6964f094f71a69fa083dbe3a6d88dc84f60b0855
hiram
  Thu Feb 25 11:44:28 2021 -0800
expanded link to other hubs table refs #23891

diff --git src/hg/makeDb/doc/asmHubs/commonHtml.pm src/hg/makeDb/doc/asmHubs/commonHtml.pm
index 0697f76..9ff8c94 100644
--- src/hg/makeDb/doc/asmHubs/commonHtml.pm
+++ src/hg/makeDb/doc/asmHubs/commonHtml.pm
@@ -1,100 +1,120 @@
 package commonHtml;
 
 # helper functions for common HTML output features
 
 use warnings;
 use strict;
 use Carp;
 use vars qw(@ISA @EXPORT_OK);
 use Exporter;
 
 @ISA = qw(Exporter);
 
 # This is a listing of the public methods and variables (which should be
 # treated as constants) exported by this module:
 @EXPORT_OK = (
   qw( otherHubLinks htmlFooter )
 );
 
 # otherHubLinks: arg one: vgpIndex, arg two: asmHubName, arg three: orderList
 # arguments allow decision on customization of the table for different
 # types of assembly hubs
 
 sub otherHubLinks($$) {
 
   my ($vgpIndex, $asmHubName) = @_;
 
+my %asmCounts;	# key is hubName, value is number of assemblies
+my @hubList = qw(primates mammals birds fish vertebrate invertebrate plants fungi);
+foreach my $hubName (@hubList) {
+  my $asmCount = `grep -v "^#" ../${hubName}AsmHub/${hubName}.orderList.tsv | wc -l`;
+  chomp $asmCount;
+  $asmCounts{$hubName} = $asmCount;
+}
+my $vgpCount = `grep -h -v "^#" ../vgpAsmHub/vgp.*.orderList.tsv | wc -l`;
+chomp $vgpCount;
+$asmCounts{'vgp'} = $vgpCount;
+my $legacyCount = `grep -h -v "^#" ../legacyAsmHub/legacy.orderList.tsv | wc -l`;
+chomp $legacyCount;
+$asmCounts{'legacy'} = $legacyCount;
+
 # different table output for VGP index
 
