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Revision 1.3 - (download) (annotate)
Thu Feb 9 21:29:04 2006 UTC (13 years, 9 months ago) by mkubal
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.2: +27 -6 lines
links for nonsubsys reactions

use FIG;
use HTML;
use raelib;
my $raelib=new raelib;
use CGI;
my $cgi=new CGI;
use LWP::Simple qw(!head); # see the caveat in perldoc LWP about importing two head methods.

my $fig;
eval {
    $fig = new FIG;
};  

    
my $html = [];
my $user = $cgi->param('user');

unshift(@$html, "<TITLE>Paint Legionella Microarray Expression Data on Subsystem Modules</TITLE>\n");

my $tag_to_id;
my $inputs;
if ($cgi->param('request') && $cgi->param('korgs') ) 
{
  my $input =$cgi->param('proteins');
  my @inputs = split("\n",$input);
  push @orgs, $cgi->param('korgs');
  $org = $orgs[0];

  if ($cgi->upload('fileupload'))
  {
     my $fh=$cgi->upload('fileupload');
     @inputs = <$fh> ;
  }

  push(@inputs,$org);
  $given = [@inputs];
  $big_return = &parse_inputs($fig,$given); 
  $id_to_tag = $big_return->[0];
  $fig_to_alias = $big_return->[1];
  $alias_to_spot_url = $big_return->[2];
  $alias_to_exp_url = $big_return->[3];
}

if ($id_to_tag && $cgi->param('request') eq "Subsystem Information") 
{
    &subsystem_info($fig,$cgi,$html,$id_to_tag,$fig_to_alias);
}
if ($id_to_tag && $cgi->param('request') eq "Paint Subsystem Connections") 
{
    &paint_connections($fig,$cgi,$html,$id_to_tag,$fig_to_alias);
}
if ($id_to_tag && $cgi->param('request') eq "Paint Subsystem Modules") 
{
    &paint_modules($fig,$cgi,$html,$id_to_tag,$fig_to_alias,$alias_to_spot_url,$alias_to_exp_url);
}

else
{
 
  &show_initial($fig,$cgi,$html);
  &HTML::show_page($cgi,$html,1);
  exit;
}

sub show_initial {
 my ($fig,$cgi,$html)=@_;
 # generate a blank page
 push @$html, 
 $cgi->start_multipart_form(),
 "<p>Select an Organism from the list.\n Enter list of tag and id pairs where the tag represents an expression level in a  microarray experiment or an isolate from a complete genome hybridization experiment and the id is a gene/protein id or alias</p>\n",
 "<p>",
 "<br><b>Choose one or more organisms from this list:</b><br>\n",
 $raelib->scrolling_org_list($cgi, "1"),
 
 "<b>Paste tag ID pairs here:</b><br>\n",
 $cgi->textarea(-name=>"proteins", -rows=>10, -columns=>40), "<br>\n", 
 "<br><b>Or choose a file here:</b><br>\n",
 $cgi->filefield(-name=>"fileupload", -size=>50), "<br>\n",
 $cgi->submit(-name=>'request', -value=>'Subsystem Information'), 
 $cgi->submit(-name=>'request', -value=>'Paint Subsystem Connections'), 
 $cgi->submit(-name=>'request', -value=>'Paint Subsystem Modules'), 
 $cgi->reset, $cgi->end_form;
 return $html;
}
sub paint_connections 
{
  my ($fig,$cgi,$html,$id_to_tag,$fig_to_alias,$alias_to_spot_url,$alias_to_exp_url)=@_;
  $new_html = [];
  $dir = "/home/mkubal/public_html";
  open(IN,"$dir/rx_to_rx.xml");
  
  open(OUT,">/home/mkubal/public_html/painted_reaction_network.html");
  my @headers = keys(%{$id_to_tag});
  
  %sid_to_coordinate_x;
  %sid_to_coordinate_y;
  %sid_to_rid;
  @sids_with_rid;

