Initial import of version 0.2

theme_tripal/node-chado_analysis.tpl.php

@@ -0,0 +1,56 @@
+<?php
+//
+// Copyright 2009 Clemson University
+//
+?>
+
+   <?php if ($picture) {
+      print $picture;
+   }?>
+    
+   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+
+   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+	<?php global $base_url;
+	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
+	</h2><?php }; ?>
+    
+	<?php if (!$teaser): ?>
+	<?php if ($submitted): ?>
+      <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+      <div>
+      <!-- tripal_analysis theme -->
+         <table>
+            <tr><th>Name</th><td><?php print $node->analysisname;?></td></tr>
+            <tr><th>Program (version)</th><td><?php print $node->program.' ('.$node->programversion.')';?></td></tr>
+            <?php
+               $ver = $node->sourceversion;
+               if ($node->sourceversion) {
+                  $ver = "($node->sourceversion)";
+               }
+               $date = preg_replace("/^(\d+-\d+-\d+) .*/","$1",$node->timeexecuted);
+            ?>
+            <tr><th>Source (version)</th><td><?php print $node->sourcename.' '.$ver;?></td></tr>
+            <tr><th>Source URI</th><td><?php print $node->sourceuri;?></td></tr>
+            <tr><th>Executed</th><td><?php print $date?></td></tr>
+            <tr><th>Description</th><td><?php print $node->description?></td></tr>
+         </table>
+      <!-- End of tripal_analysis theme-->
+	  </div> 
+    <?php endif; ?>
+    <?php endif; ?>
+    
+    <div class="content"><?php print $content?></div>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if ($teaser): ?>
+    <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
+    <?php endif; ?>
+  </div>

theme_tripal/node-chado_analysis_blast.tpl.php

@@ -0,0 +1,78 @@
+<?php
+//
+// Copyright 2009 Clemson University
+//
+?>
+
+   <?php if ($picture) {
+      print $picture;
+   }?>
+    
+   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+
+   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+	<?php global $base_url;
+	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
+	</h2><?php }; ?>
+    
+	<?php if (!$teaser): ?>
+	   <?php if ($submitted): ?>     
+      <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+      <?php endif; ?>
+      <div>
+      <!-- tripal_analysis_blast theme -->
+         <table>
+            <tr><th>Name</th><td><?php print $node->analysisname;?></td></tr>
+            <tr><th>Program (version)</th><td><?php print $node->program.' ('.$node->programversion.')';?></td></tr>
+            <?php
+               $ver = $node->sourceversion;
+               if ($node->sourceversion) {
+                  $ver = "($node->sourceversion)";
+               }
+               $date = preg_replace("/^(\d+-\d+-\d+) .*/","$1",$node->timeexecuted);
+            ?>
+            <tr><th>Source (version)</th><td><?php print $node->sourcename.' '.$ver;?></td></tr>
+            <tr><th>Source URI</th><td><?php print $node->sourceuri;?></td></tr>
+            <tr><th>Executed</th><td><?php print $date?></td></tr>
+            <tr><th>Description</th><td><?php print $node->description?></td></tr>
+            <tr><th>Blast Settings</th>
+              <td>
+                <b>Database:</b> 
+                  <?php
+                    // We want to show database name instead of database id
+                    $previous_db = db_set_active('chado');
+                    $sql = "SELECT name FROM db WHERE db_id = %d";
+                    $dbname = db_result(db_query($sql, $node->blastdb)); 
+                    print $dbname;
+                    db_set_active($previous_db);
+                  ?><br>
+                <b>File:</b>
+                  <?php print preg_replace("/.*\/(.*)/", "$1", $node->blastfile); ?><br>
+                <b>Parameters:</b>
+                  <?php print $node->blastparameters?><br>
+                  <?php if ($node->blastjob) {
+                           print "A job for parsing blast xml output will be submitted.";
+                        }
+                  ?>
+              </td>
+            </tr>
+         </table>
+      <!-- End of tripal_analysis_blast theme-->
+	  </div> 
+    
+    <?php endif; ?>
+    
+    <div class="content"><?php print $content?></div>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if ($teaser): ?>
+    <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
+    <?php endif; ?>
+  </div>