 if ((0 == $vgpIndex) && ($asmHubName ne "viral")) {
-  printf "<p>\n<table border='1'><thead>\n";
-  printf "<tr><th colspan=7 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n";
-  printf "<tr><th>Assembly hubs index pages:&nbsp;</th>\n";
-  printf "<th><a href='../primates/index.html'>Primates</a></th>\n";
-  printf "<th><a href='../mammals/index.html'>Mammals</a></th>\n";
-  printf "<th><a href='../birds/index.html'>Birds</a></th>\n";
-  printf "<th><a href='../fish/index.html'>Fish</a></th>\n";
-  printf "<th><a href='../vertebrate/index.html'>other vertebrates</a></th>\n";
-  printf "<th><a href='../legacy/index.html'>legacy/superseded</a></th>\n";
-
-  printf "</tr><tr>\n";
-  printf "<th>Hubs assembly statistics:&nbsp;</th>\n";
-  printf "<th><a href='../primates/asmStats.html'>Primates</a></th>\n";
-  printf "<th><a href='../mammals/asmStats.html'>Mammals</a></th>\n";
-  printf "<th><a href='../birds/asmStats.html'>Birds</a></th>\n";
-  printf "<th><a href='../fish/asmStats.html'>Fish</a></th>\n";
-  printf "<th><a href='../vertebrate/asmStats.html'>other vertebrates</a></th>\n";
-  printf "<th><a href='../legacy/asmStats.html'>legacy/superseded</a></th>\n";
-
-  printf "</tr><tr>\n";
-  printf "<th>Hubs track statistics:&nbsp;</th>\n";
-  printf "<th><a href='../primates/trackData.html'>Primates</a></th>\n";
-  printf "<th><a href='../mammals/trackData.html'>Mammals</a></th>\n";
-  printf "<th><a href='../birds/trackData.html'>Birds</a></th>\n";
-  printf "<th><a href='../fish/trackData.html'>Fish</a></th>\n";
-  printf "<th><a href='../vertebrate/trackData.html'>other vertebrates</a></th>\n";
-  printf "<th><a href='../legacy/trackData.html'>legacy/superseded</a></th>\n";
-
+  printf "<p>\n<table border='1' style='margin-left:auto; margin-right:auto;'><thead>\n";
+  printf "<tr><th colspan=4 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n";
+  printf "<tr><th>Collection</th>\n";
+  printf "    <th>Hub index pages:</th>\n";
+  printf "    <th>Assembly statistics:</th>\n";
+  printf "    <th>Track statistics:</th>\n";
+  printf "</tr>\n";
+  foreach my $hubName (@hubList) {
+    if ($hubName =~ m/^vertebrate/) {
+      printf "<tr><th>other vertebrates</th>\n";
+    } elsif ($hubName =~ m/fish/) {
+      printf "<tr><th>Fishes</th>\n";
+    } elsif ($hubName =~ m/invertebrate/) {
+      printf "<tr><th>Invertebrates</th>\n";
+    } else {
+      printf "<tr><th>%s</th>\n", ucfirst($hubName);
+    }
+    printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", $hubName, $asmCounts{$hubName};
+    printf "    <th><a href='../%s/asmStats.html'>assembly stats</a></th>\n", $hubName;
+    printf "    <th><a href='../%s/trackData.html'>track stats</a></th>\n", $hubName;
+    printf "</tr>\n";
+  }
+  printf "<tr><th>VGP - Vertebrate Genome Project</th>\n";
+  printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "VGP", $asmCounts{'vgp'};
+  printf "    <th><a href='../VGP/asmStats.html'>assembly stats</a></th>\n";
+  printf "    <th><a href='../VGP/trackData.html'>track stats</a></th>\n";
+  printf "</tr>\n";
+  printf "<tr><th>legacy/superseded</th>\n";
+  printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "legacy", $asmCounts{'legacy'};
+  printf "    <th><a href='../legacy/asmStats.html'>assembly stats</a></th>\n";
+  printf "    <th><a href='../legacy/trackData.html'>track stats</a></th>\n";
   printf "</tr></thead>\n</table>\n</p>\n";
 } elsif (1 == $vgpIndex) {
   printf "<p>\n<table border='1'><thead>\n";
-  printf "<tr><th colspan=5 style='text-align:center;'>Alternate sets of VGP assemblies</th></tr>\n";
+  printf "<tr><th colspan=5 style='text-align:center;'>Alternate sets of VGP assemblies</th><th style='text-align:center;'>NCBI Refseq</th></tr>\n";
   printf "<tr><th>Index pages:&nbsp;</th>\n";
   printf "<th><a href='index.html'>primary assembly</a></th>\n";
   printf "<th><a href='vgpAlt.html'>alternate/haplotype</a></th>\n";
   printf "<th><a href='vgpTrio.html'>trio mat/pat</a></th>\n";
   printf "<th><a href='vgpLegacy.html'>legacy/superseded</a></th>\n";
+  printf "<th><a href='../primates/index.html'>other NCBI Refseq assemblies</a></th>\n";
 
   printf "</tr><tr>\n";
   printf "<th>Assembly statistics:&nbsp;</th>\n";
   printf "<th><a href='asmStats.html'>primary assembly</a></th>\n";
   printf "<th><a href='vgpAltStats.html'>alternate/haplotype</a></th>\n";
   printf "<th><a href='vgpTrioStats.html'>trio mat/pat</a></th>\n";
   printf "<th><a href='vgpLegacyStats.html'>legacy/superseded</a></th>\n";
+  printf "<th><a href='../primates/asmStats.html'>other NCBI Refseq assemblies</a></th>\n";
 
   printf "</tr><tr>\n";
   printf "<th>Track statistics:&nbsp;</th>\n";
   printf "<th><a href='trackData.html'>primary assembly</a></th>\n";
   printf "<th><a href='vgpAltData.html'>alternate/haplotype</a></th>\n";
   printf "<th><a href='vgpTrioData.html'>trio mat/pat</a></th>\n";
   printf "<th><a href='vgpLegacyData.html'>legacy/superseded</a></th>\n";
+  printf "<th><a href='../primates/trackData.html'>other NCBI Refseq assemblies</a></th>\n";
 
   printf "</tr><tr>\n";
   printf "</tr></thead>\n</table>\n</p>\n";
 }
 
 }	#	sub otherHubLinks($$)
 
 ############################################################################
 # common output at the bottom of an html index page
 sub htmlFooter() {
 
 print <<"END"
 </div><!-- closing gbsPage from gbPageStartHardcoded.html -->
 </div><!-- closing container-fluid from gbPageStartHardcoded.html -->
 <!--#include virtual="\$ROOT/inc/gbFooterHardcoded.html"-->
 <script type="text/javascript" src="/js/sorttable.js"></script>
 </body></html>
 END
 }
 ############################################################################