<?php
/**
* @file
* BIPAA's theme implementation to display a single Drupal page.
*
* The doctype, html, head and body tags are not in this template. Instead they
* can be found in the html.tpl.php template normally located in the
* modules/system directory.
*
* Available variables:
*
* General utility variables:
* - $base_path: The base URL path of the Drupal installation. At the very
* least, this will always default to /.
* - $directory: The directory the template is located in, e.g. modules/system
* or themes/bipaa.
* - $is_front: TRUE if the current page is the front page.
* - $logged_in: TRUE if the user is registered and signed in.
* - $is_admin: TRUE if the user has permission to access administration pages.
*
* Site identity:
* - $front_page: The URL of the front page. Use this instead of $base_path,
* when linking to the front page. This includes the language domain or
* prefix.
* - $logo: The path to the logo image, as defined in theme configuration.
* - $site_name: The name of the site, empty when display has been disabled
* in theme settings.
* - $site_slogan: The slogan of the site, empty when display has been disabled
* in theme settings.
* - $hide_site_name: TRUE if the site name has been toggled off on the theme
* settings page. If hidden, the "element-invisible" class is added to make
* the site name visually hidden, but still accessible.
* - $hide_site_slogan: TRUE if the site slogan has been toggled off on the
* theme settings page. If hidden, the "element-invisible" class is added to
* make the site slogan visually hidden, but still accessible.
*
* Navigation:
* - $main_menu (array): An array containing the Main menu links for the
* site, if they have been configured.
* - $secondary_menu (array): An array containing the Secondary menu links for
* the site, if they have been configured.
* - $breadcrumb: The breadcrumb trail for the current page.
*
* Page content (in order of occurrence in the default page.tpl.php):
* - $title_prefix (array): An array containing additional output populated by
* modules, intended to be displayed in front of the main title tag that
* appears in the template.
* - $title: The page title, for use in the actual HTML content.
* - $title_suffix (array): An array containing additional output populated by
* modules, intended to be displayed after the main title tag that appears in
* the template.
* - $messages: HTML for status and error messages. Should be displayed
* prominently.
* - $tabs (array): Tabs linking to any sub-pages beneath the current page
* (e.g., the view and edit tabs when displaying a node).
* - $action_links (array): Actions local to the page, such as 'Add menu' on the
* menu administration interface.
* - $feed_icons: A string of all feed icons for the current page.
* - $node: The node object, if there is an automatically-loaded node
* associated with the page, and the node ID is the second argument
* in the page's path (e.g. node/12345 and node/12345/revisions, but not
* comment/reply/12345).
*
* Regions:
* - $page['header']: Items for the header region.
* - $page['featured']: Items for the featured region.
* - $page['highlighted']: Items for the highlighted content region.
* - $page['help']: Dynamic help text, mostly for admin pages.
* - $page['content']: The main content of the current page.
* - $page['sidebar_first']: Items for the first sidebar.
* - $page['triptych_first']: Items for the first triptych.
* - $page['triptych_middle']: Items for the middle triptych.
* - $page['triptych_last']: Items for the last triptych.
* - $page['footer_firstcolumn']: Items for the first footer column.
* - $page['footer_secondcolumn']: Items for the second footer column.
* - $page['footer_thirdcolumn']: Items for the third footer column.
* - $page['footer_fourthcolumn']: Items for the fourth footer column.
* - $page['footer']: Items for the footer region.
