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/trackData.pl src/hg/makeDb/doc/asmHubs/trackData.pl index bc480df..2b5c23d 100755 --- src/hg/makeDb/doc/asmHubs/trackData.pl +++ src/hg/makeDb/doc/asmHubs/trackData.pl @@ -139,70 +139,70 @@ 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= "(set of trio assemblies, maternal/paternal)"; } elsif ($orderList =~ m/vgp.legacy/) { $vgpSubset = "(set of legacy/superseded assemblies)"; } print 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, track statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Vertebrate Genomes Project assembly hubs, track 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, track statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>HPRC - Human Pangenome Reference Consortium assembly hubs, track 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="$Name genomes assembly hubs, track statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>$Name Genomes assembly hubs, track statistics</h1> <p> Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage. </p> END } } my $indexUrl = "index"; my $asmStats = "asmStats"; @@ -219,31 +219,31 @@ } # sub startHtml() # order of columns in the table # eliminated the ncbiGene track my @trackList = qw(ncbiRefSeq xenoRefGene augustus ensGene gc5Base allGaps assembly rmsk simpleRepeat windowMasker cpgIslandExtUnmasked); ### XXX beware, this trackList is going to be edited below to add or ### remove elements depending upon the situation ############################################################################## ### start the table output ############################################################################## sub startTable() { # coordinate the order of these column headings with the @trackList listed above -print '<table class="sortable" border="1"> +print '<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> '; print '<th class="sorttable_numeric">ncbiRefSeq</th> ' if ("viral" ne $asmHubName); print " <th class=\"sorttable_numeric\">ncbiGene</th>\n" if ($testOutput || ("viral" eq $asmHubName)); print ' <th class="sorttable_numeric">xenoRefGene</th> <th class="sorttable_numeric">augustus<br>genes</th> <th class="sorttable_numeric">Ensembl<br>genes</th> ' if ("viral" ne $asmHubName); print ' <th class="sorttable_numeric">gc5 base</th> '; @@ -285,31 +285,31 @@ 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); } my $columnCount = scalar(@trackList); my $colSpanFill = $columnCount - 1; if ($assemblyTotal > 1) { print <<"END" </tbody> -<tfoot><tr><th>TOTALS:</th><td align=center colspan=$colSpanFill>total assembly count ${assemblyTotal}${doneMsg}</td> +<tfoot><tr><th>TOTALS:</th><td style='text-align: center;' colspan=$colSpanFill>total assembly count ${assemblyTotal}${doneMsg}</td> </tr></tfoot> </table> END } else { print <<"END" </tbody> </table> END } } # sub endTable() ############################################################################## ### end the HTML output ############################################################################## @@ -429,33 +429,33 @@ $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId"; } $asmReport="$buildDir/download/${asmId}_assembly_report.txt"; $chromSizes = "${buildDir}/${asmId}.chrom.sizes"; $twoBit = "${buildDir}/trackData/addMask/${asmId}.masked.2bit"; $faSizeTxt = "${buildDir}/${asmId}.faSize.txt"; } # my $trackDb="$buildDir/${asmId}.trackDb.txt"; # next if (! -s "$trackDb"); # assembly build not complete if (! -s "$asmReport") { printf STDERR "# no assembly report:\n# %s\n", $asmReport; next; } if (! -s "$twoBit") { printf STDERR "# no 2bit file:\n# %s\n", $twoBit; - printf "<tr><td align=right>%d</td>\n", ++$asmCount; - printf "<td align=center>%s</td>\n", $accessionId; - printf "<th colspan=15 align=center>missing masked 2bit file</th>\n"; + printf "<tr><td style='text-align: right;'>%d</td>\n", ++$asmCount; + printf "<td style='text-align: center;'>%s</td>\n", $accessionId; + printf "<th colspan=15 style='text-align: center;'>missing masked 2bit file</th>\n"; printf "</tr>\n"; next; } if ( ! -s "$faSizeTxt" ) { printf STDERR "twoBitToFa $twoBit stdout | faSize stdin > $faSizeTxt\n"; print `twoBitToFa $twoBit stdout | faSize stdin > $faSizeTxt`; } my ($gapSize, $maskPerCent, $sizeNoGaps) = maskStats($faSizeTxt); $overallGapSize += $gapSize; my ($seqCount, $totalSize) = asmCounts($chromSizes); $overallSeqCount += $seqCount; $overallNucleotides += $totalSize; my $gapCount = gapStats($buildDir, $asmId); $overallGapCount += $gapCount; my $sciName = "notFound"; @@ -490,32 +490,32 @@ 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 ($asmId)"; if ($testOutput) { $browserUrl = "https://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=$asmId"; $hubUrl = "https://hgdownload-test.gi.ucsc.edu/goldenPath/$asmId/bigZips"; } } elsif ($testOutput) { $browserUrl = "https://genome-test.gi.ucsc.edu/h/$accessionId"; } - printf "<tr><td align=right>%d</td>\n", ++$asmCount; - printf "<td align=center><a href='%s' target=_blank>%s<br>%s</a></td>\n", $browserUrl, $browserName, $accessionId; + printf "<tr><td style='text-align: right;'>%d</td>\n", ++$asmCount; + printf "<td style='text-align: center;'><a href='%s' target=_blank>%s<br>%s</a></td>\n", $browserUrl, $browserName, $accessionId; foreach my $track (@trackList) { my $trackFile = "$buildDir/bbi/$asmId.$track"; my $trackFb = "$buildDir/trackData/$track/fb.$asmId.$track.txt"; # no ensGene file ? Then look for ebiGene file if ($track eq "ensGene" && ! -s $trackFb) { if ( -d "$buildDir/trackData/ebiGene" ) { $trackFb = "$buildDir/trackData/ebiGene/fb.ebiGene.txt" if ( -d "$buildDir/trackData/ebiGene/fb.ebiGene.txt"); $trackFile = "$buildDir/bbi/$asmId.ebiGene"; } } my $runDir = "$buildDir/trackData/$track"; my ($itemCount, $percentCover); my $customKey = ""; if ($asmId !~ m/^GC/) { $itemCount = "n/a"; @@ -613,36 +613,36 @@ ($itemCount, $percentCover) = oneTrackData($asmId, "ebiGene", $trackFile, $totalSize, $trackFb, $runDir); } elsif ($track eq "ncbiRefSeq" && $itemCount eq "n/a") { # if track ncbiRefSeq does not exist, try the ncbiGene track $runDir = "$buildDir/trackData/ncbiGene"; $trackFile = "$buildDir/bbi/$asmId.$track.bb"; ($itemCount, $percentCover) = oneTrackData($asmId, "ncbiGene", $trackFile, $totalSize, $trackFb, $runDir); } } } # else not the rmsk track } # else if ($asmId !~ m/^GC/) if (($percentCover =~ m/%/) || ($percentCover !~ m#n/a#)) { $customKey = $percentCover; $customKey =~ s/[ %]+//; } if (length($customKey)) { - printf " <td align=right sorttable_customkey='%s'>%s<br>(%s)</td>\n", $customKey, $itemCount, $percentCover; + printf " <td style='text-align: right;' sorttable_customkey='%s'>%s<br>(%s)</td>\n", $customKey, $itemCount, $percentCover; } else { if ($itemCount eq "n/a") { - printf " <td align=right>n/a</td>\n"; + printf " <td style='text-align: right;'>n/a</td>\n"; } else { - printf " <td align=right>%s<br>(%s)</td>\n", $itemCount, $percentCover; + printf " <td style='text-align: right;'>%s<br>(%s)</td>\n", $itemCount, $percentCover; } } $tracksCounted += 1 if ($itemCount ne "n/a"); } # foreach my $track (@trackList) printf "</tr>\n"; $asmCounted += 1; if ($asmId =~ m/^GC/) { printf STDERR "# %03d\t%02d tracks\t%s\n", $asmCounted, $tracksCounted, $asmId; } else { printf STDERR "# %03d\t%02d tracks\t%s_%s (%s)\n", $asmCounted, $tracksCounted, $accessionId, $asmName, $asmId; } } } ##############################################################################