d10d359c47f9f4a1245111f8b75b4c25c483c9ee
hiram
  Tue May 10 14:52:17 2022 -0700
fixup some types for cleaner html vs. W3C validator no redmine

diff --git src/hg/gar/garTable.pl src/hg/gar/garTable.pl
index 962b4b5..9f3b2b6 100755
--- src/hg/gar/garTable.pl
+++ src/hg/gar/garTable.pl
@@ -567,36 +567,34 @@
   open (FH, "cut -f1 ${refSeq} ${genBank} ${asmHubTsv}|sort -u|") or die "can not read $refSeq or $genBank or $asmHubTsv";
   while (my $asmId = <FH>) {
      chomp $asmId;
      $asmId =~ s/\.]/_/g;
      $asmId =~ s/\:/_/g;
      $asmId =~ s/\%/_/g;
      $asmId =~ s/\+/_/g;
      $asmId =~ s/\//_/g;
      $asmId =~ s/\#/_/g;
 #      $asmId =~ s/[.:%+/#]/_/g;
      $asmId =~ s/[()]//g;
      $asmId =~ s/__/_/g;
      ++$shouldBeGenArk if (defined($genArkAsm{$asmId}));
      ++$shouldBeUcsc if (defined($rrGcaGcfList{$asmId}));
      if (defined ($skipPartialGenome{$asmId})) {
-       printf STDERR "# skipping genArk %s because skipPartialGenome\n", $asmId if (defined($genArkAsm{$asmId}));
-       next;
+       next if (!defined($genArkAsm{$asmId}));
      }
      if (defined ($asmSuppressed{$asmId})) {
-       printf STDERR "# skipping genArk %s because asmSuppressed\n", $asmId if (defined($genArkAsm{$asmId}));
-       next;
+       next if (!defined($genArkAsm{$asmId}));
      }
      next if (defined ($alreadyDone{$asmId}));
      # something wrong with these two
 # GCA_900609255.1_Draft_mitochondrial_genome_of_wild_rice_W1683
 # GCA_900609265.1_Draft_mitochondrial_genome_of_wild_rice_W1679
      next if ($asmId =~ m/GCA_900609255.1|GCA_900609265.1/);
      # verify this asmId will pass the asmSize limit
      if (defined($metaInfo{$asmId})) {
       my ($asmSize, $asmContigCount, $n50Size, $n50Count, $n50ContigSize, $n50ContigCount, $n50ScaffoldSize, $n50ScaffoldCount) = split('\t', $metaInfo{$asmId});
       # if asmSize is below the minimum, don't use it
        if ($asmSize < $minimalGenomeSize{$clade}) {
          printf STDERR "# %s underSized 0 %d %s %s < %s\n", $clade, ++$underSized{$clade}, $asmId, commify($asmSize), commify($minimalGenomeSize{$clade});
      printf STDERR "# ACK would be genArk assembly %s\n", $asmId if (defined($genArkAsm{$asmId}));
      printf STDERR "# ACK would be UCSC RR %s\n", $asmId if (defined($rrGcaGcfList{$asmId}));
 printf STDERR "# ACK metaInfo: %s '%s'\n", $asmId, $metaInfo{$asmId};
@@ -741,48 +739,48 @@
 
 # count all assemblies in all clades
 my $totalAssemblies = 0;
 foreach my $c (@clades) {
   $totalAssemblies += $cladeCounts{$c};
 }
 
 printf "<!-- to get the pull-down menu items centered together -->\n";
 printf "<div style='text-align: center;'><!-- this will cause the next div to center -->\n";
 printf "  <div style='display: inline-block'>\n";
 
