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/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index 33a275a..5493a88 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -82,89 +82,89 @@ 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= "(set of trio assemblies, maternal/paternal)"; } elsif ($orderList =~ m/vgp.legacy/) { $vgpSubset = "(set of legacy/superseded assemblies)"; } print 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 hub" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Vertebrate Genomes Project assembly hub</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> $vgpSubset </p> END } else { if ($ccgpIndex) { print <<"END"; -<!DOCTYPE HTML 4.01 Transitional> +<!DOCTYPE HTML> <!--#set var="TITLE" value="CCGP - California Conservation Genomics Project " --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>CCGP - California Conservation Genomics Project assembly hub</h1> <p> <a href='https://www.ccgproject.org/' target=_blank> <img src='CCGP_logo.png' width=280 alt='CCGP logo'></a></p> <p> This assembly hub contains assemblies released by the <a href='https://www.ccgproject.org/' target=_blank> California Conservation Genomics Project.</a> </p> END } elsif ($hprcIndex) { print <<"END"; -<!DOCTYPE HTML 4.01 Transitional> +<!DOCTYPE HTML> <!--#set var="TITLE" value="HPRC - Human Pangenome Reference Consortium" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>HPRC - Human Pangenome Reference Consortium assembly hub</h1> <p> <a href='https://humanpangenome.org/' target=_blank> <img src='HPRC_logo.png' width=280 alt='HPRC logo'></a></p> <p> This assembly hub contains assemblies released by the <a href='https://humanpangenome.org/' target=_blank> Human Pangenome Reference Consortium.</a> </p> END } else { print <<"END"; -<!DOCTYPE HTML 4.01 Transitional> +<!DOCTYPE HTML> <!--#set var="TITLE" value="$Name genomes assembly hubs" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>$Name Genomes assembly hubs</h1> <p> Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage. </p> END } } print <<"END"; @@ -218,31 +218,31 @@ END } print <<"END"; The other links provide access to NCBI resources for these assemblies. END } # sub startHtml() ############################################################################## ### start the table output ############################################################################## sub startTable() { print ' -<table class="sortable" border="1"> +<table class="sortable" style="border: 1px solid black;"> <thead style="position:sticky; top:0;"><tr><th>count</th> <th><span style="float: left;">common name and<br>view in UCSC browser</span><span style="float: right;">[IGV browser]</span></th> <th>scientific name<br>and data download</th> <th>NCBI assembly</th> <th>BioSample</th> '; if ("viral" ne $asmHubName) { printf " <th>BioProject</th>\n"; } printf "<th>assembly date,<br>source link</th>\n"; if ("legacy" eq $asmHubName) { printf "<th>clade</th>\n"; } @@ -391,92 +391,92 @@ chomp $asmDate; $bioProject = `grep ^ncbiBioProject "${configRa}" | cut -d' ' -f2-`; chomp $bioProject; $bioSample = `grep ^ncbiBioSample "${configRa}" | cut -d' ' -f2-`; chomp $bioSample; $ncbiFtpLink = "https://ftp.ncbi.nlm.nih.gov/genomes/all/$accessionDir/${accessionId}_${asmName}"; } 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 ($asmId)"; } - printf "<tr><td align=right>%d</td>\n", ++$rowCount; + printf "<tr><td style='text-align: right;'>%d</td>\n", ++$rowCount; # common name and view in browser if ( $asmId =~ m/^GC/ ) { my $hubTxt = "${hubUrl}/hub.txt"; my $igvUrl = "https://igv.org/app-test/?hubURL=$hubTxt"; printf "<td><span style='float: left;'><a href='%s' target=_blank>%s</a></span><span style='float: right;'>[<a href='%s' target=_blank>IGV</a>]</span></td>\n", $browserUrl, $browserName, $igvUrl; } else { - printf "<td 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", $browserUrl, $browserName; } # scientific name and data download - 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", $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, $asmId; } # viruses do not appear to have BioSample if ($asmHubName ne "viral") { if ( $bioSample ne "notFound" ) { - printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>\n", $bioSample, $bioSample; + printf " <td style='text-align: left;'><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>\n", $bioSample, $bioSample; } else { - printf " <td align=left>n/a</td>\n"; + printf " <td style='text-align: left;'>n/a</td>\n"; } } # one broken assembly_report $bioProject= "PRJEB25768" if ($accessionId eq "GCA_900324465.2"); if ($bioProject eq "notFound") { - printf " <td align=left>%s</td>\n", $bioProject; + printf " <td style='text-align: left;'>%s</td>\n", $bioProject; } else { - printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/bioproject/?term=%s' target=_blank>%s</a></td>\n", $bioProject, $bioProject; + printf " <td style='text-align: left;'><a href='https://www.ncbi.nlm.nih.gov/bioproject/?term=%s' target=_blank>%s</a></td>\n", $bioProject, $bioProject; } - printf " <td align=center><a href='%s' target=_blank>%s</a></td>\n", $ncbiFtpLink, $asmDate; + printf " <td style='text-align: center;'><a href='%s' target=_blank>%s</a></td>\n", $ncbiFtpLink, $asmDate; if ("legacy" eq $asmHubName) { if (! defined($cladeId{$asmId})) { printf STDERR "# ERROR: missing clade definition for %s\n", $asmId; exit 255; } else { - printf " <td align=center>%s</td>\n", $cladeId{$asmId}; + printf " <td style='text-align: center;'>%s</td>\n", $cladeId{$asmId}; } } if ($ccgpIndex) { my $sciNameUnderscore = $sciName; $sciNameUnderscore =~ s/ /_/g; $sciNameUnderscore = "Strigops_habroptilus" if ($sciName =~ m/Strigops habroptila/); if (! defined($extraClass{$asmId})) { printf STDERR "# ERROR: no 'class' defined for CCGP assembly %s\n", $asmId; exit 255; } # it isn't clear how we can get these names # https://www.ccgproject.org/species/corynorhinus-townsendii-townsends-big-eared-bat - printf " <td align=center><a href='https://www.ccgproject.org/species/%s/' target=_blank>%s</a></td>\n", $sciNameUnderscore, $extraClass{$asmId} + printf " <td style='text-align: center;'><a href='https://www.ccgproject.org/species/%s/' target=_blank>%s</a></td>\n", $sciNameUnderscore, $extraClass{$asmId} } elsif ($vgpIndex) { my $sciNameUnderscore = $sciName; $sciNameUnderscore =~ s/ /_/g; $sciNameUnderscore = "Strigops_habroptilus" if ($sciName =~ m/Strigops habroptila/); if (! defined($extraClass{$asmId})) { printf STDERR "# ERROR: no 'class' defined for VGP/CCGP assembly %s\n", $asmId; exit 255; } - printf " <td align=center><a href='https://vgp.github.io/genomeark/%s/' target=_blank>%s</a></td>\n", $sciNameUnderscore, $extraClass{$asmId} + printf " <td style='text-align: center;'><a href='https://vgp.github.io/genomeark/%s/' target=_blank>%s</a></td>\n", $sciNameUnderscore, $extraClass{$asmId} } 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;