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1468 lines (1396 loc) · 54.3 KB
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? Sanger/JS5.pm
? Sanger/Graphics/GraphViz.pm
? SiteDecor/merop-edit.pm
? Website/._DBStore.pm
? Website/DBStore.pm-testing
? Website/Service
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor.pm,v
retrieving revision 6.51
retrieving revision 6.52
Merging differences between 6.51 and 6.52 into SiteDecor.pm
rcsmerge: warning: conflicts during merge
cvs update: conflicts found in SiteDecor.pm
C SiteDecor.pm
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor/blast.pm,v
retrieving revision 1.5
retrieving revision 1.6
Merging differences between 1.5 and 1.6 into blast.pm
M SiteDecor/blast.pm
M SiteDecor/ccc.pm
M SiteDecor/decipher.pm
M SiteDecor/genedb.pm
M SiteDecor/intweb.pm
cvs update: conflict: `SiteDecor/meropstest.pm' is modified but no longer in the repository
C SiteDecor/meropstest.pm
M SiteDecor/wtsi.pm
M SiteDecor/yourgenome.pm
M Website/Feedback.pm
M Website/ServiceManager.pm
M Website/webstatus
M Website/SSO/Util.pm
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/Website/Utilities/Mail.pm,v
retrieving revision 1.7
retrieving revision 1.8
Merging differences between 1.7 and 1.8 into Mail.pm
rcsmerge: warning: conflicts during merge
cvs update: conflicts found in Website/Utilities/Mail.pm
C Website/Utilities/Mail.pm
M Website/portlet/calendar.pm
? Sanger/JS5.pm
? Sanger/Graphics/GraphViz.pm
? SiteDecor/merop-edit.pm
? Website/._DBStore.pm
? Website/DBStore.pm-testing
? Website/Service
Index: SiteDecor.pm
===================================================================
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor.pm,v
retrieving revision 6.51
diff -u -r6.51 SiteDecor.pm
--- SiteDecor.pm 28 Mar 2012 10:44:53 -0000 6.51
+++ SiteDecor.pm 12 Sep 2013 14:29:20 -0000
@@ -14,22 +14,12 @@
use warnings;
use Data::Dumper;
use Config::IniFiles;
-use SiteDecor::acedb;
use SiteDecor::blast;
-use SiteDecor::bloodomics;
-use SiteDecor::ccc;
-use SiteDecor::das;
-use SiteDecor::eucomm;
-use SiteDecor::g2c;
use SiteDecor::genedb;
use SiteDecor::intweb;
use SiteDecor::intwebtest;
use SiteDecor::merops;
use SiteDecor::plain;
-use SiteDecor::sangertest;
-use SiteDecor::services;
-use SiteDecor::treefam;
-use SiteDecor::wtgc;
use SiteDecor::wtsi;
use SiteDecor::yourgenome;
use SiteDecor::Menu::jimmac;
@@ -72,29 +62,14 @@
my $handlers = {
q(.*) => 'wtsi', # default
'acedb.org' => 'acedb',
- 'bloodomics.org' => 'bloodomics',
- 'das.ensembl.org' => 'das',
- 'das(dev)?.sanger.ac.uk' => 'das',
- 'decipher(dev)?.sanger.ac.uk' => 'decipher',
- 'efamily.org.uk' => 'efamily',
- '.ensembl.org' => 'plain',
'.eucomm.org' => 'eucomm',
'genedb.org' => 'genedb',
- 'genes2cognition.org' => 'g2c',
'.hinxton.org' => 'hinxton',
'intweb(dev)?.sanger.ac.uk' => 'intweb',
'intwebtest.sanger.ac.uk' => 'intwebtest',
- 'library.sanger.ac.uk' => 'library',
- 'mw6-site1.sandbox.sanger.ac.uk' => 'merops',
- 'merops(test|.staging|.dev)?.sanger.ac.uk' => 'merops',
- 'microrna(dev)?.sanger.ac.uk' => 'microrna',
- 'mitocheck.org' => 'mitocheck',
- 'services(dev|test)?.sanger.ac.uk' => 'services',
+ 'mw6-site1.sandbox.sanger.ac.uk' => 'merops',
+ 'merops(test|.staging|.dev)?.sanger.ac.uk' => 'merops',
'test.sanger.ac.uk' => 'sangertest',
- 'trace(dev|test)?.ensembl.org' => 'trace',
- 'treefam.org' => 'treefam',
- '.wtccc.org(.uk)?' => 'ccc',
- 'wtgc.org' => 'wtgc',
'yourgenome.org' => 'yourgenome',
};
@@ -123,13 +98,13 @@
return qw(coreinifile inifile
nph noHEAD decor
redirect redirect_delay
- title description keywords robots jsfile script onload stylesheet css style cookie
+ title description keywords robots jsfile script onload stylesheet css style cookie
navigator navigator2 navigator3 navigator_header navhead heading swoosh
navigator_align navigator2_align navigator3_align
banner bannercase
author headerimg headeralt
navbar1 navbar2
- server_name
+ server_name
rss atom ical portlets
remote_addr phogolink
drp cou cgi
@@ -279,7 +254,7 @@
# remember where this request was generated
#
my ($hostname) = (hostname()) =~ /^([^\.]+)/mx;
-
+
my $route = q{};
if ($hostname =~ /.*?-.*?-.*-?/){
my @parts = split q(-), $hostname;
@@ -725,7 +700,7 @@
#
$link =~ s/XXX_(.*?)_XXX/$subs->{$1}/smgx;
$val =~ s/XXX_(.*?)_XXX/$subs->{$1}/smgx;
-
+
$link?qq(<a href="$link">$val</a>):$val;
}
} @params;