  $sid;
  $coordinate_x;
  $coordinate_y;

  while ($_ = <IN>){
      $temp = $_;
      if($temp =~ /species=\"(s\d+)\"/){$sid = $1; }
      if(!$sid_to_coordinate_x{$sid}){
	  if($temp =~ /x=\"(\d+\.\d+)\"\s+y=\"(\d+\.\d+)\"/){
	      $coordinate_x = $1; #print "sid:$sid x:$1\n"; 
	      $coordinate_y= $2;  #print "sid:$sid y:$2\n"; 
	      $sid_to_coordinate_x{$sid} = $coordinate_x;
	      $sid_to_coordinate_y{$sid} = $coordinate_y;
	  }
      }
      
      if($temp =~/id=\"(s\d+)\"\s+initialAmount.*name=\"(R\d+)\">/){
	  $sid_to_rid{$1} = $2; 
	  push(@sids_with_rid,$1);
      }
  }
  
  %rid_to_peg;
  %rid_to_tag; 
  foreach my $h (@headers)
  {
      my $p = $id_to_tag->{$h};
      my @pegs = @$p;
      foreach my $peg (@pegs){
	  if ($peg =~/(fig\|\d+.\d+.peg.\d+)/){ 
	      $peg = $1;
	      $function = $fig->function_of($peg);
	      if($function =~/EC (\d+\.\d+\.\d+\.\d+)/)
	      {
		  @rids = $fig->catalyzes($1);
		  foreach $r (@rids){
		      $rid_to_tag{$r} = $h;
		      $rid_to_peg{$r} = $peg;
		  }    
	      }	  
	  }
      }
  }

  print OUT "<HTML><HEAD>
  <TITLE>strep</TITLE>
  <META NAME='generator' CONTENT='YokMap 1.0.1'>
  <META HTTP-EQUIV='Content-Type' CONTENT='text/html; charset=iso-8859-1'>
  </HEAD>
  <BODY BGCOLOR='#ffffff'>";
  
  %rid_to_subsystems;
  open(SS_TO_RID,"$dir/ss_to_rx.txt");
  @lines = <SS_TO_RID>;
  foreach $l (@lines){
      #print "$l";
      chomp($l);
      @temp = split("\t",$l);
      if($rid_to_subsystems{$temp[1]}){
	  $list = $rid_to_subsystems{$temp[1]};
	  push(@$list,$temp[0]);
	  $rid_to_subsystems{$temp[1]}= $list;
      }
      else{
	  $rid_to_subsystems{$temp[1]}= [$temp[0]];
      }
  }
  
  @rids_on_diagram =();
  foreach $sid (@sids_with_rid){
      $rid = $sid_to_rid{$sid};
      push(@rids_on_diagram,$rid);
      $tag = $rid_to_tag{$rid};
      $peg = $rid_to_peg{$rid};
      $top = $sid_to_coordinate_y{$sid} + 10;
      $left = $sid_to_coordinate_x{$sid} + 10;
      $list= $rid_to_subsystems{$rid};
      $subsystems_text = join(" ",@$list);
      $mo = "onmouseover=\"return escape('$subsystems_text')\"";	    
      if($peg =~/fig\|\d+.\d+.peg.(\d+)/){
          my $alias = $fig_to_alias{$peg};
	  print OUT "<h5 STYLE='position: absolute; top:$top; left:$left'><font Color='red'><a href='http://theseed.uchicago.edu/FIG/protein.cgi?prot=$peg&user=' $mo>$alias</a></font></h5>\n";
      }
      #else{
#	  print OUT "<h5 STYLE='position: absolute; top:$top; left:$left'><font>no peg</font></h5>\n";
#	  }
      
      $left = $left + 40;	    
      
      if($tag){
	  print OUT "<h5 STYLE='position: absolute; top:$top; left:$left'><font Color='red'><a href='http://www.genome.jp/dbget-bin/www_bget?rn+$rid' $mo>$tag</font></h5>\n";
      }
      else{
	  print OUT "<h5 STYLE='position: absolute; top:$top; left:$left'><font Color='red'><a href='http://www.genome.jp/dbget-bin/www_bget?rn+$rid' $mo>KEGG</font></h5>\n";
      }
  
