6e2ce95748a6b80895027e24e6f5086890d169bc hiram Tue Nov 28 14:10:37 2023 -0800 correct style statements in html elements for border and text alignment and do not declare type javascript refs #29545 diff --git src/hg/makeDb/doc/asmHubs/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl index 34ead66..0079ba0 100755 --- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl +++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl @@ -64,134 +64,134 @@ my $subSetMessage = "subset of $asmHubName only"; if ($asmHubName eq "vertebrate") { $subSetMessage = "subset of other ${asmHubName}s only"; } if ($vgpIndex) { my $vgpSubset = "(set of primary assemblies)"; if ($orderList =~ m/vgp.alternate/) { $vgpSubset = "(set of alternate/haplotype assemblies)"; } elsif ($orderList =~ m/vgp.trio/) { $vgpSubset = "(set of trio assemblies, maternal/paternal)"; } elsif ($orderList =~ m/vgp.legacy/) { $vgpSubset = "(set of legacy/superseded assemblies)"; } print <<"END" -<!DOCTYPE HTML 4.01 Transitional> +<!DOCTYPE HTML> <!--#set var="TITLE" value="VGP - Vertebrate Genomes Project assembly hubs, assembly statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Vertebrate Genomes Project assembly hubs, assembly statistics</h1> <p> <a href='https://vertebrategenomesproject.org/' target=_blank> <img src='VGPlogo.png' width=280 alt='VGP logo'></a></p> <p> This assembly hub contains assemblies released by the <a href='https://vertebrategenomesproject.org/' target=_blank> Vertebrate Genomes Project.</a> $vgpSubset </p> END } else { if ($hprcIndex) { print <<"END" -<!DOCTYPE HTML 4.01 Transitional> +<!DOCTYPE HTML> <!--#set var="TITLE" value="HPRC - Human Pangenome Reference Consortium assembly hubs, assembly statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Human Pangenome Reference Consortium assembly hubs, assembly statistics</h1> <p> <a href='https://humanpangenome.org/' target=_blank> <img src='HPRC_logo.png' width=280 alt='HPRC logo'></a></p> <p> This assembly hub contains assemblies released by the <a href='https://humanpangenome.org/' target=_blank> Human Pangenome Reference Consortium.</a> </p> END } else { print <<"END" -<!DOCTYPE HTML 4.01 Transitional> +<!DOCTYPE HTML> <!--#set var="TITLE" value="$Name genomes assembly hubs, assembly statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>$Name Genomes assembly hubs, assembly statistics</h1> <p> Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage. </p> END } } print <<"END" <h3>See also: <a href='index.html'>hub access</a>, <a href='trackData.html'>track statistics</a></h3><br> <h3>Data resource links</h3> NOTE: <em>Click on the column headers to sort the table by that column</em><br> The <em>link to genome browser</em> will attach only that single assembly to the genome browser. END } ############################################################################## ### start the table output ############################################################################## sub startTable() { print <<"END" -<table class="sortable" border="1"> +<table class="sortable" style="border: 1px solid black;"> <thead style="position:sticky; top:0;"><tr><th>count</th> <th>common name<br>link to genome browser</th> <th>scientific name<br>and data download</th> <th>NCBI assembly</th> <th>sequence<br>count</th><th>genome size<br>nucleotides</th> <th>gap<br>count</th><th>unknown bases<br>(gap size sum)</th><th>masking<br>percent</th> </tr></thead><tbody> END } ############################################################################## ### end the table output ############################################################################## sub endTable() { my $commaNuc = commify($overallNucleotides); my $commaSeqCount = commify($overallSeqCount); my $commaGapSize = commify($overallGapSize); my $commaGapCount = commify($overallGapCount); my $percentDone = 100.0 * $asmCount / $assemblyTotal; my $doneMsg = ""; if ($asmCount < $assemblyTotal) { $doneMsg = sprintf(" (%d build completed, %.2f %% finished)", $asmCount, $percentDone); } if ($assemblyTotal > 1) { print " </tbody> -<tfoot><tr><th>TOTALS:</th><td align=center colspan=3>total assembly count ${assemblyTotal}${doneMsg}</td> - <td align=right>$commaSeqCount</td> - <td align=right>$commaNuc</td> - <td align=right>$commaGapCount</td> - <td align=right>$commaGapSize</td> +<tfoot><tr><th>TOTALS:</th><td style='text-align: center;' colspan=3>total assembly count ${assemblyTotal}${doneMsg}</td> + <td style='text-align: right;'>$commaSeqCount</td> + <td style='text-align: right;'>$commaNuc</td> + <td style='text-align: right;'>$commaGapCount</td> + <td style='text-align: right;'>$commaGapSize</td> <td colspan=1> </td> </tr> "; # try extra column headers as last row for this very large index page if ($vgpIndex && ($asmCount > 15)) { print "<tr><th>count</th> <th>common name<br>link to genome browser</th> <th>scientific name<br>and data download</th> <th>NCBI assembly</th> <th>sequence<br>count</th><th>genome size<br>nucleotides</th> <th>gap<br>count</th><th>unknown bases<br>(gap size sum)</th><th>masking<br>percent</th> </tr> "; } @@ -372,44 +372,44 @@ ++$itemsFound; $taxId = $line; $taxId =~ s/.*:\s+//; } } } close (FH); my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$accessionDir/$accessionId"; my $browserName = $commonName; my $browserUrl = "https://genome.ucsc.edu/h/$accessionId"; if ($asmId !~ m/^GC/) { $hubUrl = "https://hgdownload.soe.ucsc.edu/goldenPath/$asmId/bigZips"; $browserUrl = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=$asmId"; $browserName = "$commonName ($asmId)"; } - printf "<tr><td align=right>%d</td>\n", ++$asmCount; + printf "<tr><td style='text-align: right;'>%d</td>\n", ++$asmCount; # printf "<td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=%s/hub.txt&genome=%s&position=lastDbPos' target=_blank>%s</a></td>\n", $hubUrl, $accessionId, $commonName; - printf "<td align=center><a href='%s' target=_blank>%s</a></td>\n", $browserUrl, $browserName; - printf " <td align=center><a href='%s/' target=_blank>%s</a></td>\n", $hubUrl, $sciName; + printf "<td style='text-align: center;'><a href='%s' target=_blank>%s</a></td>\n", $browserUrl, $browserName; + printf " <td style='text-align: center;'><a href='%s/' target=_blank>%s</a></td>\n", $hubUrl, $sciName; if ($asmId !~ m/^GC/) { - printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s_%s</a></td>\n", $gcPrefix, $asmAcc, $accessionId, $asmName; + printf " <td style='text-align: left;'><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s_%s</a></td>\n", $gcPrefix, $asmAcc, $accessionId, $asmName; } else { - printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s/' target=_blank>%s</a></td>\n", $accessionId, $asmId; + printf " <td style='text-align: left;'><a href='https://www.ncbi.nlm.nih.gov/assembly/%s/' target=_blank>%s</a></td>\n", $accessionId, $asmId; } - printf " <td align=right>%s</td>\n", commify($seqCount); - printf " <td align=right>%s</td>\n", commify($totalSize); - printf " <td align=right>%s</td>\n", commify($gapCount); - printf " <td align=right>%s</td>\n", commify($gapSize); - printf " <td align=right>%.2f</td>\n", $maskPerCent; + printf " <td style='text-align: right;'>%s</td>\n", commify($seqCount); + printf " <td style='text-align: right;'>%s</td>\n", commify($totalSize); + printf " <td style='text-align: right;'>%s</td>\n", commify($gapCount); + printf " <td style='text-align: right;'>%s</td>\n", commify($gapSize); + printf " <td style='text-align: right;'>%.2f</td>\n", $maskPerCent; printf "</tr>\n"; } } # sub tableContents() ############################################################################## ### 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;