@@ -976,7 +951,7 @@
}
sub rlogin_data {
- # This method now returns nothing as we dont want to use this
+ # This method now returns nothing as we dont want to use this
# feature anymore. It is a potential security risk.
return q( );
}
Index: SiteDecor/blast.pm
===================================================================
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor/blast.pm,v
retrieving revision 1.5
diff -u -r1.5 blast.pm
--- SiteDecor/blast.pm 8 Apr 2011 11:14:24 -0000 1.5
+++ SiteDecor/blast.pm 12 Sep 2013 14:29:20 -0000
@@ -40,8 +40,8 @@
my $self = shift;
my $header = q(
<div id="header"><div id="logo">
- <a href="/"><img src="http://www.sanger.ac.uk/i/sanger-logo.png" alt="Wellcome Trust Sanger Institute"></a>
- </div></div>
+ <a href="/"><img src="http://www.sanger.ac.uk/s-inst/gfx/sanger-logo.png" alt="Wellcome Trust Sanger Institute"></a>
+ </div></div>
);
$header .= $self->tabs1;
$header .= $self->tabs2;
@@ -70,27 +70,32 @@
my $footer = $self->wrap_bottom;
$footer .= q(
<div id="footer">
- <ul id="footer_links">
- <li>
- <a href="http://www.sanger.ac.uk/help/">Help</a>
- </li>
- <li>|
- </li>
- <li>
- <a href="http://www.sanger.ac.uk/about/contact/">Contact us</a>
- </li>
- <li>|
- </li>
- <li>
- <a href="http://www.sanger.ac.uk/legal/">Legal</a>
- </li>
- <li>|
- </li>
- <li>
- <a href="http://www.sanger.ac.uk/datasharing/">Data sharing</a>
- </li>
- </ul><br>
- Wellcome Trust Sanger Institute, Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457<br>
+ <ul id="footer_links">
+ <li>
+ <a href="http://www.sanger.ac.uk/help/">Help</a>
+ </li>
+ <li>|
+ </li>
+ <li>
+ <a href="http://www.sanger.ac.uk/about/contact/">Contact us</a>
+ </li>
+ <li>|
+ </li>
+ <li>
+ <a href="http://www.sanger.ac.uk/legal/">Legal</a>
+ </li>
+ <li>|
+ </li>
+ <li>
+ <a href="http://www.sanger.ac.uk/datasharing/">Data sharing</a>
+ </li>
+ <li>|
+ </li>
+ <li>
+ <a href="http://www.sanger.ac.uk/legal/cookiespolicy.html">Cookie Policy</a>
+ </li>
+ </ul><br>
+ Wellcome Trust Sanger Institute, Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457<br>
</div>
);
return $footer;
@@ -117,7 +122,7 @@
my $self = shift;
my $tabs = q{
<div id="navTabs">
- <ul id="navLeft" style="margin:0;padding:0">
+ <ul id="navLeft" style="margin:0;padding:0">
};
foreach my $ent (@{$self->tabs1_cats}){
my $t = $ent->[1];
@@ -154,7 +159,7 @@
my $self = shift;
my $tabs = q{
<div id="NavTabs2">
- <ul id="Tabs2">
+ <ul id="Tabs2">
};
foreach my $ent (@{$self->tabs2_cats}){
my $t = $ent->[1];
@@ -201,4 +206,4 @@
</div>
};
}
-1;
\ No newline at end of file
+1;
Index: SiteDecor/ccc.pm
===================================================================
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor/ccc.pm,v
retrieving revision 6.34
diff -u -r6.34 ccc.pm
--- SiteDecor/ccc.pm 23 Nov 2012 11:45:55 -0000 6.34
+++ SiteDecor/ccc.pm 12 Sep 2013 14:29:20 -0000
@@ -18,8 +18,8 @@
our $VERSION = do { my @r = (q$Revision: 6.34 $ =~ /\d+/mxg); sprintf '%d.'.'%03d' x $#r, @r };
our $JSFILES = {
- '/js/urchin.js' => q(),
- };
+ '/js/urchin.js' => q(),
+ };
sub init_defaults {
my $self = shift;
@@ -37,18 +37,18 @@
sub html_headers {
my $self = shift;
- my $banner = $self->{'banner'} || "";
