a0c8e5e673c15848e6f9ab33e7e77f32c641d995
angie
  Mon Sep 18 14:38:57 2017 -0700
Big search & replace: use https instead of http for NCBI URLs.  refs #17793

diff --git src/utils/geneReviews/addGeneReviewToBed.pl src/utils/geneReviews/addGeneReviewToBed.pl
index d1f8946..6377721 100755
--- src/utils/geneReviews/addGeneReviewToBed.pl
+++ src/utils/geneReviews/addGeneReviewToBed.pl
@@ -1,53 +1,53 @@
 #!/usr/bin/perl
 use warnings;
 use strict;
 sub usage() {
     print "usage: ./addGRtoBed.pl dbName > outputFile\n";
 }
 my $argc=scalar(@ARGV);
 if ($argc != 1) {
     usage; die "ERROR: Please supply a database name for results.\n";
 }
 #get the list of (unique) of gene symbols form geneReviews table
 my @geneReviews = split('\n',
  `hgsql -N -e "select chrom, chromStart, chromEnd, name from geneReviews;" $ARGV[0]`);
 my $grBed;
 my $clickMsg = " (Click links below to search GeneReviews or GeneTests)";
 my $firstTime = 1;
 my $field;
 my $details;
 foreach $grBed(@geneReviews) {
    $details = "";
    my @col = split(/\t/, $grBed);
    #print "Processing name: ", $col[3], " <BR>";
    my @grShort = split('\n',
     `hgsql -N -e 'select  grShort, diseaseID, diseaseName from geneReviewsRefGene where geneSymbol="$col[3]"' $ARGV[0]`);
    $firstTime = 1;
    my $count = scalar(@grShort);
    my $i;
    my $j;
    for ($i=0; $i < $count; $i++) {
        my @f5 = split(/\t/, $grShort[$i]);
    if ($firstTime == 1) {
       $firstTime=0;
       $details = "";
       $details = "<BR><B>GeneReview available for " . $col[3] .  ": </B> " . $clickMsg . "<BR>";
       $details .= "<PRE><TT>";
       $details .= "Short name    Disease ID     GeneTests disease name<BR>";
       $details .= "-----------------------------------------------------------";
       $details .= "-----------------------------------------------------------";
       $details .= "----------------------------------<BR>";
       }
-      $details .= "<A HREF=\"http://www.ncbi.nlm.nih.gov/books/n/gene/" . $f5[0] . "\" TARGET=_blank><B>" . $f5[0] . "</B></A>";
+      $details .= "<A HREF=\"https://www.ncbi.nlm.nih.gov/books/n/gene/" . $f5[0] . "\" TARGET=_blank><B>" . $f5[0] . "</B></A>";
       if (length($f5[0]) <= 15) {
         for ($j = 0; $j <  15-length($f5[0]); $j ++ )
            {
               $details .= " ";
            }
          }
        $details .=  $f5[1] . "       ";
-       $details .= "<A HREF=\"http://www.ncbi.nlm.nih.gov/sites/GeneTests/review/disease/" . $f5[2] . "?db=genetests&search_param==begins_with\" TARGET=_blank>" . $f5[2]  ."<BR>";
+       $details .= "<A HREF=\"https://www.ncbi.nlm.nih.gov/sites/GeneTests/review/disease/" . $f5[2] . "?db=genetests&search_param==begins_with\" TARGET=_blank>" . $f5[2]  ."<BR>";
      }
        $details .= "</TT></PRE><BR>";
        print $col[0], "\t", $col[1], "\t", $col[2], "\t", $col[3], "\t", $details, "\n";
   }