95a16d875326cc83a774eb9f52a11c003cba36d6
hiram
  Fri Jul 15 11:00:46 2022 -0700
eliminate obsolete trimmedOrgName variable and correct date discovery refs #29734

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 9076b33..26c82f7 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -55,33 +55,30 @@
      my $loPath = "$buildDir/liftOver/${accessionId}To${OtherDb}.over.chain.gz";
       if (-s "${loPath}") {
     $liftOverGz{$otherDb} = "liftOver/${accessionId}To${OtherDb}.over.chain.gz";
       }
     }
     close (CH);
   }
   my $fileCount = 0;
   my @tdbLines;
   open (TD, "<$trackDb") or die "can not read trackDb: $trackDb";
   while (my $tdbLine = <TD>) {
      chomp $tdbLine;
      push @tdbLines, $tdbLine;
   }
   close (TD);
-  my $trimmedOrgName = $orgName;
-  $trimmedOrgName =~ s/$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\n", $orgName;
     printf $fh "twoBitPath %s.2bit\n", $accessionId;
@@ -186,44 +183,43 @@
     printf STDERR "# '%s'\n", $trackDb;
     next;
   }
   if ( ! -s "${asmReport}" ) {
     printf STDERR "# %03d missing assembly_report: %s\n", $orderKey, $asmId;
     next;
   }
   ++$buildDone;
 printf STDERR "# %03d genomes.txt %s/%s\n", $buildDone, $accessionDir, $accessionId;
   my $taxId=`grep -i "taxid:" $asmReport | head -1 | awk '{printf \$(NF)}' | tr -d \$'\\r'`;
   chomp $taxId;
   my $descr=`grep -i "organism name:" $asmReport | head -1 | tr -d \$'\\r' | sed -e 's#.*organism name: *##i; s# (.*\$##;'`;
   chomp $descr;
   my $orgName=`grep -i "organism name:" $asmReport | head -1 | tr -d \$'\\r' | sed -e 's#.* name: .* (##; s#).*##;'`;
   chomp $orgName;
-  my $asmDate=`grep -i "Date" $asmReport | head -1 | tr -d \$'\\r'`;
+  my $asmDate=`grep -i "Date:" $asmReport | head -1 | tr -d \$'\\r'`;
   chomp $asmDate;
   $asmDate =~ s/.*Date:\s+//;
   my ($year, $month, $day) = split('-', $asmDate);
+  if (defined($month)) {
     $asmDate = sprintf("%s %s", $monthNumber[$month], $year);
+  } else {
+    printf STDERR "# error: can not find month in $asmDate in $asmReport\n";
+  }
 
   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\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" ) {