- my $title = $self->{'title'} || $banner || "WTCCC: The Wellcome Trust Case Control Consortium";
+ my $banner = $self->{'banner'} || q();
+ my $title = $self->{'title'} || $banner || 'WTCCC: The Wellcome Trust Case Control Consortium';
my ($hostname) = (hostname()) =~ /^([^\.]+)/mx;
my $heads = {
- 'robots' => $self->robots() ?qq( <meta name="robots" content="@{[$self->robots()]}" />\n):q(),
- 'keywords' => $self->keywords() ?qq( <meta name="keywords" content="@{[$self->keywords()]}" />\n):q(),
- 'description' => $self->description() ?qq( <meta name="description" content="@{[$self->description()]}" />\n):q(),
- 'script' => $self->script() ?qq( <script type="text/javascript">@{[$self->script()]}</script>\n):q(),
- 'style' => $self->style() ?qq( <style type="text/css">@{[$self->style()]}</style>\n):q(),
- 'metaredirect' => q(),
- };
+ 'robots' => $self->robots() ?qq( <meta name="robots" content="@{[$self->robots()]}" />\n):q(),
+ 'keywords' => $self->keywords() ?qq( <meta name="keywords" content="@{[$self->keywords()]}" />\n):q(),
+ 'description' => $self->description() ?qq( <meta name="description" content="@{[$self->description()]}" />\n):q(),
+ 'script' => $self->script() ?qq( <script type="text/javascript">@{[$self->script()]}</script>\n):q(),
+ 'style' => $self->style() ?qq( <style type="text/css">@{[$self->style()]}</style>\n):q(),
+ 'metaredirect' => q(),
+ };
if($self->{'redirect'}) {
my $redirect = q();
@@ -57,9 +57,11 @@
}
my $redirect_delay = $self->{'redirect_delay'} || $self->{'redirect_delay'};
+ ##no critic (Literal line breaks)
$heads->{'metaredirect'} = qq(
<meta name="robots" content="noindex,follow" />
<meta http-equiv="refresh" content="$redirect_delay$redirect" />\n);
+ ##use critic (Literal line breaks)
}
###
#########
@@ -68,7 +70,7 @@
my @js;
my $j = $self->jsfile();
my $dev = $ENV{'dev'} || q();
- $dev = ($dev =~ /test/)?'dev':$dev;
+ $dev = ($dev =~ m/test/ixm)?'dev':$dev;
if($j) {
if(ref $j) {
@@ -91,7 +93,7 @@
<head>
<title>$title</title>
$heads->{'robots'}$heads->{'keywords'}$heads->{'description'}$heads->{'metaredirect'}
-@{[map {qq( <link rel="stylesheet" type="text/css" href="$_">\n); } @{$self->stylesheet()}]}
+@{[map {qq( <link rel="stylesheet" type="text/css" href="$_" />\n); } @{$self->stylesheet()}]}
@{[map {qq( <script type="text/javascript" src="$_" ></script>\n); } @{$self->jsfile()}]}
</head>
<body onload="$self->{'onload'}"><!-- host: $hostname-->);
@@ -118,6 +120,7 @@
_userv=0;
urchinTracker();
</script>
+ <div><a href="http://www.sanger.ac.uk/legal/cookiespolicy.html">Cookies Policy</a></div>
</div><!-- end main_content -->
</body>
</html>\n);
@@ -127,11 +130,11 @@
sub process_link
{
my $old_link = shift;
-if ( $old_link =~ m/^http:/ )
+if ( $old_link =~ m/^http:/ixm )
{
- $old_link =~ s/^http:/https:/ ;
+ $old_link =~ s/^http:/https:/ixm ;
}
-elsif (0 == index($old_link,'/'))
+elsif (0 == (index $old_link, q(/) ))
{
$old_link = 'https://' . $ENV{'HTTP_HOST'} . $old_link;
}
@@ -160,13 +163,13 @@
my ($text, $link) = ($_->{'text'},$_->{'link'});
my $display =0;
# Only print when not logged in.
- if (0 == index($text,'__'))
+ if (0 == (index $text,'__'))
{
- $text = substr($text,2);
- $display = 1;
+ $text = substr $text,2;
+ $display = 1;# if (not $user);
