More updates to theming

theme_tripal/css/tripal.css

@@ -1,5 +1,6 @@
 .tripal-info-box {
    width: 100%;
+   padding-bottom: 10px;
 }
 .tripal-table {
    width: 100%; 
@@ -50,8 +51,8 @@
 }
 
 .tripal-info-box-title {
-  font-size: 2em;
-  padding-top: 20px;
+  font-size: 1.5em;
+  padding-bottom: 5px;
 
 }
 /* hide the title when inside of a block on a panel */
@@ -87,3 +88,10 @@
    max-height: 300px;
    overflow: auto;
 }
+
+/* no results message */
+.tripal-no-results {
+   font-style: italic;
+   padding: 10px;
+   background-color: #FFEEEE;
+}

theme_tripal/css/tripal_feature.css

@@ -1,5 +1,5 @@
 #tripal_feature-featureloc_sequence {
-  height: 300px;
+  height: 500px;
   overflow: scroll;
    background-color: #FFFFFF;
 }
@@ -46,3 +46,14 @@ table.tripal_feature-references-table th {
    text-align: left;
 
 }
+/* feature relationship edit form */
+#tripal-feature-edit-ALL-relationships-form .form-item,
+#tripal-feature-edit-ALL-db-references-form .form-item {
+   float: left;
+   margin: 0 10px 0 0;
+   
+}
+#tripal-feature-edit-ALL-db-references-form .form-submit {
+   float: none;
+   display: block;
+}

theme_tripal/css/tripal_organism.css

@@ -1,14 +1,20 @@
-/*
- Copyright 2009 Clemson University
-*/
 
-.tripal_organism-image {
-   float: right;
+#tripal_organism-image-box {
+   float: left;
    margin-left: 10px;
    margin-bottom: 10px;
+   margin-right: 10px;
+   width: auto;
 }
-
-.tripal_organism-details {
-   position: relative;
+#tripal_organism-image-box img {
+   max-height: 200px;
 }
 
+#tripal_organism-base-box {
+   float: left;
+   width: 300px;
+}
+#tripal_organism-description-box {
+   clear: left;
+   width: auto;
+}

theme_tripal/node-chado_organism.tpl.php

@@ -1,48 +0,0 @@
-<?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?php if (!$status) { print " node-unpublished"; } ?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/tripal_feature/tripal_feature_featureloc_sequences.tpl.php

@@ -1,5 +1,5 @@
 <?php
-$featureloc_sequences =  $variables['featureloc_sequences'];
+$featureloc_sequences =  $variables['tripal_feature']['featureloc_sequences'];
 if($featureloc_sequences){
    foreach($featureloc_sequences as $seq => $attrs){ ?>
      <div id="tripal_feature-floc_seq-<?php print $attrs['type']?>-box" class="tripal_feature-info-box tripal-info-box">

theme_tripal/tripal_feature/tripal_feature_featurelocs_as_child.tpl.php

@@ -1,11 +1,11 @@
 <?php
 
-$featurelocs_as_child = $variables['featurelocs_as_child'];
+$featurelocs_as_child = $variables['tripal_feature']['featurelocs_as_child'];
 $feature = $variables['node']->feature;
 
 ?>
 <div id="tripal_feature-featurelocs_as_child-box" class="tripal_feature-info-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">Features where <?php print $feature->featurename;?> is located</div>
+  <div class="tripal_feature-info-box-title tripal-info-box-title">Locations where <?php print $feature->featurename;?> is found</div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The <?php print $feature->featurename;?> feature is located relative to the following features:</div>
   <table class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>

theme_tripal/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php

@@ -1,11 +1,11 @@
 <?php
 
-$featurelocs_as_parent = $variables['featurelocs_as_parent'];
+$featurelocs_as_parent = $variables['tripal_feature']['featurelocs_as_parent'];
 $feature = $variables['node']->feature;
 
