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patched in v4 upload page #741

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Merged
paczian merged 1 commit into from
Jul 1, 2015
Merged

patched in v4 upload page #741

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2 changes: 1 addition & 1 deletion 2 src/MGRAST/html/MGRAST-frontpage.tmpl
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Expand Up @@ -8,7 +8,7 @@
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=MetagenomeSearch"><img src='./Html/lupe.png' style='width: 20px; height: 20px;' title='Search'></a></div>
<br>
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=DownloadMetagenome"><img src='./Html/mg-download.png' style='width: 20px; height: 20px;' title=Download></a></div>
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
<div id="top_nav_links"><a class= "nav_top" href="./Html/mgmain.html?mgpage=upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
<div id="top_nav_links"><a class= "nav_top" href="http://blog.metagenomics.anl.gov/howto/" target="blank"><img src='./Html/mg-help.png' style='width: 20px; height: 20px;' title='Support'></a></div>
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Contact"><img src='./Html/mg-contact.png' style='width: 20px; height: 20px;' title='Contact'></a></div>
</div>
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2 changes: 1 addition & 1 deletion 2 src/MGRAST/html/MGRAST.tmpl
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Expand Up @@ -14,7 +14,7 @@
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=MetagenomeSearch"><img src='./Html/lupe.png' style='width: 20px; height: 20px;' title='Search'></a></div>
<br>
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=DownloadMetagenome"><img src='./Html/mg-download.png' style='width: 20px; height: 20px;' title=Download></a></div>
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
<div id="top_nav_links"><a class= "nav_top" href="./Html/mgmainv3.html?mgpage=upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
<div id="top_nav_links"><a class= "nav_top" href="http://blog.metagenomics.anl.gov/howto/" target=_blank><img src='./Html/mg-help.png' style='width: 20px; height: 20px;' title='Support'></a></div>
<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Contact"><img src='./Html/mg-contact.png' style='width: 20px; height: 20px;' title='Contact'></a></div>
</div>
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2 changes: 1 addition & 1 deletion 2 src/MGRAST/html/js/MetagenomeSearch.js
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@@ -1,4 +1,4 @@
var api_url = 'http://api.metagenomics.anl.gov/1/metagenome?verbosity=mixs&';
var api_url = RetinaConfig ? RetinaConfig.mgrast_api + "/metagenome?verbosity=mixs&" : 'http://api.metagenomics.anl.gov/1/metagenome?verbosity=mixs&';
var datastore = {};
var result = 'result'; // div where results are to be displayed
var saved_params = {};
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38 changes: 1 addition & 37 deletions 38 src/MGRAST/lib/WebPage/Home.pm
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Expand Up @@ -117,7 +117,7 @@ function forward_to_search (e) {
$content .= "<a href='?page=Register' title='Register a new account'><div style='float:left; cursor: pointer;padding-top:5px;'>".$register."</div></a>";
$content .= "<a href='?page=Contact' title='Click here for contact information'><div style='float:left; cursor: pointer;padding-top:5px;'>".$contact."</div></a>";
$content .= "<a href='http://blog.metagenomics.anl.gov' title='Click here for support and FAQs'><div style='float:left; cursor: pointer;padding-top:5px;'>".$help."</div></a>";
$content .= "<a href='?page=Upload' title='Upload a new metagenome'><div style='float:left; cursor: pointer;padding-top:5px; margin-right:20px;'>".$upload."</div></a>";
$content .= "<a href='./Html/mgmainv3.html?mgpage=upload' title='Upload a new metagenome'><div style='float:left; cursor: pointer;padding-top:5px; margin-right:20px;'>".$upload."</div></a>";
$content .= "<a href='http://blog.metagenomics.anl.gov/' target=_blank><div style='float:left; cursor: pointer;padding-top:5px;'>".$news."</div></a>";
$content .= "</div>";
$content .= "<div class='clear'></div>";
Expand Down Expand Up @@ -176,13 +176,7 @@ END

$content .= "<a href=\"http://www.biomedcentral.com/1471-2105/9/386\" target=\"_blank\"><p style='border-radius: 5px; -webkit-border-radius: 5px; -moz-border-radius: 5px; color: white; padding: 5px 0px 3px 10px; color: white; font-size:14; background-color: #5281B0; width: 100px; float: left; margin-right: 10px; top: -12px; position: relative;'>cite MG-RAST</p></a><a href=\"http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004008\" target=\"_blank\" style=\"float: right;\"><p style='border-radius: 5px; -webkit-border-radius: 5px; -moz-border-radius: 5px; color: white; padding: 5px 0px 3px 10px; color: white; font-size:14; background-color: #5281B0; width: 120px; float: left; margin-right: 10px; top: -12px; position: relative;'>cite MG-RAST API</p></a>";