theme_tripal/node-chado_analysis_interpro.tpl.php

@@ -0,0 +1,72 @@
+<?php
+//
+// Copyright 2009 Clemson University
+//
+?>
+
+   <?php if ($picture) {
+      print $picture;
+   }?>
+    
+   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+
+   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+	<?php global $base_url;
+	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
+	</h2><?php }; ?>
+    
+	<?php if (!$teaser): ?>
+	  <?php if ($submitted): ?>
+      <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+      <?php endif; ?>
+      <div>
+      <!-- tripal_analysis_interpro theme -->
+         <table>
+            <tr><th>Name</th><td><?php print $node->analysisname;?></td></tr>
+            <tr><th>Program (version)</th><td><?php print $node->program.' ('.$node->programversion.')';?></td></tr>
+            <?php
+               $ver = $node->sourceversion;
+               if ($node->sourceversion) {
+                  $ver = "($node->sourceversion)";
+               }
+               $date = preg_replace("/^(\d+-\d+-\d+) .*/","$1",$node->timeexecuted);
+            ?>
+            <tr><th>Source (version)</th><td><?php print $node->sourcename.' '.$ver;?></td></tr>
+            <tr><th>Source URI</th><td><?php print $node->sourceuri;?></td></tr>
+            <tr><th>Executed</th><td><?php print $date?></td></tr>
+            <tr><th>Description</th><td><?php print $node->description?></td></tr>
+            <tr><th>Interpro Settings</th>
+              <td>
+                <b>File:</b>
+                  <?php print preg_replace("/.*\/(.*)/", "$1", $node->interprofile); ?><br>
+                <b>Parameters:</b>
+                  <?php print $node->interproparameters?><br>
+                  <?php if ($node->interprojob) {
+                           print "A job for parsing interpro html output will be submitted.";
+                           if ($node->parsego) {
+                              print "<BR>GO terms will be parsed and stored.";
+                           }
+                        }
+                  ?>
+              </td>
+            </tr>
+         </table>
+      <!-- End of tripal_analysis_interpro theme-->
+	  </div> 
+    
+    <?php endif; ?>
+    
+    <div class="content"><?php print $content?></div>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if ($teaser): ?>
+    <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
+    <?php endif; ?>
+  </div>

theme_tripal/node-chado_analysis_kegg.tpl.php

@@ -0,0 +1,67 @@
+<?php
+//
+// Copyright 2009 Clemson University
+//
+?>
+
+   <?php if ($picture) {
+      print $picture;
+   }?>
+    
+   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+
+   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+	<?php global $base_url;
+	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
+	</h2><?php }; ?>
+    
+	<?php if (!$teaser): ?>
+	   <?php if ($submitted): ?>
+      <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+      <?php endif; ?>
+      <div>
+      <!-- tripal_analysis_kegg theme -->
+         <table>
+            <tr><th>Name</th><td><?php print $node->analysisname;?></td></tr>
+            <tr><th>Program (version)</th><td><?php print $node->program.' ('.$node->programversion.')';?></td></tr>
+            <?php
+               $ver = $node->sourceversion;
+               if ($node->sourceversion) {
+                  $ver = "($node->sourceversion)";
+               }
+               $date = preg_replace("/^(\d+-\d+-\d+) .*/","$1",$node->timeexecuted);
+            ?>
+            <tr><th>Source (version)</th><td><?php print $node->sourcename.' '.$ver;?></td></tr>
+            <tr><th>Source URI</th><td><?php print $node->sourceuri;?></td></tr>
+            <tr><th>Executed</th><td><?php print $date?></td></tr>
+            <tr><th>Description</th><td><?php print $node->description?></td></tr>
+            <tr><th>KEGG Settings</th>
+              <td>
+                <b>File:</b>
+                  <?php print preg_replace("/.*\/(.*)/", "$1", $node->hierfile); ?><br>
+                  <?php if ($node->keggjob) {
+                           print "A job for parsing KAAS heir output will be submitted.";
+                        }
+                  ?>
+              </td>
+            </tr>
+         </table>
+      <!-- End of tripal_analysis_kegg theme-->
+	  </div> 
+    
+    <?php endif; ?>
+    
+    <div class="content"><?php print $content?></div>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if ($teaser): ?>
+    <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
+    <?php endif; ?>
+  </div>