 printf "<div class='pullDownMenu'>\n";
 printf "  <span id='speciesSelectAnchor'>choose clades to view/hide &#9660;</span>\n";
 printf "  <div class='pullDownMenuContent'>\n";
 printf "  <ul id='checkBoxSpeciesSelect'>\n";
-printf "    <li><label><input class='showAll' type='checkbox' onchange='gar.visCheckBox(this)' id='allCheckBox' value='all' checked><span class='showAllLabel'> show all</span></label></li>\n";
+printf "    <li><label><input class='showAll' type='checkbox' onchange='gar.visCheckBox(this)' id='allCheckBox0' value='all' checked><span class='showAllLabel'> show all</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='primatesCheckBox' value='primates' checked><span id='primatesLabel'> primates</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='mammalsCheckBox' value='mammals' checked><span id='mammalsLabel'> mammals</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='birdsCheckBox' value='birds' checked><span id='birdsLabel'> birds</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='fishCheckBox' value='fish' checked><span id='fishLabel'> fish</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='vertebrateCheckBox' value='vertebrate' checked><span id='vertebrateLabel'> vertebrate</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='invertebratesCheckBox' value='invertebrates' checked><span id='invertebratesLabel'> invertebrates</span></label></li>\n";
-printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='plantsCheckBox' value='plants' checked><span id='plantsLabel'> plants<span></label></li>\n";
+printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='plantsCheckBox' value='plants' checked><span id='plantsLabel'> plants</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='fungiCheckBox' value='fungi' checked><span id='fungiLabel'> fungi</span></label></li>\n";
 printf "  </ul>\n";
 printf "  </div>\n";
 printf "</div>\n";
 
 printf "<div style='width: 260px;' class='pullDownMenu'>\n";
 printf "  <span style='text-align: center;' id='assemblyTypeAnchor'>select assembly type to display &#9660;</span>\n";
 printf "  <div class='pullDownMenuContent'>\n";
 printf "  <ul id='checkBoxAssemblyType'>\n";
-printf "    <li><label><input class='showAll' type='checkbox' onchange='gar.visCheckBox(this)' id='allCheckBox' value='all' checked><span class='showAllLabel'> show all</span></label></li>\n";
+printf "    <li><label><input class='showAll' type='checkbox' onchange='gar.visCheckBox(this)' id='allCheckBox1' value='all' checked><span class='showAllLabel'> show all</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='gakCheckBox' value='gak' checked><span id='gakLabel'> Existing browser</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='garCheckBox' value='gar' checked><span id='garLabel'> Request browser</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='gcaCheckBox' value='gca' checked><span id='gcaLabel'> GCA/GenBank</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='gcfCheckBox' value='gcf' checked><span id='gcfLabel'> GCF/RefSeq</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='iucnCheckBox' value='hasIucn' checked><span id='iucnLabel'> IUCN</span></label></li>\n";
 printf "   </ul>\n";
 printf "  </div>\n";
 printf "</div>\n";
 
 printf "<div style='width: 240px;' class='pullDownMenu'>\n";
 printf "  <span id='columnSelectAnchor'>show/hide columns &#9660;</span>\n";
 printf "  <div class='pullDownMenuContent'>\n";
 printf "  <ul id='checkBoxColumnSelect'>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='comNameCheckBox' value='comName' checked> English common name</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='sciNameCheckBox' value='sciName' checked> scientific name</label></li>\n";
@@ -804,35 +802,35 @@
 printf "  </div>        <!-- display inline-block to be 'text' centered -->\n";
 printf "</div>  <!-- this parent div is text-align: center to center children -->\n\n";
 
 printf "<table style='width: 100%%;' class='borderOne' id='loadingStripes'>\n";
 printf "<caption><h2>. . . please wait while page loads . . .</h2></caption>\n";
 printf "</table>\n\n";
 
 printf "<div style='text-align: center;'><!-- this will cause the next div to center -->\n";
 printf "  <div style='display: inline-block'>\n\n";
 
 printf "<h2 style='display: none;' id='counterDisplay'>%s total assemblies : use the selection menus to select subsets</h2>\n\n", commify($totalAssemblies);
 
 ##############################################################################
 ##  begin single table output, start the table and the header
 ##
-## table starts out as display: hide and will be reset to 'table' after
+## table starts out as display: none and will be reset to 'table' after
 ## page load.  Saves a lot of time for Chrome browsers, however the page
 ## is still not usable until much time later.
 ##############################################################################
-printf "<table style='display: hide;' class='sortable borderOne cladeTable' id='dataTable'>\n";
+printf "<table style='display: none;' class='sortable borderOne cladeTable' id='dataTable'>\n";
 
