2f46913934047d0f39c93be68233d2c45028f90e
hiram
  Fri Aug 30 08:02:57 2019 -0700
correctly add other liftOvers to the file listings refs #23771

diff --git src/hg/utils/automation/makePushQSql.pl src/hg/utils/automation/makePushQSql.pl
index f96b52f..f912c3a 100755
--- src/hg/utils/automation/makePushQSql.pl
+++ src/hg/utils/automation/makePushQSql.pl
@@ -135,60 +135,69 @@
   return ($seqCount <= $HgAutomate::splitThreshold);
 } # dbIsChromBased
 
 
 sub getInfrastructureEntry {
   # Make an entry hash structure for tables that are not associated with a
   # particular track -- genome browser infrastructure.
   my ($allTables) = @_;
   my @leftovers = ();
   my %entry = ();
   $entry{'shortLabel'} = "supporting tables and files";
   $entry{'priority'} = 0;
 
   # Look for the usual set of files on $dbHost:
   my $SameSpecies = ucfirst($db);  $SameSpecies =~ s/\d+$//;
+  my $sameSpecies = $db;  $sameSpecies =~ s/\d+$//;
+  my $Db = ucfirst($db);
   # 2017-03-02 - remove gc5Base.wib quality.wib quality.bw
   #              rarely, if ever, used any more
   my @gbdbFiles = map {"$HgAutomate::gbdb/$db/$_"}
     ("$db.2bit", 'html/description.html', "bbi/gc5BaseBw/gc5Base.bw", "ncbiRefSeq/ncbiRefSeqVersion.txt", "ncbiRefSeq/ncbiRefSeqOther.bb", "ncbiRefSeq/ncbiRefSeqOther.ix", "ncbiRefSeq/ncbiRefSeqOther.ixx", "ncbiRefSeq/seqNcbiRefSeq.rna.fa", "liftOver/${db}To$SameSpecies*");
 
+  my @otherGbdbFiles = map {"$HgAutomate::gbdb/${sameSpecies}*/$_"}
+    ("liftOver/${sameSpecies}*To$Db.over.chain.gz");
+
   my @goldenPathFiles = map {"$HgAutomate::goldenPath/$db/$_"}
     (qw( bigZips/* database/* chromosomes/* ),
      "liftOver/${db}To$SameSpecies*");
+
+  my @otherGoldenPathFiles = map {"$HgAutomate::goldenPath/${sameSpecies}*/$_"}
+    ("liftOver/${sameSpecies}*To$Db.over.chain.gz");
+
   my $sciUnderscore = &HgAutomate::getSpecies($dbHost, $db);
   $sciUnderscore =~ s/ /_/g;
   my $gatewayPhoto = "$HgAutomate::images/$sciUnderscore.jpg";
   if (! &HgAutomate::machineHasFile($dbHost, $gatewayPhoto)) {
      $gatewayPhoto = "$HgAutomate::images/$sciUnderscore.gif";
   }
   my @files = ();
-  foreach my $f (@gbdbFiles, @goldenPathFiles, $gatewayPhoto) {
+  foreach my $f (@gbdbFiles, @otherGbdbFiles, @goldenPathFiles, @otherGoldenPathFiles, $gatewayPhoto) {
     if (&HgAutomate::machineHasFile($dbHost, $f)) {
       push @files, $f;
     } else {
       &HgAutomate::verbose(1, "WARNING: $dbHost does not have $f\n")
 	unless ($f =~ /${db}To$SameSpecies/ ||
 		($f =~ m@/chromosomes/@ && !&dbIsChromBased()));
     }
   }
   $entry{'files'} = join('\r\n', @files);
   $entry{'redmineFiles'} = join("\n", @files);
 
   # Look for infrastructure tables in allTables hash:
-  foreach my $t qw( chromAlias chromInfo grp seq extFile hgFindSpec trackDb history
-		    tableDescriptions ) {
+  foreach my $t (qw( chromAlias chromInfo grp seq extFile hgFindSpec trackDb history
+		    tableDescriptions )) {
     if (defined $allTables->{$t}) {
       $entry{'tables'} .= "$t ";
       $entry{'redmineTables'} .= "$db.$t ";
       delete $allTables->{$t};
       &HgAutomate::verbose(3, "Deleted $t\n");
     } else {
       &HgAutomate::verbose(1, "WARNING: $db does not have $t\n");
     }
   }
   return (\%entry);
 } # getInfrastructureEntry
 
 
 sub getGenbankEntry {
   # Return an entry hash ref for genbank tables.
@@ -679,31 +688,32 @@
     &HgAutomate::verbose(0, "
 WARNING: Could not tell (from trackDb, all.joiner and hardcoded lists of
 supporting and genbank tables) which tracks to assign these tables to:\n");
     foreach my $t (@names) {
       &HgAutomate::verbose(0, "  $t\n");
     }
     &HgAutomate::verbose(0, "\n");
   }
 } # reportStragglers
 
 
 sub makePushQSql {
   my ($entries, $stragglers) = &getEntries();
   &printHeader;
   &printAllEntries($entries);
-  &printMainPushQEntry();
+# Obsolete pushQ database on hgwbeta July 2019
+#   &printMainPushQEntry();
   &reportStragglers($stragglers);
 } # makePushQSql
 
 
 sub adviseDeveloper {
   # Suggest ways to ensure completeness and correctness of output.
   &HgAutomate::verbose(1, <<_EOF_
 
  *** All done!
  *** Please edit the output to ensure correctness before using.
  *** 1. Resolve any warnings output by this script.
  *** 2. Remove any entries which should not be pushed.
  *** 3. Add tables associated with the main track table (e.g. *Pep tables
         for gene prediction tracks).
  *** 4. Add files associated with tracks.  First, look at the results