ede2fd190d25f754238a2f78b25249d400b596a3
hiram
  Thu Apr 14 22:10:55 2022 -0700
fixup the index creation to stuff in the "promoted" hub that is no longer in the tsv listings refs #29259

diff --git src/hg/makeDb/doc/asmHubs/trackData.pl src/hg/makeDb/doc/asmHubs/trackData.pl
index 3ac3983..289789c 100755
--- src/hg/makeDb/doc/asmHubs/trackData.pl
+++ src/hg/makeDb/doc/asmHubs/trackData.pl
@@ -1,19 +1,20 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
+use File::Basename;
 use FindBin qw($Bin);
 use lib "$Bin";
 use commonHtml;
 use File::stat;
 
 my $argc = scalar(@ARGV);
 if ($argc < 3) {
   printf STDERR "usage: trackData.pl Name asmHubName [two column name list] > trackData.html\n";
   printf STDERR "e.g.: trackData.pl Mammals mammals mammals.asmId.commonName.tsv > trackData.html\n";
   printf STDERR "the name list is found in \$HOME/kent/src/hg/makeDb/doc/asmHubs/\n";
   printf STDERR "\nthe two columns are 1: asmId (accessionId_assemblyName)\n";
   printf STDERR "column 2: common name for species, columns separated by tab\n";
   exit 255;
 }
 
@@ -586,31 +587,66 @@
     }	#	foreach my $track (@trackList)
     printf "</tr>\n";
     $asmCounted += 1;
     if ($asmId =~ m/^GC/) {
        printf STDERR "# %03d\t%02d tracks\t%s\n", $asmCounted, $tracksCounted, $asmId;
     } else {
        printf STDERR "# %03d\t%02d tracks\t%s_%s (%s)\n", $asmCounted, $tracksCounted, $accessionId, $asmName, $asmId;
     }
   }
 }
 
 ##############################################################################
 ### main()
 ##############################################################################
 
+# if there is a 'promoted' list, it has been taken out of the 'orderList'
+# so will need to stuff it back in at the correct ordered location
+my %promotedList;	# key is asmId, value is common name
+my $promotedList = dirname(${orderList}) . "/promoted.list";
+my @promotedList;	# contents are asmIds, in order by lc(common name)
+my $promotedIndex = -1;	# to walk through @promotedList;
+
+if ( -s "${promotedList}" ) {
+  open (FH, "<${promotedList}" ) or die "can not read ${promotedList}";
+  while (my $line = <FH>) {
+    next if ($line =~ m/^#/);
+    chomp $line;
+    my ($asmId, $commonName) = split('\t', $line);
+    $promotedList{$asmId} = $commonName;
+  }
+  close (FH);
+  foreach my $asmId ( sort { lc($promotedList{$a}) cmp lc($promotedList{$b}) } keys %promotedList) {
+     push @promotedList, $asmId;
+  }
+  $promotedIndex = 0;
+}
+
 open (FH, "<${orderList}") or die "can not read ${orderList}";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($asmId, $commonName) = split('\t', $line);
+  if ( ($promotedIndex > -1) && ($promotedIndex < scalar(@promotedList))) {
+     my $checkInsertAsmId = $promotedList[$promotedIndex];
+     my $checkInsertName = $promotedList{$checkInsertAsmId};
+     # insert before this commonName when alphabetic before
+     if (lc($checkInsertName) lt lc($commonName)) {
+       push @orderList, $checkInsertAsmId;
+       $commonName{$checkInsertAsmId} = $checkInsertName;
+       ++$assemblyTotal;
+       printf STDERR "# inserting '%s' before '%s' at # %03d\n", $checkInsertName, $commonName, $assemblyTotal;
+       ++$promotedIndex;	# only doing one at this time
+                        # TBD: will need to improve this for more inserts
+     }
+  }
   push @orderList, $asmId;
   $commonName{$asmId} = $commonName;
   ++$assemblyTotal;
 }
 close (FH);
 
 startHtml();
 startTable();
 tableContents();
 endTable();
 endHtml();