#$content .= "<p style='color:#8FBC3F;text-align:left;font-size:9px;margin-top:3px;'><em>The Metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes</em> F. Meyer, D. Paarmann, M. D'Souza, R. Olson , E. M. Glass, M. Kubal, T. Paczian , A. Rodriguez , R. Stevens, A. Wilke, J. Wilkening, R. A. Edwards<br/><em>BMC Bioinformatics 2008, 9:386
#, [<a href=\"http://www.biomedcentral.com/1471-2105/9/386\" target=\"_blank\">article</a>]</em></p>";

#$content .= "<p style='text-align: center; float: right;'><span style='font-size: 11px; color: white;'>powered by</span><br><img style='width: 50px;' src='./Html/kbase_logo.png'></p>";

my $logos = "<img src='./Html/argonne_header_logo.jpg' style='padding-top: 15px; width: 150px;'>";
# news - logos

return $content;
}
Expand All @@ -198,36 +192,6 @@ sub speedometer {
my ($speed, $mileage, $trip, $togo) = split(/\t/, $line);

$content .= "<table style='background-color: #2f2f2f; position: absolute; right: 22px; top: 78px; color: rgb(143, 188, 63); font-family: Verdana,Arial,sans-serif;'><tr><td colspan=3 align=center style='font-size: 9pt;font-weight: bold;'>pipeline status</td></tr><tr title='analysis speed in basepairs/second'><td align=right style='font-size: 8pt;'>$speed</td><td align=left style='font-size: 8pt;'>bp/s</td><td align=left style='font-size: 8pt;'>speed</td></tr><tr title='data analyzed in the last 30 days'><td align=right style='font-size: 8pt;'>$trip</td><td align=left style='font-size: 8pt;'>Mbp</td><td align=left style='font-size: 8pt;'>last 30 days</td></tr><tr title='data left to be processed'><td align=right style='font-size: 8pt;'>$togo</td><td align=left style='font-size: 8pt;'>Mbp</td><td align=left style='font-size: 8pt;'>in queue</td></tr><tr title='total amount of data analyzed'><td align=right style='font-size: 8pt;'>$mileage</td><td align=left style='font-size: 8pt;'>Mbp</td><td align=left style='font-size: 8pt;'>total</td></tr></table>";

# my @trip1 = split(//, $trip);
# while (scalar(@trip1) < 7) {
# unshift(@trip1, "0");
# }
# $trip = '<table><tr>';# style="margin-left: 36px;"
# foreach my $t (@trip1) {
# $trip .= "<td style='font-size: 10px; border: 1px solid black; background-color: white; font-weight: bold; width: 12px; text-align: center;'>$t</td>";
# }
# $trip .= '</tr></table>';
# my @togo1 = split(//, $togo);
# while (scalar(@togo1) < 7) {
# unshift(@togo1, "0");
# }
# $togo = '<table><tr>';# style="margin-left: 36px;"
# foreach my $t (@togo1) {
# $togo .= "<td style='font-size: 10px; border: 1px solid black; background-color: white; font-weight: bold; width: 12px; text-align: center;'>$t</td>";
# }
# $togo .= '</tr></table>';
# my @mileage1 = split(//, $mileage);
# while (scalar(@mileage1) < 7) {
# unshift(@mileage1, "0");
# }
# $mileage = '<table><tr>';
# foreach my $t (@mileage1) {
# $mileage .= "<td style='font-size: 10px; border: 1px solid black; background-color: white; font-weight: bold; width: 12px; text-align: center;'>$t</td>";
# }
# $mileage .= '</tr></table>';

# $content .= "<table style='background-color: #2f2f2f; position: absolute; right: 22px; top: 79px; color: rgb(143, 188, 63); font-weight: bold; font-family: Verdana,Arial,sans-serif;'><tr title='analysis speed in basepairs/second'><td style='font-size: 10px; text-align: right;'>$speed</td><td style='font-size: 10px; vertical-align: middle;'>bp/s</td><td style='font-size: 10px; vertical-align: middle;'>speed</td></tr><tr title='data analyzed in the last 30 days'><td>$trip</td><td style='font-size: 10px; vertical-align: middle;'>Mbp</td><td style='font-size: 10px; vertical-align: middle;'>last 30 days</td></tr><tr title='data left to be processed'><td>$togo</td><td style='font-size: 10px; vertical-align: middle;'>Mbp</td><td style='font-size: 10px; vertical-align: middle;'>in queue</td></tr><tr title='total amount of data analyzed'><td>$mileage</td><td style='font-size: 10px; vertical-align: middle;'>Mbp</td><td style='font-size: 10px; vertical-align: middle;'>total</td></tr></table>";
}

return $content;
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1 change: 1 addition & 0 deletions 1 src/MGRAST/lib/WebPage/MetagenomeSearch.pm
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Expand Up @@ -235,6 +235,7 @@ sub output {

my $scripts = qq~
<script type="text/javascript" src="http://maps.google.com/maps/api/js?sensor=false"></script>
<script type="text/javascript" src="js/config.js"></script>
<script type="text/javascript">
\$(document).ready( function() {
var qList = $qlist;
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