*
* @see template_preprocess()
* @see template_preprocess_page()
* @see template_process()
* @see bipaa_process_page()
* @see html.tpl.php
*/
?>
<header id="masthead" class="site-header" role="banner">
<a class="home-link" href="<?php echo $GLOBALS['base_url']; ?>" title="BIPAA" rel="home">
</a>
<div id="navbar" class="navbar">
<nav id="site-navigation" class="navigation main-navigation" role="navigation">
<button class="menu-toggle">Menu</button>
<a class="screen-reader-text skip-link" href="#content" title="Skip to content">Skip to content</a>
<div class="menu-main-container">
<ul id="primary-menu" class="nav-menu">
<?php if (getenv('ENABLE_ORTHOLOGY')): ?>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/search/phylotree">Gene families</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/organism">Organisms</a></li>
<?php elseif (getenv('ENABLE_NO_CHADO_DATA')): ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-home menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']; ?>">
<?php
if (getenv('SITE_NAME'))
echo getenv('SITE_NAME');
else
echo "Home";
?>
</a>
</li>
<?php else: ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-home menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']; ?>">
<?php
if (getenv('SITE_NAME'))
echo getenv('SITE_NAME');
else
echo "Home";
?>
</a>
<ul class="sub-menu">
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/analysis">Analyses</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/feature">Features</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/organism">Organisms</a></li>
<!--li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/elastic_search">Advanced search</a></li-->
</ul>
</li>
<?php endif; ?>
<?php if (getenv('ENABLE_GO')): ?>
<?php
if (getenv('ENABLE_GO') == "1")
$url = '/organism/';
else
$url = getenv('ENABLE_GO');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url'].$url; ?>">GO Report</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_BLAST')): ?>
<?php
if (getenv('ENABLE_BLAST') == "1")
$url = $GLOBALS['base_url'].'/blast';
else
$url = getenv('ENABLE_BLAST');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Blast</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_JBROWSE')): ?>
<?php
if (getenv('ENABLE_JBROWSE') == "1")
$url = '/jbrowse';
else
$url = getenv('ENABLE_JBROWSE');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url'].$url; ?>">JBrowse</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_APOLLO')): ?>
<?php
if (getenv('ENABLE_APOLLO') == "1")
$url = '/apollo';
else
$url = getenv('ENABLE_APOLLO');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url'].$url; ?>">Apollo</a>
<ul class="sub-menu">
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="<?php echo $GLOBALS['base_url'].'/apollo_report'; ?>">Annotation report</a></li>
</ul>
</li>
<?php endif; ?>
<?php if (getenv('ENABLE_AUREME')): ?>
<?php
if (getenv('ENABLE_AUREME') == "1")
$url = $GLOBALS['base_url'].'/aureme';
else
$url = getenv('ENABLE_AUREME');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Metabolic model</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_APHIDCYC')): ?>
<?php
if (getenv('ENABLE_APHIDCYC') == "1")
$url = 'http://aphidcyc.cycadsys.org/';
else
$url = getenv('ENABLE_APHIDCYC');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">AphidCyc</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_WIKI')): ?>
<?php
if (getenv('ENABLE_WIKI') == "1")
$url = $GLOBALS['base_url'].'/wiki/';
else
$url = getenv('ENABLE_WIKI');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Wiki</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_DOWNLOAD')): ?>
<?php
if (getenv('ENABLE_DOWNLOAD') == "1")
$url = '/download';
else
$url = getenv('ENABLE_DOWNLOAD');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url'].$url; ?>">Download</a></li>
<?php endif; ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="http://bipaa.genouest.org/is/">BIPAA</a>
<ul class="sub-menu">
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="https://bipaa.genouest.org/is/aphidbase/">AphidBase</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/parwaspdb/">ParWaspDB</a></li>
