from Boolean functions to polynomail was unsuccessful</font><br>";
                `rm -f $clientip.functionfile.txt`;
                die("Translation unsuccessful");
            }
        }
	}
	else
	{
		$filename = "$clientip.functionfile.txt";
	}
	$update_box_param = "";
	if($update_box eq 'Sequential')
	{
	   $update_box_param = "async";
	   if( ($update_value ne null) &&( $update_value ne "") )
	   {
		   $update_value =~ s/^\s+|\s+$//g; #remove all leading and trailing white spaces
		   $update_value =~  s/(\d+)\s+/$1 /g; # remove extra spaces in between the numbers
		   $update_value =~ s/ /_/g;
	   }
	   else
	   {
		 print "<br><font color=red>Sorry. Cannot accept null input for update schedule field</font><br>";
		 die("Program quitting. Empty value for update schedule field");
	   }
	}
	else
	{
		$update_box_param = "parallel";
		$update_value = "0";
	}
	if($option_box eq "All trajectories from all possible initial states") {
		print "<font color=blue><b>ANALYSIS OF THE STATE SPACE</b></font>"." [m = ".$p_value.", n = ".$n_nodes;
		if($fileuploaded == 1)
		{
			print ", file path = ". $upload_file;
		}
		print "] <br>";
        
        # only allow networks up to size 10
		if($n_nodes > 21 || ($p_value**$n_nodes >= 2**23)) {
			print "<font color=red><i>Sorry. Unable to compute statistics for very large networks. It is suggested you download the standalone version which has no limitations</i></font><br>";
		}
		else {
			if($statespace eq "State space graph")
			{
				#print  $filename ;			
				system("perl count-comps-final.pl -p $filename $p_value $n_nodes $clientip $update_box_param $update_value $SSformat"); 		
				if(-e "$clientip.out.$SSformat")
				{
					print  "<A href=\"$clientip.out.$SSformat\" target=\"_blank\"><font color=red><i>Click to view the state space graph.</i></font></A><br>";
				}
			}
			else
			{
				system("perl count-comps-final.pl $filename $p_value $n_nodes $clientip $update_box_param $update_value $SSformat");
			}
		#print $clientip.out.dot;
              `rm -f -R $clientip`;
      		  `rm -f $clientip.out.dot`;
		}
	}
	else {
  	    print "<font color=blue><b>Computing Trajectory of the given initialization</b></font>"." [m = ".$p_value.", n = ".$n_nodes."] <br>";
		if($n_nodes > 21 || ($p_value**$n_nodes >= 2**22)) {
			print "<font color=red><i>Sorry. Unable to compute statistics for very large networks. It is suggested you download the standalone version which has no limitations</i></font><br>";
		}
		else {
        if( ($trajectory_value ne null) &&( $trajectory_value ne "") ) {
                $trajectory_value =~ s/^\s+|\s+$//g;; #remove all leading and trailing white spaces
                $trajectory_value =~  s/(\d+)\s+/$1 /g; #remove extra white space between the numbers
                $trajectory_value =~ s/ /_/g;
                if($statespace eq "State space graph") {
                    system("perl sim.pl $filename $p_value $n_nodes $trajectory_value $clientip yes $update_box_param $update_value $SSformat");
                    if(-e "$clientip.graph.$SSformat")
                    {
                        print  "<A href=\"$clientip.graph.$SSformat\" target=\"_blank\"><font color=red><i>Click to view the trajectory.</i></font></A><br>";
                    }
                }
                else {
                    system("perl sim.pl $filename $p_value $n_nodes $trajectory_value $clientip no $update_box_param $update_value $SSformat");
                }
            }
            else {
                print "<br><font color=red>Sorry. Cannot accept null input for initialization field</font><br>";
                die("Program quitting. Empty value for initialization field");
            }
        }
    }
	if($regulatory eq "Dependency graph")
	{
		if($n_nodes <= 100)
		{
			system("perl regulatory.pl $filename $n_nodes $clientip $DGformat");
			if(-e "$clientip.out1.$DGformat")
			{
				print  "<A href=\"$clientip.out1.$DGformat\" target=\"_blank\"><font color=red><i>Click to view the dependency graph.</i></font></A><br>";
			}
		}
		else
		{
				print "<br><font color=red><i>Sorry. Unable to draw a graph with more than 1000 nodes in the state space.</i></font>";
				print "<br><font color = red>If you still want to see the graph, then email your function file and the parameters to hvastani@vbi.vt.edu</font>";
		}
		
	}
    `rm -f $clientip.functionfile.txt`;
    #`rm -f $clientip.trfunctionfile.txt`;

}

print end_html();