  }

  print OUT "<MAP NAME='strep'><AREA SHAPE='default' COORDS='0,0,2400,1600' NOHREF></MAP><IMG SRC='rx_to_rx.jpg' WIDTH='2400' HEIGHT='1600' USEMAP='#strep' BORDER='0'><script language='JavaScript' type='text/javascript' src='wz_tooltip.js'></script></BODY></HTML>";

  
  push(@$new_html,"<br><br>");

  push(@$new_html,"<a href='http://ci.uchicago.edu/~mkubal/painted_reaction_network.html'>painted network of reactions connecting subsystems</a>");
  
  push(@$new_html,"<br>");

  &HTML::show_page($cgi,$new_html);
  exit;
}

sub paint_modules 
{
  #print STDERR "paint_modules called\n";
  my ($fig,$cgi,$html,$id_to_tag,$fig_to_alias,$alias_to_spot_url,$alias_to_exp_url)=@_;
  $new_html = [];
  $dir = "/home/mkubal/public_html";
  
  open(IN2,"$dir/subsystem_modules.xml");
  open(IN3,"$dir/ss_connections_by_reaction.txt");
  
  open(OUT2,">/home/mkubal/public_html/painted_subsystem_modules.html");
  open(OUT3,">/home/mkubal/public_html/temp.txt");
  my @headers = keys(%{$id_to_tag});
  
  %sid_to_coordinate_x;
  %sid_to_coordinate_y;
  %sid_to_rid;
  @sids_with_rid;

  $sid;
  $coordinate_x;
  $coordinate_y;

  while ($_ = <IN2>){
      $temp = $_;
      if($temp =~ /species=\"(s\d+)\"/){$sid = $1; }
      if(!$sid_to_coordinate_x{$sid}){
	  if($temp =~ /x=\"(\d+\.\d+)\"\s+y=\"(\d+\.\d+)\"/){
	      $coordinate_x = $1; #print "sid:$sid x:$1\n"; 
	      $coordinate_y= $2;  #print "sid:$sid y:$2\n"; 
	      $sid_to_coordinate_x{$sid} = $coordinate_x;
	      $sid_to_coordinate_y{$sid} = $coordinate_y;
	  }
      }
      
      if($temp =~/id=\"(s\d+)\"\s+initialAmount.*name=\"(R\d+)\">/){
	  $sid_to_rid{$1} = $2; 
	  push(@sids_with_rid,$1);
      }
  }
  
  %rid_to_peg;
  %rid_to_tag; 
  foreach my $peg (@headers)
  {
      #print STDERR "peg:$peg\n";
      $function = $fig->function_of($peg);
      if($function =~/EC (\d+\.\d+\.\d+\.\d+)/)
      {
	  @rids = $fig->catalyzes($1);
	  foreach $r (@rids){
              $tag = $id_to_tag->{$peg};
	      $rid_to_tag{$r} = $tag;
	      $rid_to_peg{$r} = $peg;
              ##print STDERR "peg,rid,tag:$peg,$r,$tag\n";
	  }    
      }	  
  }


  print OUT2 "<HTML><HEAD>
  <TITLE>strep</TITLE>
  <META NAME='generator' CONTENT='YokMap 1.0.1'>
  <META HTTP-EQUIV='Content-Type' CONTENT='text/html; charset=iso-8859-1'>
  </HEAD>
  <BODY BGCOLOR='#ffffff'><MAP NAME='strep'>";
  
  
  %rid_to_subsystems;
  open(SS_TO_RID,"$dir/ss_to_rx.txt");
  @lines = <SS_TO_RID>;
  foreach $l (@lines){
      #print "$l";
      chomp($l);
      @temp = split("\t",$l);
      if($rid_to_subsystems{$temp[1]}){
	  $list = $rid_to_subsystems{$temp[1]};
	  $add = 1;
	  foreach $item (@$list){
	      if($item eq $temp[1]){$add = 0}
	  }
	  if($add){
	      push(@$list,$temp[0]);
	      $rid_to_subsystems{$temp[1]}= $list;
          }
      }
      else{
	  $rid_to_subsystems{$temp[1]}= [$temp[0]];
      }
  }

  
  my %rid_connects_to_ss_by;
  @lines = <IN3>;
  $counter = 0;
  #print OUT3 "Test\n";
  foreach $l (@lines){
      my $key;
      my $ss;
      my $connects_to;
      my $string;
      if($l =~/.*\t(R\d+)\t(.*)\t(R\d+)/){
          $counter = $counter + 1;
	  $key = $1;
          $ss = $2;
          $connects_to = $3;
	  $string = "$key connects to $connects_to in $ss";
	  #print OUT3 "$string\n";
	  if($rid_connects_to_ss_by{$key}){
	      $temp = $rid_connects_to_ss_by{$key};
	      $add = 1;
	      foreach $t (@$temp){
                  if($t eq $string){
		      $add= 0;
                  }
	      }
	      if($add){
		  push(@$temp,$string);
		  print OUT3 "2nd $key\t$string\n";
              }
	  }
	  else{
	      $list = [$string];
	      $rid_connects_to_ss_by{$key} = $list;
	      print OUT3 "1st $key\t$string\n";
	  }
      }  
  }	  
	  
  @rids_on_diagram =();
  foreach $sid (@sids_with_rid){
      my $rid; my $tag; my $top; my $left; my $list; my $connections;
      my $subsystems_text; my $subsystem_text; my $peg = 0;
      
      $rid = $sid_to_rid{$sid};
      push(@rids_on_diagram,$rid);
      $peg = $rid_to_peg{$rid};

      if($peg){
	  $tag = $rid_to_tag{$rid};
      	  $top = $sid_to_coordinate_y{$sid} - 10 ;
	  $left = $sid_to_coordinate_x{$sid}  - 40;
	  $list= $rid_to_subsystems{$rid};
	  $connections= $rid_connects_to_ss_by{$rid};
	  
	  $subsystems_text = join(",",@$list);
	  $connection_text = join(",",@$connections);
      
	  print OUT3 "$rid $connection_text\n";
	  $mo = "onmouseover=\"return escape('$subsystems_text')\"";
	  $mo2 = "onmouseover=\"return escape('$connection_text')\"";
            
      	  my $alias = $fig_to_alias{$peg};  
	  if($peg =~/fig\|\d+.\d+.peg.(\d+)/){
          	print OUT2 "<h5 STYLE='position: absolute; top:$top; left:$left'><font Color='red'><a href='http://theseed.uchicago.edu/FIG/protein.cgi?prot=$peg&user=' $mo>$alias</a></font></h5>\n";
              
	  }
	  
	 $top_left_x = $left + 45;	    
	 $top_left_y = $top +  15;
         $bottom_right_x = $top_left_x + 50;
         $bottom_right_y = $top_left_y + 10;
	 print OUT2 "<AREA SHAPE='RECT' COORDS='$top_left_x,$top_left_y,$bottom_right_x,$bottom_right_y' HREF='http://www.genome.jp/dbget-bin/www_bget?rn+$rid'>";   

	 $left = $left + 115;
         $spot_url = $alias_to_spot_url{$alias};
         if($tag < .10){$color ="#009900" }
	 elsif($tag < .25){$color ="#0CC00" }	
         elsif($tag < .50){$color ="#00FF00" }	
         elsif($tag < 2){$color ="#CCFF00" }
         elsif($tag < 20){$color ="#FF00FF" }
         elsif($tag < 40){$color ="#FF00CC" }
         elsif($tag < 60){$color ="#FF0099" }	
	 elsif($tag < 80){$color ="#FF0066" }
         elsif($tag < 100){$color ="#FF0033" }
         else{$color ="#FF0000" }	
	 print OUT2 "<h5 STYLE='position: absolute; top:$top; left:$left'><a href='$spot_url' ><font Color='$color'>$tag</font></h5>\n";
      
         $left = $left + 25;
         $exp_url = $alias_to_exp_url{$alias};
         print OUT2 "<h5 STYLE='position: absolute; top:$top; left:$left'><a href='$exp_url'><font Color='$color'>test_exp</font></h5>\n";
	}