 printf "<colgroup id='colDefinitions'>\n";
 printf "<col id='viewReq' span='1' class=colGViewReq>\n";
 printf "<col id='comName' span='1' class=colGComName>\n";
 printf "<col id='sciName' span='1' class=colGSciName>\n";
 printf "<col id='asmId' span='1' class=colGAsmId>\n";
 printf "<col id='asmSize' span='1' class=colGAsmSize>\n";
 printf "<col id='seqCount' span='1' class=colGAsmSeqCount>\n";
 printf "<col id='scafN50' span='1' class=colGScafN50>\n";
 printf "<col id='ctgN50' span='1' class=colGContigN50>\n";
 printf "<col id='IUCN' span='1' class=colGIUCN>\n";
 printf "<col id='taxId' span='1' class=colGTaxId>\n";
 printf "<col id='asmDate' span='1' class=colGAsmDate>\n";
 printf "<col id='bioSample' span='1' class=colGBioSample>\n";
 printf "<col id='bioProject' span='1' class=colGBioProject>\n";
@@ -1068,31 +1066,31 @@
     }
   }
 ### can override CSS settings here
 ###    $rowClass = " class='gar' style='display: none;'";
 
   # experiment with hiding all rows over 500 count to see if that helps
   # chrom browser initial loading performance
   # try out the table with out any count, just get the row started
   if (length($statusColor)) {
      my $statusClass = sprintf(" style='color:%s;", $statusColor);
      # let's see what nostatus looks like
      $statusClass = "";
      if ($asmCountInTable > 500) {
        printf "<tr%s%s style='display:none;'>", $rowClass, $statusClass;
      } else {
-       printf "<tr%s%s'>", $rowClass, $statusClass;
+       printf "<tr%s%s>", $rowClass, $statusClass;
      }
   } else {
      if ($asmCountInTable > 500) {
        printf "<tr%s style='display:none;'>", $rowClass;
      } else {
        printf "<tr%s>", $rowClass;
      }
   }
   ############# trying out a first column that is just the button or link
 
   ############# first column, common name link to browser or request button ##
   if (defined($comName{$asmId})) {
      printf "<th style='text-align:center;'><a href='%s' target=_blank>view</a></th>", $browserUrl;
      printf PC "\tview";	# output to clade.tableData.tsv
      printf "<th style='text-align:left;'>%s</th>", $commonName;
@@ -1178,41 +1176,41 @@
 
   ############# tenth column,  assembly date ################
   if (defined($asmDate{$asmId})) {
     printf "<td style='display:none;'>%s</td>", $asmDate{$asmId};
     printf PC "\t%s", $asmDate{$asmId};	# output to clade.tableData.txt
   } else {
     printf "<td style='display:none;'>n/a</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# eleventh column,  bioSample ################
   if (length($bioSample) && $bioSample !~ m#n/a#) {
     printf "<td style='display:none; text-align:left;'><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>", $bioSample, $bioSample;
     printf PC "\t%s", $bioSample;	# output to clade.tableData.txt
   } else {
-    printf "<td style='display:none; text-align=left;'>&nbsp;</td>";
+    printf "<td style='display:none; text-align:left;'>&nbsp;</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# twelveth column,  bioProject ################
   if (length($bioProject) && $bioProject !~ m#n/a#) {
     printf "<td style='display:none; text-align:left;'><a href='https://www.ncbi.nlm.nih.gov/bioproject/?term=%s' target=_blank>%s</a></td>", $bioProject, $bioProject;
     printf PC "\t%s", $bioProject;	# output to clade.tableData.txt
 
   } else {
-    printf "<td style='display:none; text-align=left;'>&nbsp;</td>";
+    printf "<td style='display:none; text-align:left;'>&nbsp;</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# eleventh column,  submitter ################
   $asmUrl = "https://www.ncbi.nlm.nih.gov/assembly/$accessionId";
   if (defined($asmSubmitter{$asmId})) {
     my $submitterSortKey = lc($asmSubmitter{$asmId});
     $submitterSortKey =~ s/ //g;
     $submitterSortKey =~ s/[^a-z0-9]//ig;
     printf "<td sorttable_customkey='%s' style='display:none;'>%s</td>", substr($submitterSortKey,0,20), $asmSubmitter{$asmId};
     printf PC "\t%s", $asmSubmitter{$asmId};	# output to clade.tableData.txt
   } else {
     printf "<td sorttable_customkey='n/a' style='display:none;'>n/a</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }