51525e645840da619740932b632116cefa9d543a
braney
  Thu Aug 2 12:58:48 2012 -0700
remove links out of the source code to the proteome browser (#5740)
diff --git src/hg/utils/mkPhotoGateway.pl src/hg/utils/mkPhotoGateway.pl
index bca44b1..3f10d36 100755
--- src/hg/utils/mkPhotoGateway.pl
+++ src/hg/utils/mkPhotoGateway.pl
@@ -1,148 +1,147 @@
 #!/usr/bin/env perl
 
 # DO NOT EDIT the /cluster/bin/scripts copy of this file -- 
 # edit ~/kent/src/hg/utils/mkPhotoGateway.pl instead.
 
 # $Id: mkPhotoGateway.pl,v 1.2 2007/06/01 19:39:14 galt Exp $
 
 use warnings;
 use strict;
 
 sub usage() {
     print "usage: ./mkPhotoGateway.pl <file.html>\n";
     print "\tthe resulting page is written to the file.html specified\n";
     print "\tCurrent contents of dbDb.hgcentraltest are used to construct\n";
     print "\tthe resulting gateway page.\n";
 }
 
 my $argc=scalar(@ARGV);
 
 if ($argc != 1) {
     usage; die "ERROR: Please supply a single file name for results.\n";
 }
 
 my $resultFile = shift;
 open (FH,">$resultFile") or die "ERROR: can not write to $resultFile";
 
 my @dbs = split('\n',
     `hgsql -N -e "select name from dbDb order by orderKey;" hgcentraltest`);
 my @sciNames = split('\n',
     `hgsql -N -e "select scientificName from dbDb order by orderKey;" hgcentraltest`);
 die "incorrect db vs. sciName count" if (scalar(@dbs) != scalar(@sciNames));
 printf STDERR "in dbDb: dbs: %d == %d scientific names\n",
 	scalar(@dbs), scalar(@sciNames);
 
 my @dbImages;
 
 for (my $i = 0; $i < scalar(@dbs); ++$i) {
     chomp ($dbs[$i]);
     chomp ($sciNames[$i]);
     next if ($dbs[$i] =~ m/hg100/);
     next if ($dbs[$i] =~ m/canHg/);
     $sciNames[$i] =~ s/ /_/g;
     my $jpgName = "$sciNames[$i].jpg";
     if ( -s "/usr/local/apache/htdocs/images/$jpgName" ) {
 	push @dbImages,$dbs[$i];
     }
 }
 
 my @useDbs;
 my $prevDb = "";
 my $prevVer = -1;
 my $latestDb = "xxx";
 for (my $i = 0; $i < scalar(@dbImages); ++$i) {
     next if ($dbImages[$i] =~ m/^rheMac[0-9][a-z]$/);
     next if ($dbImages[$i] =~ m/^pt0$/);
     if (length($prevDb) > 0) {
 	$dbImages[$i] =~ m/[0-9]+$/;
 	my $dbVersion = $&;
 	my $stripDigits = $`;
 	if ($stripDigits =~ m/^$prevDb$/) {
 	    if ($dbVersion > $prevVer) {
 		$prevVer = $dbVersion;
 		$latestDb = $dbImages[$i];
 	    }
 	} else {
 	    push @useDbs,$latestDb;
 	    $prevVer = $dbVersion;
 	    $latestDb = $dbImages[$i];
 	}
 	$prevDb = $stripDigits;
     } else {
 	$dbImages[$i] =~ m/[0-9]+$/;
 	$prevVer = $&;
 	$latestDb = $dbImages[$i];
 	$prevDb = $dbImages[$i];
 	$prevDb =~ s/[0-9]+$//;
     }
 }
 push @useDbs,$latestDb;
 
 printf STDERR "found %d images, %d latest dbs\n",
 	scalar(@dbImages), scalar(@useDbs);
 
 print FH "<HTML><HEAD><TITLE>Genome Browser Photo Gateway</TITLE>\n";
 print FH '<LINK REL="STYLESHEET" HREF="/style/HGStyle.css">', "\n";
 print FH "</HEAD>\n<BODY BACKGROUND=\"../images/floretHiram.jpg\"";
 print FH "\t",
 	'BGCOLOR="#FFF9D2" LINK="#0000CC" VLINK="#330066" ALINK="#6600FF"',
 	">\n";
 print FH "<TABLE ALIGN=LEFT BORDER=0>\n";
 print FH '<TR><TH COLSPAN=3 ALIGN=LEFT><IMG SRC="/images/title.jpg" ALT="UCSC Genome Bioinformatics"></TH></TR>', "\n";
 print FH '<TR><TD COLSPAN=2 HEIGHT=40><!-- This file generates the top menu bar on Genome Browser home page-->
 <!-- which has a different menu from the other static pages------------>
 
