few minor bug fixes, additions to CS

tripal_analysis/tripal_analysis.install

@@ -124,7 +124,10 @@ function tripal_analysis_add_cvs() {
  */
 function tripal_analysis_add_cvterms() {
 
-  tripal_insert_cv('tripal_analysis', 'Terms used for managing analyses in Tripal');
+  tripal_insert_cv(
+    'tripal_analysis', 
+    'Terms used for managing analyses in Tripal'
+  );
 
   // add analysis_date.  This is no longer used (as far as we can tell) but we don't
   // get rid of it in case it is used, so just keep it in the Tripal CV

tripal_core/theme/css/tripal.css

@@ -136,6 +136,8 @@
    margin-bottom: 10px;
  }
 
+
+
 /******************************************************************************
  * The teaser appears anywhere that a small snippet of the content is required.
  * When any node in Drupal is published to the home page a teaser is used.
@@ -230,3 +232,16 @@ div.messages.tripal-site-admin-only{
   /* border: 1px solid #7DA1D4; */
   color: black;
 }
+
+/******************************************************************************
+ * Misc CSS classes
+ *****************************************************************************/
+.tripal-dl {
+  width: 100%;
+  overflow: hidden;
+}
+.tripal-dl dt {
+  float: left;
+}
+.tripal-dl dd {
+}

tripal_feature/tripal_feature.views_default.inc

@@ -13,8 +13,8 @@ function tripal_feature_views_default_views() {
   $views = array();
 
   // User View ("Search Biological Content")
-  // Remember, if you change the name/path of this view,
-  // you also want to change it's description in tripal_feature_search_biological_data_views()
+  // Remember, if you change the name/path of this view, you also want to 
+  // change it's description in tripal_feature_search_biological_data_views()
   $view = tripal_feature_defaultvalue_user_features();
   $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;

tripal_featuremap/tripal_featuremap.module

@@ -240,7 +240,7 @@ function tripal_featuremap_theme($existing, $type, $theme, $path) {
 
     // templates for the chado_feature nodes:
     'tripal_feature_featurepos' => array(
-      'arguments' => array('node' => NULL),
+      'variables' => array('node' => NULL),
       'template' => 'tripal_feature_featurepos',
       'path' => "$path/theme/templates",
     ),

tripal_pub/theme/templates/tripal_pub_references.tpl.php

@@ -1,7 +1,6 @@
 <?php
 $pub = $variables['node']->pub;
 
-
 // expand the pub object to include the records from the pub_dbxref table
 $options = array('return_array' => 1);
 $pub = chado_expand_var($pub, 'table', 'pub_dbxref', $options);

tripal_pub/tripal_pub.module

@@ -279,8 +279,8 @@ function tripal_pub_theme($existing, $type, $theme, $path) {
 
     // instructions page for the pub module
     'tripal_pub_help' => array(
-      'template' => 'tripal_pub_help',
       'variables' =>  array(NULL),
+      'template' => 'tripal_pub_help',
       'path' => "$path/theme/templates",
     ),
 

tripal_views/views/handlers/tripal_views_handler_area_action_links.inc

@@ -123,7 +123,7 @@ class tripal_views_handler_area_action_links extends views_handler_area {
    */
   function options_submit(&$form, &$form_state) {
     parent::options_submit($form, $form_state);
-    ddl($form_state, 'form state in submit');
+    //ddl($form_state, 'form state in submit');
     $this->options['link-1']['label-1'] = $form_state['values']['options']['link-1']['label-1'];
     $this->options['link-1']['path-1'] = $form_state['values']['options']['link-1']['path-1'];