      $peg = 0;

     
  }

  foreach $k (keys(%rid_connects_to_ss_by)){
      $v = $rid_connects_to_ss_by{$k};
      $s = join(" ",@$v);
      print OUT3 "$k\t$s\n";
  }

  $start_left = 3200;
  $top = 100;

  my @all_rids = keys(%rid_to_tag);
  foreach my $ar (@all_rids){
      $left = $start_left;
      $fid = $rid_to_peg{$ar};
      ##print STDERR "peg:$fid $ar\n";
      $alias = $fig_to_alias{$fid};
      my $add = 1;
      foreach $dr (@rids_on_diagram){
	  if ($ar eq $dr){ $add = 0}
      }
      if($add){
      	 $tag = $rid_to_tag{$ar};
         $spot_url = $alias_to_spot_url{$alias};
         if($tag < .10){$color ="#009900" }
	 elsif($tag < .25){$color ="#0CC00" }	
         elsif($tag < .50){$color ="#00FF00" }	
         elsif($tag < 2){$color ="#CCFF00" }
         elsif($tag < 20){$color ="#FF00FF" }
         elsif($tag < 40){$color ="#FF00CC" }
         elsif($tag < 60){$color ="#FF0099" }	
	 elsif($tag < 80){$color ="#FF0066" }
         elsif($tag < 100){$color ="#FF0033" }
         else{$color ="#FF0000" }	
	
        print OUT2 "<h5 STYLE='position: absolute; top:$top; left:$left'><a href='http://theseed.uchicago.edu/FIG/protein.cgi?prot=$fid&user='><font Color='$color'>$alias</font></a></h5>\n";
        
	$left = $left + 50;  
	print OUT2 "<h5 STYLE='position: absolute; top:$top; left:$left'><a href='$spot_url'><font Color='$color'>$tag</font></h5>\n";
      	 
	$left = $left + 50;
        $exp_url = $alias_to_exp_url{$alias};
        print OUT2 "<h5 STYLE='position: absolute; top:$top; left:$left'><a href='$exp_url'><font Color='$color'>test_exp</font></h5>\n";
 
	$left = $left + 50;
	print OUT2 "<h5 STYLE='position: absolute; top:$top; left:$left'><a href='http://www.genome.jp/dbget-bin/www_bget?rn+$ar'><font Color='$color'>$ar</font></h5>\n";

	$top = $top + 25;
        if($top > 2000){$top = 100; $start_left = $start_left + 400}
      }
  }
  
  print OUT2 "</MAP><IMG SRC='subsystem_modules.jpg' WIDTH='3600' HEIGHT='2400' USEMAP='#strep' BORDER='0'><script language='JavaScript' type='text/javascript' src='wz_tooltip.js'></script></BODY></HTML>";

  #print OUT2 "<MAP NAME='strep'><AREA SHAPE='default' COORDS='0,0,3600,2400' NOHREF></MAP><IMG SRC='subsystem_modules.jpg' WIDTH='3600' HEIGHT='2400' USEMAP='#strep' BORDER='0'><script language='JavaScript' type='text/javascript' src='wz_tooltip.js'></script></BODY></HTML>";
  
  push(@$new_html,"<br><br>");

  push(@$new_html,"<a href='http://ci.uchicago.edu/~mkubal/painted_subsystem_modules.html'>painted subsystem modules</a>");
  
  &HTML::show_page($cgi,$new_html);
  exit;
}


sub subsystem_info 
{
  my ($fig,$cgi,$html,$id_to_tag)=@_;
  
  my $html = [];
  my $table = [];
  my @headers = keys(%{$id_to_tag});
  my $ss_counter;
  my @all_subsystems;
  my @pegs_with_no_ss;

  push (@$html,"<br><br>");
  my $first_header = 1;
  my $pegs_to_color_suffix;
  foreach my $h (@headers)
  {
     my $p = $id_to_tag->{$h};
     my @pegs = @$p;
     foreach my $peg (@pegs) 
     {
         if($first_header){$pegs_to_color_suffix = $pegs_to_color_suffix."&color=$peg"}
         if ($peg =~/(fig\|\d+.\d+.peg.\d+)/){ $peg = $1};
         my @subsystems = $fig->subsystems_for_peg($peg);

