1290eaf14faaf78d5ba17002f6e218a861f995a4
hiram
  Wed Jul 6 14:06:28 2022 -0700
the description is used in the pull down menu on gateway page should be common name then use organism for extra assembly info refs #29545

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 4a72ab7..9076b33 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -71,40 +71,40 @@
   $trimmedOrgName =~ s/$commonName{$asmId}//i;
   $trimmedOrgName = $orgName if (length($trimmedOrgName) < 1);
   my $assemblyName = $asmId;
   $assemblyName =~ s/${accessionId}_//;
   foreach my $fh (@fhN) {
     printf $fh "hub %s genome assembly\n", $accessionId;
     printf $fh "shortLabel %s\n", $orgName;
     printf $fh "longLabel %s/%s/%s genome assembly\n", $orgName, $descr, $asmId;
     printf $fh "useOneFile on\n";
     printf $fh "email hclawson\@ucsc.edu\n";
     printf $fh "descriptionUrl html/%s.description.html\n", $asmId;
     printf $fh "\n";
     printf $fh "genome %s\n", $accessionId;
     printf $fh "taxId %s\n", $taxId if (length($taxId) > 1);
     printf $fh "groups groups.txt\n";
-    printf $fh "description %s %s\n", $assemblyName, $asmDate;
+    printf $fh "description %s\n", $orgName;
     printf $fh "twoBitPath %s.2bit\n", $accessionId;
     printf $fh "twoBitBptUrl %s.2bit.bpt\n", $accessionId;
     printf $fh "chromSizes %s.chrom.sizes.txt\n", $accessionId;
     if ( -s "${buildDir}/${asmId}.chromAlias.bb" ) {
       printf $fh "chromAliasBb %s.chromAlias.bb\n", $accessionId;
     } else {
       printf $fh "chromAlias %s.chromAlias.txt\n", $accessionId;
     }
-    printf $fh "organism %s\n", $commonName{$asmId};
+    printf $fh "organism %s %s\n", $assemblyName, $asmDate;
     printf $fh "defaultPos %s\n", $defPos;
     printf $fh "scientificName %s\n", $descr;
     printf $fh "htmlPath html/%s.description.html\n", $asmId;
     # until blat server host is ready for hgdownload, avoid these lines
     if ($blatHosts[$fileCount] ne $downloadHost) {
       printf $fh "blat %s%s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatHostDomain, $blatPorts[$fileCount];
       printf $fh "transBlat %s%s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatHostDomain, $blatPorts[$fileCount];
       printf $fh "isPcr %s%s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatHostDomain, $blatPorts[$fileCount];
     }
     foreach my $otherDb (sort keys %liftOverGz) {
        printf $fh "liftOver.%s %s\n", $otherDb, $liftOverGz{$otherDb};
     }
     printf $fh "\n";
     foreach my $tdbLine (@tdbLines) {
       printf $fh "%s\n", $tdbLine;
@@ -207,43 +207,43 @@
   if (defined($commonName{$asmId})) {
      $orgName = $commonName{$asmId};
   }
   my $trimmedOrgName = $orgName;
   $trimmedOrgName =~ s/$commonName{$asmId}//i;
   $trimmedOrgName =~ s/^\s+//;
   $trimmedOrgName =~ s/\s+$//;
   $trimmedOrgName = $orgName if (length($trimmedOrgName) < 1);
   my $assemblyName = $asmId;
   $assemblyName =~ s/${accessionId}_//;
 
   printf "genome %s\n", $accessionId;
   printf "taxId %s\n", $taxId if (length($taxId) > 1);
   printf "trackDb ../%s/%s/trackDb.txt\n", $accessionDir, $accessionId;
   printf "groups groups.txt\n";
-  printf "description %s %s\n", $assemblyName, $asmDate;
+  printf "description %s\n", $orgName;
   printf "twoBitPath ../%s/%s/%s.2bit\n", $accessionDir, $accessionId, $accessionId;
   printf "twoBitBptUrl ../%s/%s/%s.2bit.bpt\n", $accessionDir, $accessionId, $accessionId;
   printf "chromSizes ../%s/%s/%s.chrom.sizes.txt\n", $accessionDir, $accessionId, $accessionId;
 