theme_tripal/node-chado_feature.tpl.php

@@ -0,0 +1,151 @@
+<?php
+/*
+* Copyright 2009 Clemson University
+*/
+?>
+
+   <?php if ($picture) {
+      print $picture;
+   }?>
+
+   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+
+   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+	<?php global $base_url;
+	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
+	</h2><?php }; ?>
+
+	<?php if (!$teaser): ?>
+	   <?php if ($submitted): ?>
+      <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+      <?php endif; ?>
+      <!-- theme_tripal_feature_feature_id -->
+      <!--<div id="feature_notice"><img src="sites/all/modules/tripal_analysis_blast/images/info-128x128.png"><br><i>Feature information and annotations have moved. See below</i></div>-->
+      <div id="feature-view">
+         <?php
+            $aprefix = variable_get('chado_feature_accession_prefix','ID');
+            $feature = $node->feature;
+            if($feature->is_obsolete == 't'){
+            drupal_set_message(t('This feature is obsolete and no longer used in analysis, but is here for reference.'));
+         }?>
+         <table class="tripal_table_vert">
+            <tr><th>Name</th><td><?php print $feature->featurename; ?></td></tr>
+            <tr><th>Accession</th><td><?php print variable_get('chado_feature_accession_prefix','ID'); print $feature->feature_id; ?></td></tr>
+            <tr><th valign="top">Sequence</th><td><pre><?php print ereg_replace("(.{50})","\\1<br>",$feature->residues); ?></pre></td></tr>
+            <tr><th>Length</th><td><?php print $feature->seqlen ?></td></tr>
+            <tr><th>Type</th><td><?php print $feature->cvname; ?></td>
+            </tr>
+            <?php $org_url = url("node/$org_nid")?>
+            <tr>
+            	<th>Organism</th>
+            	<td>
+            		<?php if ($org_nid) {?>
+            				<a href="<?php print $org_url?>"><?php print $feature->common_name?></a>
+            		<?php
+            		      } else {
+            		         if ($feature->common_name) {
+                               print $feature->common_name;
+            		         } else {
+            		           // This sql is for the preview to show organism common_name
+            		           $sql = "SELECT common_name FROM organism WHERE organism_id = $node->organism_id";
+                               $previous_db = db_set_active('chado');
+                               $org_commonname = db_result(db_query($sql));
+                               print $org_commonname;
+                               db_set_active($previous_db);
+            		         }
+            		      }
+            		?>
+            	</td>
+           	</tr>
+           	
+           	<!-- Add library information which this feature belongs to-->
+           	<?php if ($node->lib_additions) { ?>
+               <tr><th>Library</th><td>
+                  <?php
+                     $libraries = $node->lib_additions;
+                     foreach ($libraries as $lib_url => $lib_name) {
+                        // Check if library exists as a node in drupal
+                        if ($lib_url) {
+                  ?>
+                     <a href="<?php print $lib_url?>"><?php print $lib_name?></a><BR>
+                  <?php
+                        } else {
+                           print $lib_name;
+                        }
+                     }
+                  ?>
+               </td></tr>
+            <?php } ?>
+            <!-- End of library addition -->
+            
+            <!-- theme_tripal_feature_feature_synonyms -->
+            <?php
+               $synonyms = $node->synonyms;
+               if(count($synonyms) > 0){
+            ?>
+      			<tr><th>Synonyms</th><td>
+                  <?php
+                  // iterate through each synonym
+                  if (is_array($synonyms)) {
+                     foreach ($synonyms as $result){
+                        print $result->name."<br>";
+                     }
+                  } else {
+                     print $synonyms;
+                  }
+                  ?>
+               	</td></tr>
+            <?php } ?>
+      		<!-- End of theme_tripal_feature_feature_synonyms -->
+         </table>
+      </div>
+      <!-- End of theme_tripal_feature_feature_id -->
+
+   <?php endif; ?>
+
+   <div class="content">
+   <?php if (!$teaser): ?>
+     <!-- Control link for the expandableBoxes -->
+       <br><a id="tripal_expandableBox_toggle_button" onClick="toggleExpandableBoxes()">[-] Collapse All</a><br><br>
+     <!-- End of Control link for the expandableBoxes -->
+     <!-- theme_tripal_feature_feature_references -->
+      <?php
+         $references = $node->references;
+         if(count($references) > 0){
+      ?>
+      <div id="feature-references" class="tripal_feature-info-box">
+      <div class="tripal_expandableBox"><h3>References</h3></div>
+      <div class="tripal_expandableBoxContent">
+      <table>
+         <tr>
+            <th>Dababase</th>
+            <th>Accession</th>
+         </tr>
+      <?php
+         foreach ($references as $result){
+      ?>
+         <tr>
+            <td><?php print $result->db_name?></td>
+            <td><?php if($result->urlprefix){ ?><a href="<?php print $result->urlprefix.$result->accession?>"><?php print $result->accession?></a><?php } else { print $result->accession; } ?></td>
+         </tr>
+      <?php  } ?>
+         </table></div></div>
+      <?php } ?>
+     <!-- End of theme_tripal_feature_feature_references -->
+   <?php endif; ?>
+   <?php print $content?>
+   </div>
+   
+   <?php if (!$teaser): ?>
+   <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
+   <?php endif; ?>
+
+   <?php if ($teaser): ?>
+   <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
+   <?php endif; ?>
+
+   <?php if (!$teaser): ?>
+   <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
+   <?php endif; ?>
+
+   </div>