}
# Only print when logged in.
- elsif (0 == index($text,'_'))
+ elsif (0 == (index $text,'_'))
{
# $text = substr($text,1);
# $display = 1 if ($user && $url_cache->allowed_url($link));
@@ -184,9 +187,10 @@
}
else {
$subject = $_; # used later when we get a hash
- my $legend = ($user && 'Registered access' eq $subject) ? qq( title="$user logged in") : '';
+# my $legend = ($user && 'Registered access' eq $subject) ? qq( title="$user logged in") : q();
+ my $legend = q();
$menu{$_} = " <div$legend>$_</div>\n";
- $popup{$_} = "";
+ $popup{$_} = q();
push @subjects,$_;
}
} # next content
@@ -219,12 +223,12 @@
foreach (@_)
{
if ('ARRAY' eq ref $_)
- {
+ {
foreach (@{$_})
{
push @{$self->{'stylesheet'}}, $_
}
- }
+ }
else
{
push @{$self->{'stylesheet'}}, $_
@@ -248,7 +252,7 @@
{ push @flatten, $_ }
}
- my %defined = map { $_, 1 } @{$self->{'jsfile'}};
+ my %defined = map { $_ => 1 } @{$self->{'jsfile'}};
push @{$self->{'jsfile'}},grep { not $defined{$_} } @flatten;
}
return $self->{'jsfile'};
Index: SiteDecor/decipher.pm
===================================================================
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor/decipher.pm,v
retrieving revision 1.9
diff -u -r1.9 decipher.pm
--- SiteDecor/decipher.pm 24 Aug 2009 15:40:37 -0000 1.9
+++ SiteDecor/decipher.pm 12 Sep 2013 14:29:20 -0000
@@ -132,6 +132,8 @@
sub site_headers {
my $self = shift;
+ $self->read_ini;
+
if($self->decor() eq 'printable') {
return $self->site_banner();
}
@@ -195,7 +197,7 @@
<div id="login_box" style="display:none">
<form autocomplete="off" name="ssologin" action="https://enigma$dev.sanger.ac.uk/LOGIN" method="post" >
<input type="hidden" name="destination" value="$protocol://$ENV{'SERVER_NAME'}$uri" />
- <label for="credential_0">Username:</label>
+ <label for="credential_0">UserName:</label>
<input type="text" name="credential_0" maxlength="128" class="field"/>
<label for="credential_1">Password:</label>
<input type="password" name="credential_1" maxlength="20" class="field"/>
@@ -260,6 +262,7 @@
#########
# need to add check here to see if navigator is present. if not hide navtab and expand main
#
+
if(@{$nav_entries->{'1'}} || @{$nav_entries->{'2'}} || $self->heading()) {
$site_headers .= qq( <div id="main" @{[$is_hidden?qq(class="expanded"):qq(class="collapsed")]}>);
} else {
@@ -284,6 +287,7 @@
}
$site_headers .= $self->site_banner($banner);
}
+
return $site_headers;
}
@@ -336,7 +340,7 @@
</div>
<div id="legal">
<p class="right">$lastmod</p>
- <p class="left">Registered charity number 210183</p>
+ <p class="left">Registered charity number 1021457</p>
<p class="middle">@{[($self->decor() eq "printable")?q():qq(<a href="http://www$dev.sanger.ac.uk/notices/release-policy.shtml">Data Release Policy</a> | <a href="http://www$dev.sanger.ac.uk/notices/use-policy.shtml">Conditions of Use</a> | <a href="http://www$dev.sanger.ac.uk/notices/copyright.shtml">Copyright</a>)]}</p>
</div>
</div> <!-- end of collapseFOOT div -->
Index: SiteDecor/genedb.pm
===================================================================
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor/genedb.pm,v
retrieving revision 6.2
diff -u -r6.2 genedb.pm
--- SiteDecor/genedb.pm 27 Apr 2009 10:20:36 -0000 6.2
+++ SiteDecor/genedb.pm 12 Sep 2013 14:29:20 -0000
@@ -21,17 +21,26 @@
sub html_headers {
my $self = shift;
my $title = $self->{'title'} || "";
- return qq[
+ return q[
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head>
-<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
- <title>${title} - GeneDB</title>
-
- <link rel="stylesheet" href="http://beta.genedb.org/includes/style/alternative.css" type="text/css">
- <link rel="stylesheet" href="http://beta.genedb.org/includes/style/menu.css" type="text/css">
-<link rel="stylesheet" type="text/css" href="http://beta.genedb.org/includes/style/wtsi.css">
-<link rel="stylesheet" type="text/css" href="http://beta.genedb.org/includes/style/genedb/genePage.css">
+<html>
+<head>
+ <title>Homepage - GeneDB</title>
+
+ <script type="text/javascript" src="http://js.sanger.ac.uk/urchin.js"></script>
+
+ <link rel="stylesheet" href="/includes/style/genedb/main.css" type="text/css" />
+ <script type="text/javascript" src="/includes/scripts/jquery/jquery-genePage-combined.js"></script>
+
+ <script type="text/javascript">
+ $(function(){
+ $("#nav > li")
+ .mouseover(function(){$(this).addClass("over");})
+ .mouseout (function(){$(this).removeClass("over");});
