27a61987f2692b2fad37a9faada47b927f568e1e
hiram
  Fri May 24 10:11:44 2024 -0700
correct ftp to https for references to ftp.ncbi.nih.gov no redmine

diff --git src/hg/utils/automation/asmHubHtml.pl src/hg/utils/automation/asmHubHtml.pl
index 5a27bc8..7a36cf7 100755
--- src/hg/utils/automation/asmHubHtml.pl
+++ src/hg/utils/automation/asmHubHtml.pl
@@ -1,107 +1,107 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 use AsmHub;
 use File::Basename;
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 2) {
   printf STDERR "usage: hubHtml.pl <hubLink> <pathTo>/<base> >> hubIndex.html\n";
   printf STDERR "will look for files <pathTo>/<base>/html/<base>.names.tab and\n";
   printf STDERR "<pathTo>/html/<base>.build.stats.txt\n";
   exit 255;
 }
 
 my $hubLink = shift;
 my $baseName = shift;
 my $asmId = basename($baseName);
 my $ftpName = dirname($baseName);
 $ftpName =~ s#/hive/data/inside/ncbi/##;
 my $namesFile = "$baseName/html/$asmId.names.tab";
 my $statsFile = "$baseName/html/$asmId.build.stats.txt";
 my $faCountFile = "$baseName/$asmId.faCount.signature.txt";
 my $geneStatsFile = "$baseName.ncbiGene.ncbi.stats.txt";
 my $contigCount = 0;
 my $genomeSize = 0;
 my $n50 = 0;
 my $totalNucleotides = 0;
 my $adenine = 0;
 my $cytosine = 0;
 my $guanine = 0;
 my $thymine = 0;
 my $gapsN = 0;
 my $CpG = 0;
 my $gcContent = 0;
 my $NperCent = 0;
 
 # single line file, three numbers: contigCount genomeSize N50
 open (FH, "<$statsFile") or die "can not read $statsFile";
 while (my $line = <FH>) {
   chomp $line;
   ($contigCount, $genomeSize, $n50) = split('\s+', $line);
 }
 close (FH);
 
 # single line file, the last line, the 'total' line output of faCount:
 # #seq    len     A       C       G       T       N       cpg
 # total   16569   5124    5181    2169    4094    1       435
 
 my $geneCount = 0;
 my $genePercentCoverage = 0;
 my $geneBasesCovered = 0;
 
 if ( -s $geneStatsFile ) {
   my $geneStats=`cat $geneStatsFile | awk '{printf "%d\\n", \$2}' | xargs echo`;
   chomp $geneStats;
   ($geneCount, $geneBasesCovered) = split('\s+', $geneStats);
   $genePercentCoverage = 0;
   if ($genomeSize > 0) {
   $genePercentCoverage = sprintf("%.3f", 100.0 * $geneBasesCovered/$genomeSize);
   }
 }
 
 open (FH, "grep '^total' $faCountFile 2> /dev/null|tail -1|") or die "can not read $faCountFile";
 while (my $line = <FH>) {
   chomp $line;
   (undef, $totalNucleotides, $adenine, $cytosine, $guanine, $thymine, $gapsN, $CpG) = split('\s+', $line);
   $gcContent = 100.0*($cytosine+$guanine)/$totalNucleotides if ($totalNucleotides > 0);
   $NperCent = 100.0*$gapsN/$totalNucleotides if($totalNucleotides > 0);
 }
 close (FH);
 
 
 my $hubText = "hub.txt";
 # first line is a comment, second line is the set of names data
 open (FH, "grep -v '^#' $namesFile|") or die "can not read $namesFile";
 while (my $line = <FH>) {
   chomp $line;
   my ($taxId, $commonName, $submitter, $asmName, $sciName, $bioSample, $asmType, $asmLevel, $asmDate, $asmAccession) = split('\t', $line);
   $asmDate =~ s/ /&nbsp;/g;
   $sciName =~ s/ *\(.*//;
   $sciName =~ s/ /&nbsp;/g;
   printf "<tr align=\"right\"><td><a href=\"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%d\" target=_\"_blank\"> %d</a>", $taxId, $taxId;
   printf "<td>%s</td>", $asmDate;
   printf "<td><a href='' class='hgGateway' hubTxt='%s/%s'  asmId='%s_%s' target='_blank'>%s</a></td>", $hubLink, $hubText, $asmAccession, $asmName, $commonName;
   printf "<td>%s</td>", $sciName;
   if ($bioSample ne "(n/a)") {
     printf "<td><a href=\"https://www.ncbi.nlm.nih.gov/biosample/?term=%s\" target=\"_blank\"> %s</a></td>", $bioSample, $bioSample;
   } else {
     printf "<td>(n/a)</td>";
   }
   printf "<td align=\"right\">%s</td>", &AsmHub::commify($contigCount);
   printf "<td align=\"right\">%s</td>", &AsmHub::commify($genomeSize);
   printf "<td align=\"right\">%s</td>", &AsmHub::commify($n50);
   printf "<td align=\"right\">%%&nbsp;%.2f</td>", $gcContent;
   printf "<td align=\"right\">%s<br>%%&nbsp;%.2f</td>", &AsmHub::commify($gapsN), $NperCent;
   printf "<td align=\"right\">%s<br>%s<br>%%&nbsp;%.2f</td>", &AsmHub::commify($geneCount), &AsmHub::commify($geneBasesCovered), $genePercentCoverage;
   printf "<td><a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\" target=\"_blank\">%s</a></td>", $asmAccession, $asmAccession;
-  printf "<td><a href=\"ftp://ftp.ncbi.nlm.nih.gov/%s\" target=\"_blank\">%s</a></td>", $ftpName, $asmName;
+  printf "<td><a href=\"https://ftp.ncbi.nlm.nih.gov/%s\" target=\"_blank\">%s</a></td>", $ftpName, $asmName;
   printf "<td>%s</td>", $asmType;
   printf "<td>%s</td>", $asmLevel;
   printf "<td>%s</td></tr>\n", $submitter;
 }
 close (FH);