2c720ad5f45b1111583f17a95b58cc9750f4c5c5
hiram
  Tue Aug 6 09:44:15 2019 -0700
fixup links to hgdownload for AGP and JPG image refs #23734

diff --git src/hg/utils/automation/asmHubGatewayPage.pl src/hg/utils/automation/asmHubGatewayPage.pl
index 0d4eca3..5f0d543 100755
--- src/hg/utils/automation/asmHubGatewayPage.pl
+++ src/hg/utils/automation/asmHubGatewayPage.pl
@@ -144,36 +144,39 @@
   if ( -s $jpgImage ) {
     $imageSize = `identify $jpgImage | awk '{print \$3}'`;
     chomp $imageSize;
     ($imageWidth, $imageHeight) = split('x', $imageSize);
     $imageName = basename($jpgImage);
   }
 }
 
 # transform this path name into a chrom.sizes reference
 
 my $thisDir = `pwd`;
 chomp $thisDir;
 printf STDERR "# thisDir $thisDir\n";
 my $ftpName = dirname($thisDir);
 my $asmId = basename($ftpName);;
+my ($gcXPrefix, $accession, $rest) = split('_', $asmId, 3);
+my $newStyleUrl = sprintf("%s/%s/%s/%s/%s", $gcXPrefix, substr($accession,0,3),
+   substr($accession,3,3), substr($accession,6,3), $asmId);
 $ftpName =~ s#/hive/data/outside/ncbi/##;
 $ftpName =~ s#/hive/data/inside/ncbi/##;
 $ftpName =~ s#/hive/data/genomes/asmHubs/##;
 printf STDERR "# ftpName $ftpName\n";
-my $urlDirectory = `basename $ftpName`;
-chomp $urlDirectory;
+# my $urlDirectory = `basename $ftpName`;
+# chomp $urlDirectory;
 my $speciesSubgroup = $ftpName;
 my $asmType = "genbank";
 $asmType = "refseq" if ( $speciesSubgroup =~ m#refseq/#);
 $speciesSubgroup =~ s#genomes/$asmType/##;;
 $speciesSubgroup =~ s#/.*##;;
 
 my %taxIdCommonName;  # key is taxId, value is common name
                       # from NCBI taxonomy database dump
 open (FH, "<$ENV{'HOME'}/kent/src/hg/utils/automation/genbank/taxId.comName.tab") or die "can not read taxId.comName.tab";
 while (my $line = <FH>) {
   chomp $line;
   my ($taxId, $comName) = split('\t', $line);
   $taxIdCommonName{$taxId} = $comName;
 }
 close (FH);
@@ -265,81 +268,81 @@
 printf STDERR "%s\t", $asmName;
 printf STDERR "%s\t", $orgName;
 printf STDERR "%s\t", $bioSample;
 printf STDERR "%s\t", $descrAsmType;
 printf STDERR "%s\t", $asmLevel;
 printf STDERR "%s\t", $asmDate;
 printf STDERR "%s\n", $asmAccession;
 
 # printf "<script type='text/javascript'>var asmId='%s';</script>\n", $asmId;
 
 if (length($imageName)) {
 printf "<!-- Display image in righthand corner -->
 <table align=right border=0 width=%d height=%d>
   <tr><td align=RIGHT><a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\"
     target=_blank>
-    <img src=\"/hubs/VGP/genomes/%s/html/%s\" width=%d height=%d alt=\"%s\"></a>
+    <img src=\"https://%s/hubs/VGP/genomes/%s/html/%s\" width=%d height=%d alt=\"%s\"></a>
   </td></tr>
   <tr><td align=right>
     <font size=-1> <em>%s</em><BR>
     </font>
     <font size=-2> (Photo courtesy of
       <a href=\"%s\" target=_blank>%s</a>)
     </font>
   </td></tr>
 </table>
-\n", $imageWidth+$imageWidthBorder, $imageHeight, $asmAccession, $asmId, $imageName, $imageWidth, $imageHeight, $commonName, $orgName, $photoCreditURL, $photoCreditName;
+\n", $imageWidth+$imageWidthBorder, $imageHeight, $asmAccession, $sourceServer, $asmId, $imageName, $imageWidth, $imageHeight, $commonName, $orgName, $photoCreditURL, $photoCreditName;
 }
 
 my $sciNameUnderscore = $orgName;
 $sciNameUnderscore =~ s/ /_/g;
 $sciNameUnderscore = "Strigops_habroptilus" if ($orgName =~ m/Strigops habroptila/);
 
 printf "<p>
 <b>Common name:</b>&nbsp;%s<br>
 <b>Taxonomic name: %s, taxonomy ID:</b> <a href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s' target='_blank'> %s</a><br>
 <b>Sequencing/Assembly provider ID:</b> %s<br>
 <b>Vertebrate Genomes Project information:</b> <a href='https://vgp.github.io/genomeark/%s/' target=_blank>%s</a><br>
 <b>Assembly date:</b> %s<br>
 <b>Assembly type:</b> %s<br>
 <b>Assembly level:</b> %s<br>
 <b>Biosample:</b> <a href=\"https://www.ncbi.nlm.nih.gov/biosample/?term=%s\" target=\"_blank\">%s</a><br>
 <b>Assembly accession ID:</b> <a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\" target=\"_blank\">%s</a><br>
 <b>Assembly FTP location:</b> <a href=\"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/%s\" target=\"_blank\">%s</a><br>
 \n", $commonName, $orgName, $taxId, $taxId, $submitter, $sciNameUnderscore, $orgName, $asmDate, $descrAsmType,
-  $asmLevel, $bioSample, $bioSample, $asmAccession, $asmAccession, $urlDirectory, $urlDirectory;
+  $asmLevel, $bioSample, $bioSample, $asmAccession, $asmAccession, $newStyleUrl, $newStyleUrl;
 
 chromSizes($chromSizes);
 
 printf "</p>\n<hr>
 <p>
 <b>Download files for this assembly hub:</b><br>
 To use the data from this assembly for a local hub instance at your
 institution, download these data as indicated by these instructions.<br>
 See also: <a href='/goldenPath/help/hgTrackHubHelp.html' target=_blank>track hub help</a> documentation.<br>
 <br>
 To download this assembly data, use this <em>rsync</em> command:
 <pre>
   rsync -a -P rsync://$sourceServer/hubs/VGP/genomes/$asmId/ ./$asmId/
 
   which creates the local directory: ./$asmId/
 </pre>
 or this <em>wget</em> command:
 <pre>
   wget --timestamping -m -nH -x --cut-dirs=4 -e robots=off -np -k \\
     --reject \"index.html*\" -P \"$asmId\" \\
-       http://$sourceServer/hubs/VGP/genomes/$asmId/
+       https://$sourceServer/hubs/VGP/genomes/$asmId/
 
   which creates a local directory: ./$asmId/
 </pre>
 <br>
 There is an included $asmId.genomes.txt file in that download
 data to use for your local track hub instance.<br>
 You will need to add a hub.txt file to point to this genomes.txt file.<br>
 Something like:
 <pre>
 hub myLocalHub
 shortLabel myLocalHub
 longLabel genomes from Vertebrate Genomes Project assemblies
 genomesFile $asmId.genomes.txt
 email yourEmail\@yourdomain.edu
 descriptionUrl html/$asmId.description.html