+ });
+ </script>
+
</head>
];
}
@@ -39,27 +48,128 @@
sub site_headers {
my $self = shift;
my $title = $self->{'title'} || "GeneDB";
- return qq[
-<body class="genePage">
-
-<table id="header"><tbody>
- <tr id="top-row">
- <td id="logo" rowspan="2" align="left" valign="top"><a href="http://beta.genedb.org/Homepage"><img src="http://beta.genedb.org/includes/images/genedb-logo.gif" alt="GeneDB" border="0" height="51" width="171"></a></td>
- <td id="name">${title}</td>
- <td id="search">
- <form name="searchForm" action="http://beta.genedb.org/Query" method="GET">
- <input name="taxons" value="" type="hidden">
- <input name="q" value="allNameProduct" type="hidden">
- <input name="pseudogenes" value="true" type="hidden">
- <input name="product" value="true" type="hidden">
- <input name="allNames" value="true" type="hidden">
- <input id="query" name="search" align="middle" type="text">
- <input id="submit" value="Search" title="Search" align="middle" type="submit"><br>
- </form>
- </td>
- </tr>
-</tbody></table>
-
+ return q[
+<body>
+<div id="container">
+<div id="header">
+<a href="/Homepage"><img src="/includes/image/GeneDB-logo.png" border="0" alt="GeneDB" class="float-left-and-offset" id="logo" /></a>
+
+<div class="float-right" >
+<div class="baby-blue-top"></div>
+<div id="search" class="baby-blue">
+<form action="/QuickSearchQuery" method="get">
+<table cellpadding="0" cellspacing="0" width="100%" class="search-table">
+<tr>
+<td>
+<input type="hidden" name="pseudogenes" value="true" />
+<input type="hidden" name="product" value="true" />
+<input type="hidden" name="allNames" value="true" />
+<input type="text" name="searchText" class="search-box" /></td><td align="right"><input type="image" src="/includes/image/button-search.gif" /></td>
+</tr>
+<tr>
+<td colspan="2">
+
+<select name="taxons">
+<option class="Level0DropDown" value="Root"> All Organisms</option>
+<option class="Level1DropDown" value="Bacteria"> Bacteria</option>
+<option class="Level2DropDown" value="Bfragilis_NCTC9343"> B. fragilis NCTC9343</option>
+<option class="Level2DropDown" value="Bordetella"> Bordetella</option>
+<option class="Level3DropDown" value="Bbronchiseptica"> B. bronchiseptica</option>
+<option class="Level3DropDown" value="Bparapertussis"> B. parapertussis</option>
+<option class="Level2DropDown" value="Burkholderia"> Burkholderia</option>
+<option class="Level3DropDown" value="Bcenocepacia"> B. cenocepacia</option>
+<option class="Level3DropDown" value="Bpseudomallei"> B. pseudomallei</option>
+<option class="Level2DropDown" value="Cabortus"> C. abortus</option>
+<option class="Level2DropDown" value="Cdiphtheriae"> C. diphtheriae</option>
+<option class="Level2DropDown" value="Cjejuni"> C. jejuni</option>
+<option class="Level2DropDown" value="Ecarotovora"> E. carotovora</option>
+<option class="Level2DropDown" value="Rleguminosarum"> R. leguminosarum</option>
+<option class="Level2DropDown" value="Salmonella"> Salmonella</option>
+<option class="Level3DropDown" value="Styphi"> S. typhi</option>
+<option class="Level3DropDown" value="Styphimurium"> S. typhimurium</option>
+<option class="Level2DropDown" value="Scoelicolor"> S. coelicolor</option>
+<option class="Level2DropDown" value="Staphylococcus"> Staphylococcus</option>
+<option class="Level3DropDown" value="Saureus_MRSA252"> S. aureus MRSA252</option>
+<option class="Level3DropDown" value="Saureus_MSSA476"> S. aureus MSSA476</option>
+<option class="Level2DropDown" value="Streptococcus"> Streptococcus</option>
+<option class="Level3DropDown" value="Spyogenes"> S. pyogenes</option>
+<option class="Level1DropDown" value="Helminths"> Helminths</option>
+<option class="Level2DropDown" value="Platyhelminths"> Platyhelminths</option>
+<option class="Level3DropDown" value="Sjaponicum"> S. japonicum</option>
+<option class="Level3DropDown" value="Smansoni"> S. mansoni</option>
+<option class="Level1DropDown" value="Protozoa"> Protozoa</option>
+<option class="Level2DropDown" value="Apicomplexa"> Apicomplexa</option>
+<option class="Level3DropDown" value="Etenella"> E. tenella</option>
+<option class="Level3DropDown" value="Ncaninum"> N. caninum</option>
+<option class="Level3DropDown" value="Plasmodium"> Plasmodium</option>
+<option class="Level4DropDown" value="Pchabaudi"> P. chabaudi</option>
+<option class="Level4DropDown" value="Pfalciparum"> P. falciparum</option>
+<option class="Level4DropDown" value="Pknowlesi"> P. knowlesi</option>