 ?>
 <div id="tripal_feature-featurelocs_as_parent-box" class="tripal_feature-info-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">Features Located on <?php print $feature->featurename;?></div>
+  <div class="tripal_feature-info-box-title tripal-info-box-title">Features located relative to <?php print $feature->featurename;?></div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The features shown below are located relative to <?php print $feature->featurename;?></div>
   <table class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>

theme_tripal/tripal_feature/tripal_feature_properties.tpl.php

@@ -0,0 +1,31 @@
+<?php
+$properties = $variables['tripal_feature']['properties'];
+$feature = $variables['node']->feature;
+?>
+<div id="tripal_feature-properties-box" class="tripal_feature-info-box tripal-info-box">
+  <div class="tripal_feature-info-box-title tripal-info-box-title">Properties</div>
+  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' is also known by these names</div>
+  <?php if(count($properties) > 0){ ?>
+  <table class="tripal_feature-table tripal-table tripal-table-horz">
+    <tr>
+      <th>Synonym</th>
+    </tr>
+    <?php
+    $i = 0; 
+    foreach ($properties as $result){
+      $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
+      if($i % 2 == 0 ){
+         $class = 'tripal_feature-table-odd-row tripal-table-even-row';
+      }
+      ?>
+      <tr class="<?php print $class ?>">
+        <td><?php print $result->name?></td>
+      </tr>
+      <?php
+      $i++;  
+    } ?>
+  </table>
+  <?php } else { ?>
+    <div class="tripal-no-results">There are no properties for this feature</div> 
+  <?php }?>
+</div>

theme_tripal/tripal_feature/tripal_feature_references.tpl.php

@@ -57,5 +57,7 @@ $feature = $variables['node']->feature;
       $i++;  
     } ?>
   </table>
-  <?php } ?>
+  <?php } else { ?>
+    <div class="tripal-no-results">There are no references for this feature</div> 
+  <?php }?>
 </div>

theme_tripal/tripal_feature/tripal_feature_relationships_as_object.tpl.php

@@ -1,6 +1,6 @@
 <?php
 
-$object_relationships = $variables['object_relationships'];
+$object_relationships = $variables['tripal_feature']['object_relationships'];
 $feature = $variables['node']->feature;
 
 ?>

theme_tripal/tripal_feature/tripal_feature_relationships_as_subject.tpl.php

@@ -1,6 +1,6 @@
 <?php
 
-$subject_relationships = $variables['subject_relationships'];
+$subject_relationships = $variables['tripal_feature']['subject_relationships'];
 $feature = $variables['node']->feature;
 
 ?>

theme_tripal/tripal_feature/tripal_feature_synonyms.tpl.php

@@ -1,19 +1,31 @@
-<!-- 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 $synonyms;
-                  }
-                  ?>
-               	</td></tr>
-            <?php } ?>
-      		<!-- End of theme_tripal_feature_feature_synonyms -->
+<?php
+$synonyms = $variables['tripal_feature']['synonyms'];
+$feature = $variables['node']->feature;
+?>
+<div id="tripal_feature-synonyms-box" class="tripal_feature-info-box tripal-info-box">
+  <div class="tripal_feature-info-box-title tripal-info-box-title">Synonyms</div>
+  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' has the following properites</div>
+  <?php if(count($synonyms) > 0){ ?>
+  <table class="tripal_feature-table tripal-table tripal-table-horz">
+    <tr>
+      <th>Synonym</th>
+    </tr>
+    <?php
+    $i = 0; 
+    foreach ($synonyms as $result){
+      $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
+      if($i % 2 == 0 ){
+         $class = 'tripal_feature-table-odd-row tripal-table-even-row';
+      }
+      ?>
+      <tr class="<?php print $class ?>">
+        <td><?php print $result->name?></td>
+      </tr>
+      <?php
+      $i++;  
+    } ?>
+  </table>
+  <?php } else { ?>
+    <div class="tripal-no-results">There are no synonyms for this feature</div> 
+  <?php }?>
+</div>