         if(!$subsystems[0]){push(@pegs_with_no_ss,$peg)};
         foreach my $ssr (@subsystems)
         {
             $ss = $ssr->[0];
	     my $key = $ss."_".$h;
             if($ss_counter{$key}){$ss_counter{$key} = $ss_counter{$key} + 1}
             else{$ss_counter{$key} = 1}
             my $add = 1;
             foreach my $s (@all_subsystems){if($s eq $ss){$add= 0}}
             if($add){push(@all_subsystems,$ss)}
         }
     }
     $first_header = 0;
  }
 
  my $prefix = &FIG::cgi_url() . "/display_subsys.cgi?user=&ssa_name=";
  my $suffix = "&request=show_ssa".$pegs_to_color_suffix;	
  push(@$table,"<TABLE><TR><TH>Subsystems</TH>");
  foreach my $h (@headers)
  {
      push(@$table,"<TH>\t$h\t</TH>");
  }
  push(@$table,"</TR>");

  foreach my $ss (@all_subsystems)
  {
      my $url = "<a href="."$prefix"."$ss"."$suffix>$ss</a>";	    
      push(@$table,"<TR><TD>$url</TD>");
      foreach my $h (@headers)
      {
         $key = $ss."_".$h;
         if(!$ss_counter{$key}){$cell = "0"}else{$cell=$ss_counter{$key}}  
     	 push(@$table,"<TD>$cell</TD>");
      }
      push(@$table,"</TR>");
        
   }     
         
   push(@$table,"</TABLE>");
   push @$html, &HTML::make_table($table), "\n";
         
   push(@$html,$cgi->h3("Pegs Not in Subsystem"));
   push(@$html,"<TABLE>");
	
   foreach my $p (@pegs_with_no_ss)
   {
        my $cgi = &FIG::cgi_url();
	my $url =qq(<a href="$cgi/protein.cgi?prot=$p&user=">$p</a>);
	push(@$html,"<TR><TD>$url</TD></TR>");
   }
	 
   push(@$html,"</TABLE>");

    &HTML::show_page($cgi,$html);
    exit;
}

=head2 parse_inputs

Given a list of of tab-separated tags and protein ids
return a hash with the tag as key and the value is a list of values
=cut

sub parse_inputs 
{

 my ($fig,$given) =@_;
 my $org = pop(@$given);
 my $hash;
 my $fig_to_alias;
 my $alias_to_fig;
 my $alias_to_spot_url;
 my $alias_to_exp_url;  
 
 open(ID2PEG,"/home/mkubal/public_html/lpg_to_peg.txt");
 @lines = <ID2PEG>;
 foreach $l (@lines){
     chomp($l);
     @temp = split("\t",$l);
     $alias_to_fig{$temp[0]} = $temp[1];
     $fig_to_alias{$temp[1]} = $temp[0];
 }

 foreach my $g (@$given)
 {
     my $id ="";		
     if ($g =~/(.*?)(\s+|\t)(.*?)(\s+|\t)(http.*?)(\s+|\t)(http.*)/){
       	
	$temp_id = $1;
        $tag = $3; 
	$spot_url = $5;
        print STDERR "spot_url:$spot_url\n";
        $exp_url = $7;
        print STDERR "exp_url:$exp_url\n";
	$alias_to_spot_url{$temp_id} = $spot_url;
        $alias_to_exp_url{$temp_id} = $exp_url; 
 
        if($temp_id !~/fig/){ 
             $id = $alias_to_fig{$temp_id};
             $hash{$id} = $tag;
         }
         else{
           $id = $temp_id;
           $fig_to_alias{$id} = $id;
           $hash{$id} = $tag;  
         }
     }

 }
 
 return [\%hash,\%fig_to_alias,\%alias_to_spot_url,\%alias_to_exp_url];

}
 

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