+<option class="Level4DropDown" value="Pvivax"> P. vivax</option>
+<option class="Level4DropDown" value="Pyoelii"> P. yoelii</option>
+<option class="Level2DropDown" value="Kinetoplastida"> Kinetoplastida</option>
+<option class="Level3DropDown" value="Leishmania"> Leishmania</option>
+<option class="Level4DropDown" value="Lbraziliensis"> L. braziliensis</option>
+<option class="Level4DropDown" value="Linfantum"> L. infantum</option>
+<option class="Level4DropDown" value="Lmajor"> L. major</option>
+<option class="Level4DropDown" value="Lmexicana"> L. mexicana</option>
+<option class="Level3DropDown" value="Trypanosoma"> Trypanosoma</option>
+<option class="Level4DropDown" value="Tbruceibrucei427"> T. brucei brucei 427</option>
+<option class="Level4DropDown" value="Tbruceibrucei927"> T. brucei brucei 927</option>
+<option class="Level4DropDown" value="Tbruceigambiense"> T. bruceigambiense</option>
+<option class="Level4DropDown" value="Tcongolense"> T. congolense</option>
+<option class="Level4DropDown" value="Tcruzi"> T. cruzi</option>
+<option class="Level4DropDown" value="Tvivax"> T. vivax</option>
+</select>
+</td>
+</tr>
+</table>
+</form>
+</div>
+<div class="baby-blue-bot"></div>
+</div><!-- end float right of search box -->
+<br class="clear" />
+</div><!-- end header block -->
+
+<br class="clear" />
+
+<div id="navigation">
+<ul id="nav">
+<li><a href="/Homepage">Home</a>
+</li>
+
+<li><a href="/Page/aboutUs">About us</a></li>
+<li class="has-sub"><a href="/Query">Searches</a>
+<ul class="sub-menu">
+<li><a href="/Query/geneType?taxons=" >By Gene Type</a></li>
+<li><a href="/Query/geneLocation?taxons=" >By Location</a></li>
+<li><a href="/Query/proteinLength?taxons=" >By Protein Length</a></li>
+<li><a href="/Query/proteinMass?taxons=">By Molecular Mass</a></li>
+<li><a href="/Query/proteinNumTM?taxons=">By No. TM domains</a></li>
+<li><a href="/Query/proteinTargetingSeq?taxons=">By Targeting Seqs.</a></li>
+<li><a href="/Query/simpleName?taxons=">Gene names</a></li>
+<li><a href="/Query/product?taxons=">Product</a></li>
+
+<li><a href="/Query/go?taxons=">GO term/id</a></li>
+<li><a href="/Query/ec?taxons=">EC number</a></li>
+<li><a href="/Query/pfam?taxons=">Pfam ID or keyword</a></li>
+</ul>
+<!-- end sub menu -->
+</li>
+<li class="has-sub"><a href="">Browse</a>
+<ul class="sub-menu">
+<li><a href="/category/genedb_products?taxons=">Products</a></li>
+<li><a href="/category/ControlledCuration?taxons=">Controlled Curation</a></li>
+<li><a href="/category/biological_process?taxons=">Biological Process</a></li>
+<li><a href="/category/cellular_component?taxons=">Cellular Component</a></li>
+<li><a href="/category/molecular_function?taxons=">Molecular Function</a></li>
+</ul>
+</li>
+<li><a href="/History">History</a></li>
+<!-- end sub menu -->
+</ul>
+</div><!-- end navigation block -->
+<div style="font-size:1.3em">
];
}
@@ -71,17 +181,35 @@
sub site_footers {
my $self = shift;
- return qq[
- <br>
-<br>
-<table class="footer" width="100%">
- <tbody><tr height="20">
- <td style="" align="left" width="33%">Hosted by the <a href="http://www.sanger.ac.uk/">Sanger Institute</a></td>
- <td style="" align="center" width="34%"><!-- Curator feedback --></td>
- <td style="" align="right" width="33%"><!-- Technical feedback--></td>
- </tr>
-</tbody></table>
-</body></html>
+ return q[
+</div>
+<br class="clear" />
+
+<div id="footer">
+<div class="footer-top"></div>
+<div class="light-grey">
+<table cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="top" align="left">
+<p>© 2009 and hosted by the <a href="http://www.sanger.ac.uk/">Sanger Institute</a></p>
+</td>
+
+<td valign="top" align="right">
+<p>Comments/Questions: <a href="mailto:webmaster@genedb.org">Email us</a>
+</td>
+</tr>
+</table>
+</div>
+<div class="footer-bot"></div>
+</div><!-- end footer -->
+</div><!-- end container -->
+
+<script type="text/javascript">
+_userv=0;
+urchinTracker();
+</script>
+</body>
+</html>
];
}
Index: SiteDecor/intweb.pm
===================================================================
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor/intweb.pm,v
retrieving revision 1.12
diff -u -r1.12 intweb.pm
--- SiteDecor/intweb.pm 11 Nov 2011 10:34:52 -0000 1.12
+++ SiteDecor/intweb.pm 12 Sep 2013 14:29:20 -0000
@@ -176,7 +176,7 @@
</div><!--search box end-->
</div> <!-- end of collapseHEAD div -->
<div id="nav_bar">