   <TABLE BGCOLOR="000000" CELLPADDING="1" CELLSPACING="1" WIDTH="100%" HEIGHT="27">
     <TR BGCOLOR="2636D1"><TD VALIGN="middle">
       <TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 BGCOLOR="2636D1" HEIGHT="24">
 	<TR><TD VALIGN="middle"><FONT COLOR="#89A1DE">&nbsp;&nbsp;
 
 	  <A HREF="/index.html" class="topbar">HOME</A>&nbsp;&nbsp;-&nbsp;&nbsp;
 	  <A HREF="/cgi-bin/hgGateway" class="topbar">Genomes</A>&nbsp;&nbsp;-&nbsp;&nbsp;
  	  <A HREF="/cgi-bin/hgBlat?command=start" class="topbar">Blat</A>&nbsp;&nbsp;-&nbsp;&nbsp; 
 	  <A HREF="/cgi-bin/hgTables?command=start" class="topbar">Tables</A>&nbsp;&nbsp;-&nbsp;&nbsp; 
 	  <A HREF="/cgi-bin/hgNear" class="topbar">Gene Sorter</A>&nbsp;&nbsp;-&nbsp;&nbsp; 
 	  <A HREF="/cgi-bin/hgPcr?command=start" class="topbar">PCR</A>&nbsp;&nbsp;-&nbsp;&nbsp; 
 	  <A HREF="/cgi-bin/hgVisiGene?command=start" class="topbar">VisiGene</A>&nbsp;&nbsp;-&nbsp;&nbsp; 
-	  <A HREF="/cgi-bin/pbGateway?command=start" class="topbar">Proteome</A>&nbsp;&nbsp;-&nbsp;&nbsp; 
 	  <A HREF="/FAQ/" class="topbar">FAQ</A>&nbsp;&nbsp;-&nbsp;&nbsp; 
 	  <A HREF="/goldenPath/help/hgTracksHelp.html" class="topbar">Help</A>
 
 	</FONT></TD></TR>
       </TABLE>
     </TD></TR>
   </TABLE>
 <!-- end topbar -->
 </TD></TR>', "\n";
 
 my $done = 0;
 while ($done < scalar(@useDbs)) {
     print FH "<TR>\n";
     for (my $i = 0; $i < 3; ++$i) {
 	if ($done < scalar(@useDbs)) {
 	    my $href=`hgsql -N -e 'select genome,name from dbDb where name="$useDbs[$done]";' hgcentraltest`;
 	    chomp $href;
 	    my $genomeOrg = $href;
 	    $genomeOrg =~ s/\t/ - /;
 	    $href =~ s/\t/&db=/;
 	    $href =~ s/ /+/g;
 	    my $sciName=`hgsql -N -e 'select scientificName from dbDb where name="$useDbs[$done]";' hgcentraltest`;
 	    chomp $sciName;
 	    $sciName =~ s/ /_/g;
 	    printf    " <TD>%s</TD>", $genomeOrg;
 	    printf FH "  <TD ALIGN=CENTER><A HREF=\"/cgi-bin/hgTracks?org=%s\" TARGET=_blank>\n", $href;
 	    printf FH "   <IMG SRC=\"/images/%s.jpg\"></A><BR>", $sciName;
 	    printf FH "    %s</A><BR>\n", $genomeOrg;
 	    printf FH "    (<A HREF=\"/cgi-bin/hgGateway?org=%s\">photo credits</A>)</TD>\n", $href;
 	    ++$done;
 	} else {
 	    printf "  <TD>&nbsp;</TD>";
 	    print FH "  <TD>&nbsp;</TD>\n";
 	}
     }
     printf "\n";
     print FH "</TR>\n";
 }
 print FH "</BODY></HTML>\n";
 
 close (FH);