<li id="menu-item-78" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-78"><a href="https://bipaa.genouest.org/is/lepidodb/">LepidoDB</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/coleoptera/">Coleoptera</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/crustacea/">Crustacea</a></li>
<li id="menu-item-130" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-130"><a href="https://bipaa-galaxy.genouest.org/">Galaxy</a></li>
<li id="menu-item-138" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-138"><a href="https://bipaa.genouest.org/account/">BIPAA account</a></li>
</ul>
</li>
</ul>
</div>
<?php if (!getenv('ENABLE_ORTHOLOGY')): ?>
<?php print render($page['header']["tripal_elasticsearch_elasticsearch_website_search_box"]); ?>
<?php endif; ?>
</nav><!-- #site-navigation -->
</div><!-- #navbar -->
</header><!-- #masthead -->
<div id="main" class="site-main">
<div id="primary" class="content-area">
<div id="content" class="site-content" role="main">
<article class="page type-page status-publish hentry">
<div class="entry-content">
<?php if ($page['highlighted']): ?><div id="highlighted"><?php print render($page['highlighted']); ?></div><?php endif; ?>
<a id="main-content"></a>
<header class="entry-header">
<?php print render($title_prefix); ?>
<h1 class="entry-title" id="page-title">
<?php print getenv('SITE_NAME'); ?>
</h1>
<?php print render($title_suffix); ?>
</header>
<?php if ($tabs): ?>
<div class="tabs">
<?php print render($tabs); ?>
</div>
<?php endif; ?>
<?php print render($page['help']); ?>
<?php if ($action_links): ?>
<ul class="action-links">
<?php print render($action_links); ?>
</ul>
<?php endif; ?>
<?php
if (file_exists('/welcome.html'))
include('/welcome.html');
?>
<?php if (getenv('ENABLE_ORTHOLOGY')): ?>
<p>This section contains orthology data.</p>
<p>Browse the available <a href="<?php echo $GLOBALS['base_url']; ?>/search/phylotree">gene families</a></p>
<?php elseif (getenv('ENABLE_NO_CHADO_DATA')): ?>
<?php else: ?>
<?php $search_form = drupal_get_form('website_search_box_form'); print drupal_render($search_form); ?>
<?php endif; ?>
<div id="front_content">
<div id="front_organisms">
<h2>Available organisms</h2>
<?php foreach ($page['organisms'] as $org_id => $org): ?>
<div class="tripal-organism-teaser tripal-teaser">
<div class="tripal-organism-teaser-title tripal-teaser-title">
<p class='data_highlight'>
<?php
print "<a href=\"".$GLOBALS['base_url']."/organism/".str_replace(' ', '-', $org->genus)."/".str_replace(' ', '-', $org->species)."\"><i>$org->genus $org->species</i>";
if (strtolower($org->common_name) != strtolower($org->genus[0].$org->species))
print " ($org->common_name)";
print "</a>";
?>
</p>
</div>
<div class="tripal-organism-teaser-text tripal-teaser-text"><?php
print substr($org->comment, 0, 650);
if (strlen($org->comment) > 650) {
print "... ";
}
?>
</div>
</div>
<?php endforeach; ?>
<?php if (file_exists('/var/www/html/species.png')): ?>
<img src="<?php echo $GLOBALS['base_url']; ?>/species.png" width=200 height=150 class="org_img" />
<?php elseif (file_exists('/var/www/html/species.jpg')): ?>
<img src="<?php echo $GLOBALS['base_url']; ?>/species.jpg" width=200 height=150 class="org_img" />
<?php endif; ?>
<?php if (file_exists('/var/www/html/species_legend.html')): ?>
<?php include('/var/www/html/species_legend.html'); ?>
<?php endif; ?>
<p style="font-style:italic; margin:0; padding:0">Other organisms are available on the <a href="https://bipaa.genouest.org/">BIPAA website</a>.</p>
</div>
<div id="front_analyses">
<h2>Available datasets</h2>
<?php foreach ($page['analyses'] as $org_id => $ans): ?>
<?php if ($page['analyses'] > 1): ?>
<?php if (($org_id != "multi") && ($org_id != "none")): ?>
<h4>
<?php
$org = $page['organisms'][$org_id];
print "<i>$org->genus $org->species</i>";
if (strtolower($org->common_name) != strtolower($org->genus[0].$org->species))
print " ($org->common_name)";
?>
</h4>
<?php else: ?>
<h4>Other analyses</h4>
<?php endif; ?>
<div class="sub_analysis">
<?php else: ?>
<div class="no_sub_analysis">
<?php endif; ?>