- <a href="http://www$dev.sanger.ac.uk/feedback/"><img src="/icons/navigation/email.gif" alt="Contact WTSI Webmaster" title="Contact WTSI Webmaster" /></a>
+ <a href="mailto:web\@sanger.ac.uk"><img src="/icons/navigation/email.gif" alt="Contact WTSI Webmaster" title="Contact WTSI Webmaster" /></a>
<a href="$printlink"><img src="/icons/navigation/printer.gif" alt="Printer friendly format" title="Printer friendly format" /></a>
<a href="$ssokey" $loginjs><img src="/icons/navigation/$icons" alt="$login_title" title="$login_title" /></a>
<a href="http://www$dev.sanger.ac.uk/shared/news-report/atom/20020211150255"><img src="/icons/navigation/rss.gif" alt="WTSI RSS feed" title="WTSI RSS feed" /></a>
Index: SiteDecor/meropstest.pm
===================================================================
RCS file: /repos/cvs/webcore/SHARED_docs/lib/core/SiteDecor/Attic/meropstest.pm,v
retrieving revision 1.34
diff -u -r1.34 meropstest.pm
--- SiteDecor/meropstest.pm 14 Dec 2009 16:18:57 -0000 1.34
+++ SiteDecor/meropstest.pm 12 Sep 2013 14:29:20 -0000
@@ -8,7 +8,11 @@
package SiteDecor::meropstest;
use strict;
use warnings;
+use Carp;
use base qw(SiteDecor);
+use Website::DBStore;
+our $H_CACHE = {};
+our $H_ID = {};
sub init_defaults {
my $self = shift;
@@ -28,7 +32,7 @@
sub fields {
my $self = shift;
my @fields = $self->SUPER::fields;
- push @fields, qw( body_class content_class );
+ push @fields, qw( lastmod body_class content_class );
return @fields;
}
@@ -38,38 +42,51 @@
#############################################
# Determine $config_file
-
- my $inifile = $self->{'inifile'};
- my $req_uri = $ENV{'REQUEST_URI'} || q();
-
if($self->ini_loaded()) {
return;
}
+ my ($sidebar,$id) = $self->stuff();
+
+ my $content = ($self->{content_class})?$self->{content_class}:'content';
+ $html_headers .= qq( <div class="sidebar"$id>
+ $sidebar
+ </div><!-- end sidebar -->
+ <div class="$content">\n);
+
+ return $html_headers;
+}
+
+sub stuff {
+ my $self = shift;
+
+# key = $req_uri+$ENV{'DOCUMENT_ROOT'}+$inifile
+
+ my $inifile = $self->{'inifile'};
+ my $req_uri = $ENV{'REQUEST_URI'} || q(); # path to script
if(!$inifile && $req_uri =~ /^\/(perl|cgi\-bin)/mx) {
# return;
}
- my ($header,$header_global);
+ my ($header,$header_direct,$header_global);
+# my $header_file = 'default_sidebar.yml';
if($inifile) {
#########
# determine full path to configured header files
#
-
- my $req = $ENV{'REQUEST_URI'}; # path to script
-
my $tld;
# Strip cgi-bin or perl:
- if($req =~ m{/(cgi-bin|perl)/([^/]+)/}mx) {
+ if($req_uri =~ m{/(cgi-bin|perl)/([^/]+)/}mx) {
$tld = $2;
- } elsif($req !~ /(cgi-bin|perl)/mx) {
- ($tld) = $req =~ m{/([^/]+)/$}mx; # last part of path (?)
+ } elsif($req_uri !~ /(cgi-bin|perl)/mx) {
+ ($tld) = $req_uri =~ m{/([^/]+)/$}mx; # last part of path (?)
}
$tld = $tld?"$tld/":q(); # add a backslash
($header) = $inifile =~ /([a-zA-Z0-9\/\_\-\.]+)/mx; # anything from inifile
my $dr = $ENV{'DOCUMENT_ROOT'} ||q();
+ $header_direct = qq($dr/$header);
$header = qq($dr/$tld$header);
$header_global = qq($dr/default_sidebar.yml); # just look at root for default sidebar
}
@@ -86,49 +103,80 @@
$header_global = qq($dr/default_sidebar.yml);
}
- $header =~ s|//|/|mxg;
+ $header =~ s{//}{/}mxg;
+
- my $sidebar = q();
+ my $sidebar = q();
my $sidebar_id = q();
- my $header_file = q();
- if(-f $header) {
- $header_file = $header;
- }
- elsif (-f $header_global) {
- $header_file = $header_global;
- }
- if ($header_file) {
- eval {
- my $config = YAML::LoadFile($header_file);
- $sidebar = q();
- for my $entry (@{$config}) {
- if ($entry->{'html_sidebar_id'}) {
- $sidebar_id = q( id=').$entry->{'html_sidebar_id'}.q(');
- }
- else {
- $sidebar .= $self->create_menu($entry);
+ my $header_file = q();#/Users/mw6/webcvs/MEROPS_docs/htdocs/default_sidebar.yml);
+
+ # Only use files that exist = a file op.
+# if ($header && -f $header) {
+# $header_file = $header;
+# }
+# elsif ($header_direct && -f $header_direct) {
+# $header_file = $header_direct;
+# }
+# elsif (-f $header_global) {
+# $header_file = $header_global;
+# }
+ $header_file = $header || $header_direct || $header_global;
+ unless (-f $header_file) {
+ $header_file = $header_direct || $header_global;
+ unless (-f $header_file) {
+ $header_file = $header_global;
+ unless (-f $header_file) {
+ $header_file = q();
+ $sidebar = q(You need a default_sidebar.yml);
+ carp "Not found: $header_file";
+ return ($sidebar,$sidebar_id);
}
}
- };
- if ($@) {
- warn "Problems : $@";
}
- $self->ini_loaded(1);
- }