   # wait until code gets out for v429 release before using chromAlias.bb
   # for the chromInfoPage display of hgTracks
   if ( -s "${buildDir}/${asmId}.chromAlias.bb" ) {
     printf "chromAliasBb ../%s/%s/%s.chromAlias.bb\n", $accessionDir, $accessionId, $accessionId;
   } else {
     printf "chromAlias ../%s/%s/%s.chromAlias.txt\n", $accessionDir, $accessionId, $accessionId;
   }
-  printf "organism %s\n", $commonName{$asmId};
+  printf "organism %s %s\n", $assemblyName, $asmDate;
   my $chrName=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`;
   chomp $chrName;
   my $bigChrom=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$NF}'`;
   chomp $bigChrom;
   my $oneThird = int($bigChrom/3);
   my $tenK = $oneThird + 10000;
   $tenK = $bigChrom if ($tenK > $bigChrom);
   my $defPos="${chrName}:${oneThird}-${tenK}";
   if ( -s "$buildDir/defaultPos.txt" ) {
     $defPos=`cat "$buildDir/defaultPos.txt"`;
     chomp $defPos;
   }
   printf "defaultPos %s\n", $defPos;
   printf "orderKey %d\n", $buildDone;
   printf "scientificName %s\n", $descr;
@@ -272,40 +272,40 @@
   # try creating single file hub.txt, one for hgwdev, one for hgdownload
   my $downloadHubTxt = "$buildDir/${asmId}.download.hub.txt";
   open (DL, ">$downloadHubTxt") or die "can not write to $downloadHubTxt";
   $localHubTxt = "$buildDir/${asmId}.singleFile.hub.txt";
   open (HT, ">$localHubTxt") or die "can not write to $localHubTxt";
 
   singleFileHub(\*HT, \*DL, $accessionId, $orgName, $descr, $asmId, $asmDate,
 	$defPos, $taxId, $trackDb, $accessionDir, $buildDir);
 
   my $localGenomesFile = "$buildDir/${asmId}.genomes.txt";
   open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
   printf GF "genome %s\n", $accessionId;
   printf GF "taxId %s\n", $taxId if (length($taxId) > 1);
   printf GF "trackDb trackDb.txt\n";
   printf GF "groups groups.txt\n";
-  printf GF "description %s %s\n", $assemblyName, $asmDate;
+  printf GF "description %s\n", $orgName;
   printf GF "twoBitPath %s.2bit\n", $accessionId;
   printf GF "twoBitBptUrl %s.2bit.bpt\n", $accessionId;
   printf GF "chromSizes %s.chrom.sizes.txt\n", $accessionId;
   if ( -s "${buildDir}/${asmId}.chromAlias.bb" ) {
     printf GF "chromAliasBb %s.chromAlias.bb\n", $accessionId;
   } else {
     printf GF "chromAlias %s.chromAlias.txt\n", $accessionId;
   }
-  printf GF "organism %s\n", $commonName{$asmId};
+  printf GF "organism %s %s\n", $assemblyName, $asmDate;
   printf GF "defaultPos %s\n", $defPos;
   printf GF "scientificName %s\n", $descr;
   printf GF "htmlPath html/%s.description.html\n", $asmId;
   # until blat server host is ready for hgdownload, avoid these lines
   if ($blatHost ne $downloadHost) {
     if ( -s "${destDir}/$accessionId.trans.gfidx" ) {
       printf GF "blat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
       printf GF "transBlat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
      printf GF "isPcr $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
     }
   }
   close (GF);
 
   my $localGroups = "$buildDir/${asmId}.groups.txt";
   open (GR, ">$localGroups") or die "can not write to $localGroups";