theme_tripal/node-chado_library.tpl.php

@@ -0,0 +1,47 @@
+<?php
+/*
+ Copyright 2009 Clemson University
+*/
+?>
+
+   <?php if ($picture) { print $picture; }?>
+    
+   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+
+   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+	<?php global $base_url;
+	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
+	</h2><?php }; ?>
+    
+	<?php if (!$teaser): ?>
+   	<?php if ($submitted): ?>
+        <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+      <?php endif;?>
+      <div>
+      <!-- tripal library theme -->
+         <table>
+            <tr><th>Unique Name</th><td><?php print $node->uniquename;?></td></tr>
+            <tr><th>Organism</th><td><?php print $node->genus.' '.$node->species.' ('.$node->common_name.')';?></td></tr>
+            <tr><th>Libraray Type</th><td><?php print $node->library_type?></td></tr>
+            <!--<tr><th>Number of ESTs</th><td><?php print $node->sequence_num?></td></tr>-->
+            <tr><th>Description</th><td><?php print $node->library_description?></td></tr>
+         </table>
+      <!-- End of tripal library theme-->
+	  </div> 
+    <?php endif; ?>
+    
+    <div class="content"><?php print $content?></div>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if ($teaser): ?>
+    <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
+    <?php endif; ?>
+    
+    <?php if (!$teaser): ?>
+    <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
+    <?php endif; ?>
+  </div>
+

theme_tripal/node-chado_organism.tpl.php

@@ -0,0 +1,54 @@
+<?php
+//
+// Copyright 2009 Clemson University
+//
+?>
+
+<?php if($teaser){ ?>
+    <a href="<?php print $node_url?>"><?php print $title?></a>
+<?php } else { ?>
+   <?php $features  = $node->features ?>
+   <?php $libraries = $node->libraries ?>
+   <div class="node<?php if ($sticky) { print " sticky"; } ?>
+                   <?php if (!$status) { print " node-unpublished"; } ?>">
+   <?php if ($picture) { print $picture; }?>
+   <?php if ($page == 0) { ?>
+     <h2 class="title"><a href="<?php print $node_url?>"><?php print $title?></a></h2>
+   <?php }; ?>
+   <span class="taxonomy"><?php print $terms?></span>
+   <div class="content">
+     <div class="tripal_organism-image">
+        <img src=<?php print file_create_url(file_directory_path() . "/tripal/tripal_organism/images/".$node->genus."_".$node->species.".jpg")?>>
+     </div>
+     <?php if ($submitted): ?>     
+        <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+     <?php endif; ?>
+     <div class="tripal_organism-details">
+        <h3>Details</h3>
+           <table class="tripal_table_vert">
+              <tr>
+                 <th nowrap>Common Name</th>
+                 <td><?php print $node->common_name?></td>
+              </tr>
+              <tr>
+                 <th>Genus</th>
+                 <td><?php print $node->genus?></td>
+              </tr>
+              <tr>
+                 <th>Species</th>
+                 <td><?php print $node->species?></td>
+              </tr>
+           </table>
+           <?php if($node->description){ ?>
+              <b>Description</b>
+              <p class="organism"><?php print $node->description?></p>
+           <?php }; ?>
+        </div>
+     </div>
+     <div class="content"><?php print $content ?></div>
+     <?php if ($links) { ?>
+       <div class="links"> <?php print $links?></div>
+     <?php }; ?>
+  </div>
+<?php }; ?>
+

theme_tripal/node.tpl.php

@@ -0,0 +1,17 @@
+<?php
+//
+// Copyright 2009 Clemson University
+//
+?>
+
+  <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+    <?php if ($picture) {
+      print $picture;
+    }?>
+    <?php if ($page == 0) { ?><h2 class="title"><a href="<?php print $node_url?>"><?php print $title?></a></h2><?php }; ?>
+  
+   
+    <div class="content"><?php print $content?></div>
+	  <div class="postmeta"><span class="submitted"><?php print $submitted?></span> <span class="taxonomy"><?php print $terms?></span></div>
+    <?php if ($links) { ?><div class="links"> <?php print $links?></div><?php }; ?>
+  </div>

theme_tripal/tripal.info

@@ -0,0 +1,18 @@
+name = Tripal Theme
+description = A Tripal specific theme for use with any other theme.  Requires customization to .info file of the primary theme.
+version = 6.x-0.1b
+core = 6.x
+engine = phptemplate
+;base theme = admire_gray
+
+stylesheets[all][] = css/tripal.css
+stylesheets[all][] = css/tripal_analysis_blast.css
+stylesheets[all][] = css/tripal_organism.css
+
+scripts[] = js/tripal.js
+
+regions[header] = Header
+regions[sidebar_left] = Sidebar left
+regions[content_top] = Content top
+regions[sidebar_right] = Sidebar right
+regions[footer_block] = Footer block