- else {
- $sidebar = q(You need a default_sidebar.yml);
- warn "Not found: $header_file";
- }
- my $content = ($self->{content_class})?$self->{content_class}:'content';
+ # warn 'H='.$header_file;
+ if ($H_CACHE->{$header_file}) {
+ # warn "got from self";
+ my $sidebar = $H_CACHE->{$header_file}->{sidebar};
+ my $sidebar_id = $H_CACHE->{$header_file}->{id};
+ return ($sidebar,$sidebar_id);
+ }
+
+ # if (!$self->{dbstore}) {
+ # $self->{dbstore} = Website::DBStore->new();
+ # }
+ # my $dbstore= $self->{dbstore};
+ # if ($sidebar = $dbstore->get($header_file)) {
+ # warn "got from database";
+ # $self->{sidebar}->{$header_file} = $sidebar;
+ # } else {
+
+ eval {
+ my $config = YAML::LoadFile($header_file);
+ $sidebar = q();
+ for my $entry (@{$config}) {
+ if ($entry->{'html_sidebar_id'}) {
+ $sidebar_id = q( id=').$entry->{'html_sidebar_id'}.q(');
+ } else {
+ $sidebar .= $self->create_menu($entry);
+ }
+ }
+ };
+ if ($@) {
+ carp "Problems : $@";
+ }
- $html_headers .= qq( <div class="sidebar"$sidebar_id>
- $sidebar
- </div><!-- end sidebar -->
- <div class="$content">\n);
+ # warn " $header_file / sidebar = ".length($sidebar);
- return $html_headers;
+ # warn "Saving..";
+ # $dbstore->set($sidebar,$header_file,5); # 5 minutes
+ $H_CACHE->{$header_file}->{sidebar} = $sidebar;
+ $H_CACHE->{$header_file}->{id} = $sidebar_id || q();
+# warn "$sidebar_id | $header_file";
+
+ $self->ini_loaded(1);
+ return ($sidebar,$sidebar_id);
}
sub site_body_tag {
@@ -140,7 +188,7 @@
if(grep { m{/js/sidebar.js}mx } @{$self->jsfile()}) {
$onload = "sidebar_default(); $onload;";
}
- $onload = $onload?q( onload="$onload"):q();
+ $onload = $onload?qq( onload="$onload"):q();
return sprintf q( <body%s%s>), $class, $onload;
}
@@ -150,12 +198,12 @@
if(defined $self->{'banner'}) {
my $banner = q();
- if($self->{'bannercase'} eq "uc") {
- $banner = uc($self->{'banner'});
- } elsif($self->{'bannercase'} eq "ucfirst") {
- $banner = ucfirst($self->{'banner'});
+ if($self->{'bannercase'} eq 'uc') {
+ $banner = uc $self->{'banner'};
+ } elsif($self->{'bannercase'} eq 'ucfirst') {
+ $banner = ucfirst $self->{'banner'};
} else {
- $banner = lc($self->{'banner'});
+ $banner = lc $self->{'banner'};
}
$site_headers .= $self->site_banner($banner);
}
@@ -183,21 +231,32 @@
my $lastmod = q();
my $req_uri = $ENV{'REQUEST_URI'} || q();
- if($ENV{'LAST_MODIFIED'}) {
+ if ($self->{lastmod}) {
+ $lastmod = q(Page created ).($self->{'lastmod'}->{'text'} || (get_time($self->{'lastmod'}->{'time'})));
+ }
+ elsif($ENV{'LAST_MODIFIED'}) {
$lastmod = qq(Last Modified $ENV{'LAST_MODIFIED'});
-
}
- else {
+ elsif($req_uri =~ m{/(cgi-bin|perl)/([^/]+)}mx) {
+ eval {
+ my ($conf_file) = ($ENV{'DOCUMENT_ROOT'}.'/../data/sitedefs.yml') =~ m{([a-z\d\./_]+)}mix;
+ my $config = YAML::LoadFile($conf_file);
+ my $date = $config->{merops_rel_date};
+ if ($date) { $lastmod = 'Page created '.$date }
+ };
+ }
+
+ if (not $lastmod) {
#########
# Look for the request_uri document
#
- my ($fn) = "$ENV{'DOCUMENT_ROOT'}/$req_uri" =~ m|([a-z\d\./_]+)|mix;
+ my ($fn) = "$ENV{'DOCUMENT_ROOT'}/$req_uri" =~ m{([a-z\d\./_]+)}mix;
#########
# If that doesn't exist try the script_filename
#
if($fn && !-e $fn) {
- ($fn) = $ENV{'SCRIPT_FILENAME'}||q() =~ m|([a-z\d\./_]+)|mix;
+ ($fn) = $ENV{'SCRIPT_FILENAME'}||q() =~ m{([a-z\d\./_]+)}mix;
}
if($fn && -e $fn) {
@@ -213,7 +272,7 @@
<div class="footer">
<p class="right"><a href='/cgi-bin/feedback'>feedback</a><br />$lastmod</p>
<p class="left"><img src="/gfx/wtlogo.gif" alt="Wellcome Trust logo" /><br />Funding from the <a href="http://www.wellcome.ac.uk">Wellcome Trust</a></p>
- <p class="middle">© 2009 WTSI<br /><a href="/about/availability.shtml">Terms of use</a></p>
+ <p class="middle">© 2011 WTSI<br /><a href="/about/availability.shtml">Terms of use</a></p>
</div>
</div><!-- end class content -->
<script type="text/javascript">
@@ -227,17 +286,17 @@
sub create_menu {
my ($self,$entry) = @_;
my $output = q{};
- while ((my $key, my $value) = each %$entry) {
+ while ((my $key, my $value) = each %{$entry}) {
if (ref $value eq 'HASH') {
my $is_li = 0;
- my ($has_children_s,$has_children_e) = ('','');
- if ($value->{'class'} && $value->{'class'} ne 'title' && $value->{'class'} ne 'switch' && $value->{'class'} !~ /^bigtext/ )
+ my ($has_children_s,$has_children_e) = (q(),q());
+ if ($value->{'class'} && $value->{'class'} ne 'title' && $value->{'class'} ne 'switch' && $value->{'class'} !~ /^bigtext/xm )
{