<?php foreach ($ans as $an_num => $an): ?>
<?php if ($an->human_kind == 'assembly'): ?>
<div class="tripal_analysis_blast-teaser tripal-teaser">
<div class="tripal-analysis-blast-teaser-title tripal-teaser-title">
<?php
print "Genome assembly: <span class='data_highlight'>".$an->name;
?></span>
</div>
<div class="tripal-analysis-blast-teaser-text tripal-teaser-text"><?php
print substr($an->description, 0, 650);
if (strlen($an->description) > 650) {
print "... " . l("[more]", "node/$an_num");
}
print "<p class=\"sub_analysis\"><b>" .$an->feature_count . "</b> features";
print ", performed on <b>".explode(' ', $an->timeexecuted)[0]."</b></p>";
?>
</div>
</div>
<?php endif; ?>
<?php endforeach; ?>
<?php foreach ($ans as $an_num => $an): ?>
<?php if ($an->human_kind != 'assembly'): ?>
<div class="tripal_analysis_blast-teaser tripal-teaser">
<div class="tripal-analysis-blast-teaser-title tripal-teaser-title">
<?php
if ($an->human_kind == 'functional') {
print "Functional annotation: <span class='data_highlight'>".$an->name;
}
else if ($an->human_kind == 'structural') {
print "Structural annotation: <span class='data_highlight'>".$an->name;
}
else if ($an->human_kind == 'transcriptome') {
print "Transcriptome: <span class='data_highlight'>".$an->name;
}
else {
print "Analysis: <span class='data_highlight'>".$an->name;
}
?></span>
</div>
<div class="tripal-analysis-blast-teaser-text tripal-teaser-text"><?php
print substr($an->description, 0, 650);
if (strlen($an->description) > 650) {
print "... " . l("[more]", "node/$an_num");
}
print "<p class=\"sub_analysis\"><b>" .$an->feature_count . "</b> features";
print ", performed on <b>".explode(' ', $an->timeexecuted)[0]."</b></p>";
?>
</div>
</div>
<?php if (count($an->children) >= 1): ?>
<div class="sub_analysis">
<p><b>Associated functional annotation:</b></p>
<?php foreach ($an->children as $an_num2 => $an2): ?>
<div class="tripal_analysis_blast-teaser tripal-teaser">
<div class="tripal-analysis-blast-teaser-title tripal-teaser-title">
<p class="data_highlight"><?php print $an2->name; ?></p>
</div>
<div class="tripal-analysis-blast-teaser-text tripal-teaser-text"><?php
print substr($an2->description, 0, 650);
if (strlen($an2->description) > 650) {
print "... " . l("[more]", "node/$an_num2");
}
print "<p class=\"sub_analysis\"><b>" .$an2->feature_count . "</b> features";
print ", performed on <b>".explode(' ', $an2->timeexecuted)[0]."</b></p>";
?>
</div>
</div>
<?php endforeach; ?>
</div>
<?php endif; ?>
<?php endif; ?>
<?php endforeach; ?>
</div>
<?php endforeach; ?>
</div>
</div>
<?php if ($page['sidebar_second']): ?>
<div id="sidebar-second" class="column sidebar"><div class="section">
<?php print render($page['sidebar_second']); ?>
</div></div> <!-- /.section, /#sidebar-second -->
<?php endif; ?>
</div><!-- #entry-content -->
</article>
</div><!-- #content -->
</div><!-- #primary -->
<div id="tertiary" class="sidebar-container" role="complementary">
<div class="sidebar-inner">
<div class="widget-area">
</div><!-- .widget-area -->
</div><!-- .sidebar-inner -->
</div><!-- #tertiary -->
</div><!-- #main -->
<footer id="colophon" class="site-footer" role="contentinfo">
<div id="secondary" class="sidebar-container" role="complementary">
<div class="widget-area masonry" style="position: relative; height: 250px;">
<aside id="meta-2" class="widget widget_meta masonry-brick" style="position: absolute; left: 248px; top: 0px;"><h3 class="widget-title">Links</h3> <ul>
<?php if (!$logged_in): ?>
<li><a href="<?php echo $GLOBALS['base_url']."/user" ?>">Log in</a></li>
<?php endif; ?>
<li><a href="<?php echo $GLOBALS['base_url']."/rss.xml" ?>">Content <abbr title="Really Simple Syndication">RSS</abbr></a></li>
<li><a href="https://bipaa.genouest.org/">BIPAA website</a></li>
</aside>
<aside id="text-4" class="widget widget_text masonry-brick" style="position: absolute; left: 496px; top: 0px;">
<div class="textwidget"><img src="<?php echo $GLOBALS['base_url']."/".drupal_get_path('theme', 'bipaa');?>/images/bipaa/bipaa.png"></div>
</aside>
</div><!-- .widget-area -->
</div><!-- #secondary -->